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Optimal citation database matching #8

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kousu opened this issue Oct 16, 2021 · 6 comments
Open

Optimal citation database matching #8

kousu opened this issue Oct 16, 2021 · 6 comments

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@kousu
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kousu commented Oct 16, 2021 •
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I went down a rabbit hole and want to pin this idea in case someone wants to take it up later: optimal fuzzy matches between the gsheet and CCV databases (or potentially any other database formats we support in the future).

find_matching_ref() does a basic JOIN then uses a simple heuristic to handle rare conflicts:

https://github.com/jcohenadad/bibeasy/blob/637635b5e14ccc30bf71a9af491a1e8484393864/bibeasy/utils.py#L163-L177

replace_ref_in_text() goes its own way and uses isin() to give a degree of toleration:

https://github.com/jcohenadad/bibeasy/blob/637635b5e14ccc30bf71a9af491a1e8484393864/bibeasy/utils.py#L403-L405

Both work well enough because the data is fairly accurate, and find_matching_ref warns about any data it doesn't understand so they can be manually corrected.

As the database grows and time to maintain it shortens though this gets harder.

There's a generic solution to this in the literature: use difflib.SequenceMatcher.ratio() (or another kind of fuzzy matcher; there's other metrics available in fuzzywuzzy) to get a score for every pair of titles and pick the best. For example, you could directly replace the line in find_matching_ref with:

id_ccv = df_ccv[df_ccv['Title'].isin(difflib.get_close_matches(row['Title'], df_ccv['Title']))].index.values

which would then be able to tolerate misspellings, changes in capitalization, abbreviations, and punctuation variations. The current code will warn that all of these situations are "MISSED".

We can even match on multiple fields using this trick: average their scores: sum(ratio(df_ccv[row,field],row[field]) for field in fields))/len(fields) (you could also play with using a weighted average, so that say the Publisher is worth half as much as the Year which is three-quarters as much as the Title. But to get that feature you need to rewrite difflib.get_close_matches().

And we can do even better than that. So far what I've described allows for collisions; they are rare, but they can happen if the same article was published in multiple venues with small title variations. Optimally, we want a best guess for the complete database of what goes to what, with no redundant matchings. This is the Assignment Problem, and there's a solution here available as scipy.optimize.linear_sum_assignment().
@kousu
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kousu commented Oct 16, 2021 •
edited
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The matches would be improved, too, in our case by doing them case insensitively. So, e.g., rewrite difflib.get_close_matches to

--- /tmp/a	2021-10-16 19:36:44.887957974 -0400
+++ /tmp/b	2021-10-16 19:36:54.873261759 -0400
@@ -33,9 +33,9 @@
         raise ValueError("cutoff must be in [0.0, 1.0]: %r" % (cutoff,))
     result = []
     s = SequenceMatcher()
-    s.set_seq2(word)
+    s.set_seq2(word.lower())
     for x in possibilities:
-        s.set_seq1(x)
+        s.set_seq1(x.lower())
         if s.real_quick_ratio() >= cutoff and \
            s.quick_ratio() >= cutoff and \
            s.ratio() >= cutoff:

or if not using get_close_matches() directly but instead, say, using linear_sum_assignment(), at least make sure to call .lower() before computing the ratios. And another optimization -- effective for us but maybe not for every situation? -- is to write ratio() something like

def ratio(a,b):
   if a == b: return 1.0
   return SequenceMatcher(None, a, b).ratio()

because we have a lot of exact matches and == is faster than SequenceMatcher

Another optimization might be to clamp pairs below a threshold to 0.0? Maybe that doesn't save any time though.

@kousu
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kousu commented Oct 16, 2021

Another optimization is to install https://github.com/miohtama/python-Levenshtein and use its drop-in-compatible SequenceMatcher. It's written in C so it's much faster at string searching.

@kousu
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kousu commented Oct 17, 2021 •
edited
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id_ccv = df_ccv[df_ccv['Title'].isin(difflib.get_close_matches(row['Title'], df_ccv['Title']))].index.values

EDIT: you need to use

id_ccv = df_ccv[df_ccv['Title'].isin(difflib.get_close_matches(row['Title'],df_ccv_unmatched['Title']))].index.values

and also patch

-                        id_ccv = np.array(id_ccv_single)
+                        id_ccv = np.array([id_ccv_single])

I tried this out. I ran

bibeasy -x CCV.xml

on master and on my edit, which I'm not posting as a branch because it's just a quick prototype to see how it would affect the output. Here's the diff:

--- a	2021-10-16 20:09:42.729544314 -0400
+++ b	2021-10-16 20:08:24.733071066 -0400
@@ -19,10 +19,9 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J5	CCV J148	Investigations on spinal cord fMRI of cats under ketamine
   Mismatched fields: Authors, Journal/Conference
-GSHEET J6	CCV J149	Characterization of cardiac-related noise in fMRI of the cervical spinal cord
+GSHEET J6	CCV J57	Characterization of cardiac-related noise in fMRI of the cervical spinal cord
   Mismatched fields: Authors
-GSHEET J7	CCV J145	BOLD signal responses to controlled hypercapnia in human spinal cord
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J7	CCV dupl	BOLD signal responses to controlled hypercapnia in human spinal cord
 GSHEET J8	CCV J147	Characterization of the hemodynamic response in the vivo rat lumbar spinal cord by intrinsic optical imaging and laser speckle microscopy
   Mismatched fields: Authors
 GSHEET J9	CCV J146	Human cervical spinal cord funiculi: investigation with magnetic resonance diffusion tensor imaging
@@ -65,14 +64,11 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J30	CCV J117	What can we learn from T2* maps of the cortex?
   Mismatched fields: Journal/Conference
-GSHEET J31	CCV J122	The current state-of-the-art of spinal cord imaging: methods
-  Mismatched fields: Journal/Conference
-GSHEET J32	CCV J118	The current state-of-the-art of spinal cord imaging: applications
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J31	CCV dupl	The current state-of-the-art of spinal cord imaging: methods
+GSHEET J32	CCV dupl	The current state-of-the-art of spinal cord imaging: applications
 GSHEET J33	CCV J116	Nineteen-channel receive array and four-channel transmit array coil for cervical spinal cord imaging at 7T
   Mismatched fields: Authors
-GSHEET J34	CCV J124	Effect of respiration on the B0 field in the human spinal cord at 3T
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J34	CCV dupl	Effect of respiration on the B0 field in the human spinal cord at 3T
 GSHEET J35	CCV J114	Robust, accurate and fast automatic segmentation of the spinal cord
   Mismatched fields: Authors, Journal/Conference
 GSHEET J36	CCV J115	Multi-parametric spinal cord MRI as potential progression marker in amyotrophic lateral sclerosis
@@ -124,8 +120,7 @@
   Mismatched fields: Authors
 GSHEET J61	CCV J91	Is the Relationship between Cortical and White Matter Pathologic Changes in Multiple Sclerosis Spatially Specific? A Multimodal 7-T and 3-T MR Imaging Study with Surface and Tract-based Analysis
   Mismatched fields: Authors
-GSHEET J62	CCV J94	Segmentation of the human spinal cord
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J62	CCV dupl	Segmentation of the human spinal cord
 GSHEET J63	CCV J90	ZOOM or Non-ZOOM? Assessing Spinal Cord Diffusion Tensor Imaging Protocols for Multi-Centre Studies
   Mismatched fields: Authors, Journal/Conference
 GSHEET J64	CCV J88	Brainhack: a collaborative workshop for the open neuroscience community
@@ -138,8 +133,7 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J68	CCV J79	Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter
   Mismatched fields: Authors
-GSHEET J69	CCV J86	g-Ratio weighted imaging of the human spinal cord in vivo
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J69	CCV dupl	g-Ratio weighted imaging of the human spinal cord in vivo
 GSHEET J70	CCV J82	Functional Magnetic Resonance Imaging of the Spinal Cord: Current Status and Future Developments
   Mismatched fields: Journal/Conference
 GSHEET J71	CCV J83	SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data
@@ -152,16 +146,14 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J75	CCV J81	A Novel MRI Biomarker of Spinal Cord White Matter Injury: T2*-Weighted White Matter to Gray Matter Signal Intensity Ratio
   Mismatched fields: Authors, Journal/Conference
-GSHEET J76	CCV J85	Spinal cord grey matter segmentation challenge
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J76	CCV dupl	Spinal cord grey matter segmentation challenge
 GSHEET J77	CCV J84	Brain processing of the temporal dimension of acute pain in short-term memory
   Mismatched fields: Authors
 GSHEET J78	CCV J76	In vivo characterization of cortical and white matter neuroaxonal pathology in early multiple sclerosis
   Mismatched fields: Authors, Journal/Conference
 GSHEET J79	CCV J75	AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter
   Mismatched fields: Authors, Journal/Conference
-GSHEET J80	CCV J80	Axon and Myelin Morphology in Animal and Human Spinal Cord
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J80	CCV dupl	Axon and Myelin Morphology in Animal and Human Spinal Cord
 GSHEET J81	CCV J54	A pneumatic phantom for mimicking respiration-induced artifacts in spinal MRI
   Mismatched fields: Authors, Journal/Conference
 GSHEET J82	CCV J67	PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space
@@ -186,14 +178,13 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J92	CCV J53	AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks
   Mismatched fields: Authors, Journal/Conference
-GSHEET J93	CCV J57	Effect of cardiac-related translational motion in diffusion MRI of the spinal cord
+GSHEET J93	CCV J149	Effect of cardiac-related translational motion in diffusion MRI of the spinal cord
   Mismatched fields: Authors
 GSHEET J94	CCV J63	Microstructural imaging in the spinal cord and validation strategies
   Mismatched fields: Journal/Conference
 GSHEET J95	CCV J61	Can microstructural MRI detect subclinical tissue injury in subjects with asymptomatic cervical spinal cord compression? A prospective cohort study
   Mismatched fields: Authors, Journal/Conference
-GSHEET J96	CCV J62	Spinal cord gray matter segmentation using deep dilated convolutions
-  Mismatched fields: Authors, Journal/Conference
+GSHEET J96	CCV dupl	Spinal cord gray matter segmentation using deep dilated convolutions
 GSHEET J97	CCV J56	Monitoring for myelopathic progression with multiparametric quantitative MRI
   Mismatched fields: Authors, Journal/Conference
 GSHEET J98	CCV J72	Postmortem diffusion MRI of the entire human spinal cord at microscopic resolution
@@ -261,8 +252,10 @@
   Mismatched fields: Authors, Journal/Conference
 GSHEET J133	CCV J18	HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy
 GSHEET J134	CCV J25	Injury Volume Extracted from MRI Predicts Neurologic Outcome in Acute Spinal Cord Injury: A Prospective TRACK-SCI Pilot Study
-GSHEET J135	CCV missed	Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation
-GSHEET J136	CCV missed	Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools
+GSHEET J135	CCV J1	Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation
+  Mismatched fields: Authors
+GSHEET J136	CCV J5	Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools
+  Mismatched fields: Authors, Journal/Conference
 GSHEET J137	CCV J3	Associations between relative morning blood pressure, cerebral blood flow, and memory in older adults treated and controlled for hypertension
   Mismatched fields: Authors
 GSHEET J138	CCV J16	SoftSeg: Advantages of soft versus binary training for image segmentation
@@ -271,30 +264,36 @@
   Mismatched fields: Authors
 GSHEET J140	CCV J11	Generic acquisition protocol for quantitative MRI of the spinal cord
   Mismatched fields: Authors
-GSHEET J141	CCV missed	Atlas-based Quantification of DTI measures in Typically Developing Pediatric Spinal Cord
-GSHEET J142	CCV missed	Quantitative magnetic resonance imaging of spinal cordmicrostructure in adults with cerebral palsy
+GSHEET J141	CCV J14	Atlas-based Quantification of DTI measures in Typically Developing Pediatric Spinal Cord
+  Mismatched fields: Authors, Journal/Conference
+GSHEET J142	CCV J13	Quantitative magnetic resonance imaging of spinal cordmicrostructure in adults with cerebral palsy
+  Mismatched fields: Journal/Conference
 GSHEET J143	CCV J17	ivadomed: A Medical Imaging Deep Learning Toolbox
   Mismatched fields: Journal/Conference
-GSHEET J144	CCV missed	A simple and robust method for automating analysis of naïve and regenerating peripheral nerves
+GSHEET J144	CCV J9	A simple and robust method for automating analysis of naïve and regenerating peripheral nerves
+  Mismatched fields: Authors, Journal/Conference
 GSHEET J145	CCV J6	Tracking White and Gray Matter Degeneration along the Spinal Cord Axis in Degenerative Cervical Myelopathy
-GSHEET J146	CCV missed	Diffusion MRI reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression
+GSHEET J146	CCV J8	Diffusion MRI reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression
 GSHEET J147	CCV J4	Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps
-GSHEET J148	CCV missed	Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning
-GSHEET J149	CCV missed	The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure
-GSHEET J151	CCV missed	Quantitative 7-Tesla imaging of cortical myelin changes in early multiple sclerosis
+GSHEET J148	CCV J7	Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning
+  Mismatched fields: Authors, Journal/Conference
+GSHEET J149	CCV J12	The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure
+  Mismatched fields: Authors, Journal/Conference
+GSHEET J151	CCV J15	Quantitative 7-Tesla imaging of cortical myelin changes in early multiple sclerosis
+  Mismatched fields: Authors, Journal/Conference
 GSHEET J152	CCV missed	A comprehensive structural characterization of the Sapap3 knockout mouse for repetitive behaviours
-GSHEET [missed]	CCV J1	Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation.
-GSHEET [missed]	CCV J5	Spinal Cord Morphology in Degenerative Cervical Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools
-GSHEET [missed]	CCV J7	Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning.
-GSHEET [missed]	CCV J8	Diffusion magnetic resonance imaging reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression.
-GSHEET [missed]	CCV J9	A simple and robust method for automating analysis of naïve and regenerating peripheral nerves.
-GSHEET [missed]	CCV J12	The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure.
-GSHEET [missed]	CCV J13	Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy.
-GSHEET [missed]	CCV J14	Atlas-Based Quantification of DTI Measures in a Typically Developing Pediatric Spinal Cord.
-GSHEET [missed]	CCV J15	Quantitative 7-Tesla Imaging of Cortical Myelin Changes in Early Multiple Sclerosis.
 GSHEET [missed]	CCV J26	A Cross-Sectional Study on the Impact of Arterial Stiffness on the Corpus Callosum, a Key White Matter Tract Implicated in Alzheimer's Disease
 GSHEET [missed]	CCV J27	Injury volume extracted from MRI predicts neurologic outcome in acute spinal cord injury: A prospective TRACK-SCI pilot study
 GSHEET [missed]	CCV J41	Deep Active Learning for Axon-Myelin Segmentation on Histology Data
+GSHEET [missed]	CCV J62	Spinal cord gray matter segmentation using deep dilated convolutions
+GSHEET [missed]	CCV J80	Axon and Myelin Morphology in Animal and Human Spinal Cord
+GSHEET [missed]	CCV J85	Spinal cord grey matter segmentation challenge
+GSHEET [missed]	CCV J86	g-Ratio weighted imaging of the human spinal cord in vivo
+GSHEET [missed]	CCV J94	Segmentation of the human spinal cord
+GSHEET [missed]	CCV J118	The current state-of-the-art of spinal cord imaging: applications
+GSHEET [missed]	CCV J122	The current state-of-the-art of spinal cord imaging: methods
+GSHEET [missed]	CCV J124	Effect of respiration on the B0 field in the human spinal cord at 3T
+GSHEET [missed]	CCV J145	BOLD signal responses to controlled hypercapnia in human spinal cord
 
 Publication type: 'nonreferred'
 
@@ -650,7 +649,7 @@
 GSHEET N6	CCV missed	Bound Pool Fractions Complement Diffusion Measures in Characterizing White Matter Micro and Macrostructure
 GSHEET N7	CCV missed	A Robust Methodology for T1 Mapping
 
-Results for type: 'article': Found: 141 | Not in CCV: 10 | Duplicate: 0 | Not in Gsheet: 12
+Results for type: 'article': Found: 141 | Not in CCV: 1 | Duplicate: 9 | Not in Gsheet: 12
 
 
 Results for type: 'nonreferred': Found: 0 | Not in CCV: 9 | Duplicate: 0 | Not in Gsheet: 0

So the main change was that it matched 9 articles it previously didn't recognize as duplicates. I haven't looked at which ones they are yet (and might not bother) but I guess that's a reasonable thing for it to do?

-Results for type: 'article': Found: 141 | Not in CCV: 10 | Duplicate: 0 | Not in Gsheet: 12
+Results for type: 'article': Found: 141 | Not in CCV: 1 | Duplicate: 9 | Not in Gsheet: 12

It was also a lot slower. It took double the time. I think the inner .isin() is killing the runtime, because get_close_matches is an O(n) search, isin() is an O(n) search, and so the whole thing is O(2*n^2).

@jcohenadad
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these are great investigations and suggestions, Nick. Exactly addressing the limitations on the implementation that i’ve been aware of for many years but never took the time to address them.

@kousu
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kousu commented Oct 17, 2021 •
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This should be helpful for feeding the linear-solver:

def quick_quick_ratio(a, b, threshold=0.6):
    """
    *Quickly* compute the similarity ratio of two strings.
    
    The speed comes from using approximations: if the ratio
    is below the given threshold return 0.0 early. This means
    that strings that are obviously different do not need the
    full computation performed.
    
    Most uses of ratio() are interested in *similar* strings not
    *dissimilar* ones.
    
    Equivalent to:
    
    difflib.SequenceMatcher(None, a, b).ratio() \
      if difflib.SequenceMatcher(None, a, b).ratio() >= threshold \
      else 0.0
    """
    
    if a == b: return 1.0 # TODO: test if having this here is faster or slower
    
    m = difflib.SequenceMatcher(None, a, b)
    if m.real_quick_ratio() < threshold: return 0.0
    if m.quick_ratio() < threshold: return 0.0
    r = m.ratio()
    if r < threshold: return 0.0
    return r

@kousu
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kousu commented Oct 18, 2021 •
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I'm getting ahead of myself here, but I worked out a prototype. I first did a pure-python version and then I used scipy.optimize.linear_sum_assignment; they get the same results on the current citation database, but linear_sum_assignment is faster and, in theory, more accurate in the case of ambiguous data.

data.py 
titlesA = ['Activation detection in diffuse optical imaging by means of the general linear model', 'Development of clinical diffusion tensor MRI of the spinal cord in a context of spinal cord injury', 'In vivo DTI of the healthy and injured cat spinal cord at high spatial and angular resolution', 'Detection of multiple pathways in the spinal cord using q-ball imaging', 'Investigations on spinal cord fMRI of cats under ketamine', 'Characterization of cardiac-related noise in fMRI of the cervical spinal cord', 'BOLD signal responses to controlled hypercapnia in human spinal cord', 'Characterization of the hemodynamic response in the vivo rat lumbar spinal cord by intrinsic optical imaging and laser speckle microscopy', 'Human cervical spinal cord funiculi: investigation with magnetic resonance diffusion tensor imaging', 'In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis', 'Quality assessment of high angular resolution diffusion imaging data using bootstrap on Q-ball reconstruction', '32-channel RF coil optimized for brain and cervical spinal cord at 3 T', 'Demyelination and degeneration in the injured human spinal cord detected with diffusion and magnetization transfer MRI', 'Wallerian degeneration after spinal cord lesions in cats detected with diffusion tensor imaging', 'Impact of outliers on diffusion tensor and Q-ball imaging: clinical implications and correction strategies', 'Focal cortical lesion detection in multiple sclerosis: 3 Tesla DIR versus 7 Tesla FLASH-T2', 'T2* mapping and B0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex', 'Improving diffusion MRI using simultaneous multi-slice echo planar imaging', 'Reduction of physiological noise with independent component analysis improves the detection of nociceptive responses with fMRI of the human spinal cord', 'Cervical spinal cord injection of epidural corticosteroids: comprehensive longitudinal study including multiparametric magnetic resonance imaging', '7T MRI of spinal cord injury', 'Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries', '7-T MRI of the spinal cord can detect lateral corticospinal tract abnormality in amyotrophic lateral sclerosis', 'Fast diffusion tensor imaging and tractography of the whole cervical spinal cord using point spread function corrected echo planar imaging', 'Involvement of spinal sensory pathway in ALS and specificity of cord atrophy to lower motor neuron degeneration', 'Visualizing integrative functioning in the human brainstem and spinal cord with spinal functional magnetic resonance imaging', 'The Human Connectome Project and beyond: initial applications of 300 mT/m gradients', 'Pushing the limits of in vivo diffusion MRI for the Human Connectome Project', 'Identification of discrete functional subregions of the human periaqueductal gray', 'What can we learn from T2* maps of the cortex?', 'The current state-of-the-art of spinal cord imaging: methods', 'The current state-of-the-art of spinal cord imaging: applications', 'Nineteen-channel receive array and four-channel transmit array coil for cervical spinal cord imaging at 7T', 'Effect of respiration on the B0 field in the human spinal cord at 3T', 'Robust, accurate and fast automatic segmentation of the spinal cord', 'Multi-parametric spinal cord MRI as potential progression marker in amyotrophic lateral sclerosis', 'Automatic labeling of vertebral levels using a robust template-based approach', 'Recovery of locomotion after partial spinal cord lesions in cats: assessment using behavioral, electrophysiological and imaging techniques', 'Framework for integrated MRI average of the spinal cord white and gray matter: the MNI-Poly-AMU template', 'Validation of a semiautomated spinal cord segmentation method', 'Spinal diffusion tensor imaging: A comprehensive review with emphasis on spinal cord anatomy and clinical applications', 'Characterizing the location of spinal and vertebral levels in the human cervical spinal cord', 'Reproducibility of T2* mapping in the human cerebral cortex in vivo at 7 Tesla MRI', 'The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter', 'A gradient in cortical pathology in multiple sclerosis by in vivo quantitative 7 T imaging', 'High resolution imaging of the central nervous system: how novel imaging methods combined with navigation strategies will advance patient care', 'Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe', 'Simultaneous Brain-Cervical Cord FMRI Reveals Intrinsic Spinal Cord Plasticity during Motor Sequence Learning', 'A reliable spatially normalized template of the human spinal cord--Applications to automated white matter/gray matter segmentation and tensor-based morphometry (TBM) mapping of gray matter alterations occurring with age', 'Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling', 'Multivariate combination of magnetization transfer, T2* and B0 orientation to study the myelo-architecture of the in vivo human cortex', 'In vivo mapping of human spinal cord microstructure at 300mT/m', 'White matter atlas of the human spinal cord with estimation of partial volume effect', 'Real diffusion-weighted MRI enabling true signal averaging and increased diffusion contrast', 'In vivo histology of the myelin g-ratio with magnetic resonance imaging', 'Quantitative analysis of the myelin g-ratio from electron microscopy images of the macaque corpus callosum', 'Spinal Cord Segmentation by One Dimensional Normalized Template Matching: A Novel, Quantitative Technique to Analyze Advanced Magnetic Resonance Imaging Data', 'Fully automated segmentation of the cervical cord from T1-weighted MRI using PropSeg: Application to multiple sclerosis', 'Translating state-of-the-art spinal cord MRI techniques to clinical use: A systematic review of clinical studies utilizing DTI, MT, MWF, MRS, and fMRI', 'Quantitative magnetization transfer imaging made easy with qMTLab: Software for data simulation, analysis, and visualization', 'Is the Relationship between Cortical and White Matter Pathologic Changes in Multiple Sclerosis Spatially Specific? A Multimodal 7-T and 3-T MR Imaging Study with Surface and Tract-based Analysis', 'Segmentation of the human spinal cord', 'ZOOM or Non-ZOOM? Assessing Spinal Cord Diffusion Tensor Imaging Protocols for Multi-Centre Studies', 'Brainhack: a collaborative workshop for the open neuroscience community', 'A 24-channel shim array for the human spinal cord: Design, evaluation, and application', 'AxonSeg: open source software for axon and myelin segmentation and morphometric analysis', 'Modeling white matter microstructure', 'Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter', 'g-Ratio weighted imaging of the human spinal cord in vivo', 'Functional Magnetic Resonance Imaging of the Spinal Cord: Current Status and Future Developments', 'SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data', 'MRI Atlas-Based Measurement of Spinal Cord Injury Predicts Outcome in Acute Flaccid Myelitis', 'Topologically preserving straightening of spinal cord MRI', 'Clinically Feasible Microstructural MRI to Quantify Cervical Spinal Cord Tissue Injury Using DTI, MT, and T2*-Weighted Imaging: Assessment of Normative Data and Reliability', 'A Novel MRI Biomarker of Spinal Cord White Matter Injury: T2*-Weighted White Matter to Gray Matter Signal Intensity Ratio', 'Spinal cord grey matter segmentation challenge', 'Brain processing of the temporal dimension of acute pain in short-term memory', 'In vivo characterization of cortical and white matter neuroaxonal pathology in early multiple sclerosis', 'AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter', 'Axon and Myelin Morphology in Animal and Human Spinal Cord', 'A pneumatic phantom for mimicking respiration-induced artifacts in spinal MRI', 'PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space', 'Promise and pitfalls of g-ratio estimation with MRI', 'Spinal Cord Gray Matter Atrophy in Amyotrophic Lateral Sclerosis', 'Scan-rescan of axcaliber, macromolecular tissue volume, and g-ratio in the spinal cord', 'Automatic spinal cord localization, robust to MRI contrasts using global curve optimization', 'Test-retest reliability of myelin imaging in the human spinal cord: Measurement errors versus region- and aging-induced variations', 'Design and construction of an optimized transmit/receive hybrid birdcage resonator to improve full body images of medium-sized animals in 7T scanner', 'Real-time correction of respiration-induced distortions in the human spinal cord using a 24-channel shim array', 'Neuroinflammation of the spinal cord and nerve roots in chronic radicular pain patients', 'Changes in structural network are associated with cortical demyelination in early multiple sclerosis', 'AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks', 'Effect of cardiac-related translational motion in diffusion MRI of the spinal cord', 'Microstructural imaging in the spinal cord and validation strategies', 'Can microstructural MRI detect subclinical tissue injury in subjects with asymptomatic cervical spinal cord compression? A prospective cohort study', 'Spinal cord gray matter segmentation using deep dilated convolutions', 'Monitoring for myelopathic progression with multiparametric quantitative MRI', 'Postmortem diffusion MRI of the entire human spinal cord at microscopic resolution', 'Size-adaptable 13-channel receive array for brain MRI in human neonates at 3 T', 'What Has Been Learned from Magnetic Resonance Imaging Examination of the Injured Human Spinal Cord: A Canadian Perspective', 'Inter-Vendor Reproducibility of Myelin Water Imaging Using a 3D Gradient and Spin Echo Sequence', 'The spinal and cerebral profile of adult spinal-muscular atrophy: A multimodal imaging study', 'Linearity, Bias, Intrascanner Repeatability, and Interscanner Reproducibility of Quantitative Multidynamic Multiecho Sequence for Rapid Simultaneous Relaxometry at 3 T: A Validation Study With a Standardized Phantom and Healthy Controls', 'Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks', 'Axons morphometry in the human spinal cord', 'Spatial distribution of multiple sclerosis lesions in the cervical spinal cord', 'Arterial stiffness and white matter integrity in the elderly: A diffusion tensor and magnetization transfer imaging study', 'Unsupervised domain adaptation for medical imaging segmentation with self-ensembling', 'Promises and limitations of deep learning for medical image segmentation', 'Convolutional Neural Network-Based Automated Segmentation of the Spinal Cord and Contusion Injury: Deep Learning Biomarker Correlates of Motor Impairment in Acute Spinal Cord Injury', 'Signal Intensity within Cerebral Venous Sinuses on Synthetic MRI', 'Open-source pipeline for multi-class segmentation of the spinal cord with deep learning', 'Arterial stiffness and brain integrity: A review of MRI findings', 'Guidelines for the conduct of clinical trials in spinal cord injury: Neuroimaging biomarkers', 'Gray Matter Alterations in Early and Late Relapsing-Remitting Multiple Sclerosis Evaluated with Synthetic Quantitative Magnetic Resonance Imaging', 'Presymptomatic spinal cord pathology in c9orf72 mutation carriers: A longitudinal neuroimaging study', 'Brainstem and spinal cord MRI identifies altered sensorimotor pathways post-stroke', 'Profiles of cortical inflammation in multiple sclerosis by 11C-PBR28 MR-PET and 7 Tesla imaging', 'Traumatic and nontraumatic spinal cord injury: pathological insights from neuroimaging', 'Construction of a rat spinal cord atlas of axon morphometry', 'Arterial stiffness cut-off value and white matter integrity in the elderly', 'Validation of Rapid Magnetic Resonance Myelin Imaging in Multiple Sclerosis', 'Multi-parametric quantitative in vivo spinal cord MRI with unified signal readout and image denoising', 'Imaging mechanisms of disease progression in multiple sclerosis: beyond brain atrophy', 'Machine learning and multi-parametric brain MRI to differentiate hereditary diffuse leukodystrophy with spheroids from multiple sclerosis', 'Multiple sclerosis lesions in motor tracts from the brain to the cervical cord: spatial distribution and correlation with disability', '7 T imaging reveals a gradient in spinal cord lesion distribution in multiple sclerosis', 'Deep Semantic Segmentation of Natural and Medical Images: A Review', 'Resting-state brain and spinal cord networks in humans are functionally integrated', 'qMRLab: Quantitative MRI analysis, under one umbrella', 'Cortico-spinal imaging to study pain', 'An interactive meta-analysis of MRI biomarkers of myelin', 'HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy', 'Injury Volume Extracted from MRI Predicts Neurologic Outcome in Acute Spinal Cord Injury: A Prospective TRACK-SCI Pilot Study', 'Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation', 'Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools', 'Associations between relative morning blood pressure, cerebral blood flow, and memory in older adults treated and controlled for hypertension', 'SoftSeg: Advantages of soft versus binary training for image segmentation', 'Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers', 'Generic acquisition protocol for quantitative MRI of the spinal cord', 'Atlas-based Quantification of DTI measures in Typically Developing Pediatric Spinal Cord', 'Quantitative magnetic resonance imaging of spinal cordmicrostructure in adults with cerebral palsy', 'ivadomed: A Medical Imaging Deep Learning Toolbox', 'A simple and robust method for automating analysis of naïve and regenerating peripheral nerves', 'Tracking White and Gray Matter Degeneration along the Spinal Cord Axis in Degenerative Cervical Myelopathy', 'Diffusion MRI reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression', 'Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps', 'Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning', 'The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure', 'Quantitative 7-Tesla imaging of cortical myelin changes in early multiple sclerosis', 'A comprehensive structural characterization of the Sapap3 knockout mouse for repetitive behaviours', 'High-Resolution DWI in Brain and Spinal Cord with syngo RESOLVE', 'Deep Active Learning for Axon-Myelin Segmentation on Histology Data', 'ivadomed: A Medical Imaging Deep Learning Toolbox', 'Spine intervertebral disc labeling using a fully convolutional redundant counting model', 'Automatic segmentation of spinal multiple sclerosis lesions: How to generalize across MRI contrasts?', 'Multiclass Spinal Cord Tumor Segmentation on MRI with Deep Learning', 'Effectiveness of regional diffusion MRI measures in distinguishing multiple sclerosis abnormalities within the cervical spinal cord', 'Evaluation of distortion correction methods in diffusion MRI of the spinal cord', 'Reproducibility and Evolution of Diffusion MRI Measurements within the Cervical Spinal Cord in Multiple Sclerosis', 'Knowledge modeling in image guided neurosurgery: application in understanding intra-operative brain shift', 'Application of the general linear model to hemodynamic response estimation in diffuse optical imaging', 'Accelerated Diffusion Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries', 'Automatic 3D segmentation of spinal cord MRI using propagated deformable models', 'A Temperature Phantom to Probe the Ensemble Average Propagator Asymmetry: an In-Silico Study', 'Deep semi-supervised segmentation with weight-averaged consistency targets', 'Geometric evaluation of distortion correction methods in diffusion MRI of the spinal cord', 'Fixed-Point U-Net Quantization for Medical Image Segmentation', 'Benefits of Linear Conditioning with Metadata for Image Segmentation', 'Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling', 'TouchMe - Distribution and Management of Medical Videos in Clinical Routine', 'Modélisation des connaissances en neurochirurgie guidée par l’image : application à l’étude des déformations anatomiques intra-opératoires', 'Methodology to study functional MRI of the cat lumbar spinal cord', 'A functional MRI methodology to map the neuronal activity in the spinal cord of cats', 'In vivo diffusion MRI of the cat spinal cord following injury', 'Spinal cord in vivo diffusion tensor imaging of healthy human and spinalized cats', 'Methodology for MR diffusion tensor imaging of the cat spinal cord', 'Impact of realignment on spinal functional MRI time series', 'In vivo diffusion tensor imaging of the spinal cord', 'In vivo assessment of spinal cord integrity by diffusion tensor imaging', 'A dual lesion paradigm to study spinal cord injury (SCI) in cats using electrophysiological and imaging methods', 'BOLD signal responses to controlled hypercapnia in human spinal cord', 'Characterizing and controlling for physiological noise in human cervical spinal fMRI in response to  noxious stimuli', 'Q-ball imaging of the spinal cord', 'Characterization of the healthy and injured spinal cord using q-ball imaging', 'Detection of multiple pathways in the spinal cord white matter using q-ball imaging', 'Diffusion Tensor Imaging and Tractography of the spinal cord in animals and humans', 'Locomotor recovery after spinal lesions in the cat using behavioral and imaging techniques', 'The importance of the spinal CPG in the recovery of locomotion after partial spinal cord lesions', 'Optimizing locomotion after spinal lesions', 'Sex differences in corpus callosum fractional anisotropy in schizophrenia patients: A pilot tractography study using Diffusion Tensor Imaging', 'Slice-by-slice motion correction in spinal cord fMRI: SliceCorr', 'Comparison of hypercapnia-induced BOLD changes in the brain and spinal cord', 'Point spread function mapping for distortion correction of spinal cord diffusion weighted MRI', 'Investigation of venous effects in spinal cord fMRI using hypercapnia', 'Distortion correction in spinal cord DTI: What’s the best approach?', 'Evaluation of q-ball metrics for assessing the integrity of the injured spinal cord', 'High angular resolution diffusion MRI of spinal cord injured cats', 'Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury', 'Venous effect in spinal cord fMRI: insights from intrinsic optical imaging and laser speckle', 'Studying the sensorimotor pathways: brain - brainstem - spinal cord imaging', 'Improving high-resolution Q-Ball imaging with a head insert gradient: Bootstrap and SNR analysis', 'Improving diffusion and functional MRI of the brain and spinal cord using a new 32ch coil', 'Surface-based analysis of subpial T2* signal changes at 7T in multiple sclerosis', 'Assessing the quality of HARDI data using bootstrap on Q-Ball reconstruction', 'Subpial Pathology as a Substrate for Cortical Thinning in Multiple Sclerosis: a 7T MRI study', 'Evidence of distributed subpial T2* signal changes at 7T in multiple sclerosis: an histogram based approach', 'A 32 Channel receive-only 3T array optimized for brain and cervical spine imaging', 'Improving Sensitivity in Low SNR Diffusion Imaging Using Optimal SNR Coil Combinations', 'Improving SNR per unit time in Diffusion Imaging using a blipped-CAIPIRINHA simultaneous multi-slice EPI acquisition', 'Impact of Outliers in DTI and Q-Ball Imaging - Clinical Implications and Correction Strategies', 'Straightening the spinal cord using fiber tractography', 'Characterisation of cortical pathology using T2* mapping at 7T', 'Characterization of cortical pathology using T2* mapping at 7T', 'Quantitative characterization of cortical pathology in multiple sclerosis using surface-based analysis of T2* relaxation at 7T', 'Evidence of Wallerian degeneration in the human spinal cord using in vivo high-resolution DTI and magnetization transfer', 'Diffusion and magnetization transfer imaging detects spinal cord lesions in amyotrophic lateral sclerosis', 'Demyelination in the injured human spinal cord detected with diffusion and magnetization transfer imaging', 'Involvement of spinal sensory pathway in amyotrophic lateral sclerosis detected with DTI and magnetization transfer', 'Cortical surface and depth analysis of T2* in the human brain', 'Mechanism-Based Neuroimaging Using 7-T MRI in Amyotrophic Lateral Sclerosis (ALS)', 'In Vivo Human Brain Measurements of Axon Diameter Distributions in the Corpus Callosum using 300 mT/m Maximum Gradient Strengths', '19-channel Rx array coil and 4-channel Tx loop array for cervical spinal cord imaging at 7T MRI', 'In vivo imaging of fiber pathways of the human brain with ultra-high gradients', 'Improving SNR in high b-value diffusion imaging using Gmax=300mT/m human gradients', 'Improved Q-Ball imaging using a 300 mT/m human gradient', 'B0-orientation dependence can characterize cortical and sub-cortical fibers in vivo at 7T', 'In Vivo Human Brain Measurements of Axon Diameter Using 300 mT/m Maximum Gradient Strengths', 'Demonstration of a novel prospective motion correction technique for diffusion neuroimaging', 'Reproducibility of surface-based laminar measures of T2* relaxation decay in the cortex at 7 Tesla MRI', 'Spinal MRI atrophy study in amyotrophic lateral sclerosis and spinal muscular atrophy', 'Preliminary clinical utility of advanced spinal-cord MRI', '7T MRI of the pathological spinal cord', 'Simultaneous Diffusion-Weighted MRI of Brain and Cervical Spinal Cord using a 64-Channel Head-Neck Array Coil at 3T', 'Low-Rank Basis Smoothing for the Denoising of Diffusion Weighted Images', 'A gradient in cortical T2* relaxation decay changes at 7 Tesla MRI in patients with multiple sclerosis', 'Laminar-specific variations of T2* relaxation decay in the cortex at 7 Tesla MRI', 'Imaging the Grid Structure of the Brain with DSI and QBI with the 3T Connectom Instrument: Conditional Validation of in vivo MRI Tractography in Humans', '7T MRI of the human spinal cord', 'MTR and T2* analysis of subpial demyelination', 'Intracortical laminar pathology in the motor cortex is associated with proximal underlying white matter injury in multiple sclerosis: a multimodal 7 T and 3 T MRI study', 'Validation of a cord atrophy measurements method in motor neuron diseases', 'Resolving the anatomic variability of the human cervical spinal cord: a solution to facilitate advanced neural imaging', 'Validation of a 2D Spinal Cord probabilistic atlas: Application to FA measurement and VBM study of the GM atrophy occurring with age', 'ZOOM and non-ZOOM Spinal Cord Diffusion Tensor Imaging protocols for multi-centre studies', 'Effect of spatial smoothing and cardiac gating on physiological noise in spinal cord fMRI', 'Comparison between 7T T2* and 3T MTR in the in vivo human cortex', 'Atlas of white-matter tracts in the human spinal cord', 'Multisite DTI of the spinal cord with integrated template and white matter atlas processing pipeline', 'The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter', 'In vivo estimation of axon diameter in the human spinal cord using 300 mT/m gradients', 'MNI-Poly-AMU average anatomical template for automatic spinal cord measurements', 'Intracortical laminar pathology in the motor cortex is associated with tractographically connected white matter injury in multiple sclerosis: a multimodal 7T and 3T MRI study', 'PropSeg: automatic spinal cord segmentation method for MR images using propagated deformation models', 'Spinal Cord Toolbox: an open-source framework for processing spinal cord MRI data', 'Exploring the link between resting-state functional connectivity in the default mode network and subpial pathology in MS using multimodal 7 Tesla MRI', 'Multivariate combination of magnetization transfer ratio and quantitative T2* to detect subpial demyelination in multiple sclerosis', 'Fully automated segmentation of the cervical spinal cord using PropSeg: application to multiple sclerosis', 'Spinal cord gray and white matter segmentation using atlas deformation', 'A 24-channel shim array for real-time shimming of the human spinal cord: Characterization and proof-of-concept experiment', 'Template-based analysis of multi-parametric MRI data with the Spinal Cord Toolbox', 'Slice-by-slice regularized registration for spinal cord MRI: SliceReg', 'Validation of MRI microstructure measurements with Coherent Anti-Stokes Raman Scattering (CARS)', 'Impact of noise bias with parallel imaging for axon diameter estimation with q-space MR', 'T1 and T2 template of the human brainstem and spinal cord', 'Large-FOV Tractography of the Brain and Spinal Cord with Reduced Scan Time: A Study using Diffusion-Weighted, Readout-Segmented EPI and Simultaneous Multi-Slice Acceleration', 'Comparison of NOGSE and PGSE sequences for axon diameter estimation', 'Spinal Cord Toolbox: Automated Software For Processing Quantitative MRI Data Of The Spinal Cord', 'In vivo mapping of myelin g-ratio in the human spinal cord', 'Next-generation MRI of the human spinal cord: Translating measures of microarchitecture and function to clinical utilization', 'Next-Generation MRI of the Human Spinal Cord: Quantitative Imaging Biomarkers for Cervical Spondylotic Myelopathy (CSM)', 'Multivariate combination of quantitative T2* and T1 at 7T MRI detects in vivo subpial demyelination in the early stages of MS', 'A Prospective Longitudinal Study in Degenerative Cervical Myelopathy Using Quantitative Microstructural MRI with Tract-Specific Metrics', 'Translating State-Of-The-Art Spinal Cord MRI Techniques To Clinical Use: A Systematic Review Of Clinical Studies Utilizing DTI, MT, MWF, MRS, and fMRI', 'Fully-\xadintegrated T1\u200b, T2\u200b, T2\u200b*, white and gray matter atlases of the spinal cord', 'Optimization of geometry for combined RF/shim coil arrays for the spinal cord', 'Mapping the myelin g-ratio: promises and pitfalls', 'Quantitative Magnetization Transfer Imaging Made Easy with qMTLab: Software for Data Simulation, Analysis and Visualisation', 'Very-high order shimming in the human spinal cord using a dedicated 24-channel array coil', 'Fully-integrated framework for registration of spinal cord white and gray matter', 'Validation of quantitative MRI metrics using full slice histology with automatic axon segmentation', 'Association between cortical demyelination and structural connectomics in early multiple sclerosis', 'A clinically feasible quantitative MRI protocol to assess tissue injury in the cervical spinal cord using DTI, MT, and T2*-weighted imaging: reliability and variations with confounding variables', 'Microstructural MRI Quantifies Tract-Specific Injury and Correlates With Global Disability and Focal Neurological Deficits in Degenerative Cervical Myelopathy', 'Bringing the T1 mapping sequences together: A study of the T2 effects in ex vivo pig hearts', 'Toward Clinical Translation of Quantitative Spinal Cord MRI: Serial Monitoring to Identify Disease Progression in Patients with Degenerative Cervical Myelopathy', 'Multi-Parametric Spinal Cord MRI Detects Subclinical Tissue Injury in Asymptomatic Cervical Spinal Cord Compression', 'Multi-Parametric Cervical Spinal Cord MRI Provides an Accurate Diagnostic Tool for Detecting Clinical Myelopathy', 'Changes in structural network connectivity in early-stage multiple sclerosis are associated with cortical demyelination', 'Repeatability and reproducibility of spinal cord atrophy measurements in a multiple sclerosis population using the Spinal Cord Toolbox', 'PAM50: Multimodal template of the brainstem and spinal cord compatible with the ICBM152 space', 'Exploring complementary in multi-modal imaging of cortex microstructure: a diffusion and relaxometry study', 'Partial volume effect correction for surface-based cortical mapping', 'Robust and automatic spinal cord detection on multiple MRI contrasts using machine learning', 'Making myelin water imaging mainstream: Multi-site and multi-vendor reproducibility', 'Fast multivariate relaxometry can differentiate neurodegenerative disease processes and phenotypes', 'Size-adaptable 13-channel receive array for brain imaging in human neonates at 3T', 'Real-time shimming of the human spinal cord using a 24-channel shim array coil', 'Fully automatic segmentation of spinal cord gray matter on patients with degenerative cervical myelopathy', 'Statistical combinations of T1, MTR, MTsat and Macromolecular Tissue Volume to improve myelin content estimation in the human spinal cord at 3T', 'Translating AxCaliber on a clinical system : 600mT/m versus optimized 80mT/m protocol', 'Scan-rescan of AxCaliber, macromolecular tissue volume and g-ratio in the spinal cord', 'On the Precision of Myelin Imaging: Characterizing Ex vivo Dog Spinal Cord with MRI and Histology', 'Histological validation of microstructural measures derived from the PICASO model', 'Evaluation of Axonal and Myelin Integrity with Advanced MRI Methods in Multiple Sclerosis', 'Volumetric Analysis of Pediatric Spinal Cord Structural MRI data using SCT', 'Development of a standardized normative pediatric spinal cord structural template: demonstration of an automatic estimation of spinal cord cross sectional area measurements (SCCSA)', 'Comparison of cervical cord results from a quantative 3D multi-parameter mapping (MPM) protocol of the whole brain with a dedicated cervical cord protocol', 'Spatial Distribution of Multiple Sclerosis lesions in the Cervical Cord', 'A unified signal readout improves denoising of multi- modal spinal cord MRI', 'Magnitude versus complex-valued images for spinal cord diffusion MRI: which one is best?', 'Consensus acquisition protocol for quantitative MRI of the cervical spinal cord at 3T', 'A statistical framework for evaluating the reliability of myelin imaging', 'Accuracy and precision of Synthetic MRI', 'Machine learning and rapid multi-parametric relaxometry can differentiate demyelinating disorders with high accuracy', 'Quantitative MRI made easy with qMRLab', 'Automatic MS lesion segmentation in the spinal cord using deep learning', 'Integrated B0/Rx coil array for improved spinal cord imaging at 3T', 'Convolutional neural network based segmentation of the spinal cord and intramedullary injury in acute blunt spinal cord trauma', 'Rapid simultaneous acquisition of QSM and MTV', 'Spinal cord contribution to long-term motor skill learning', 'Corticospinal Tract Morphometry at the Cervical Spinal Cord in Chronic Hemiparetic Stroke', 'Clinical and histological validation of rapid magnetic resonance myelin imaging in multiple sclerosis', 'Characterization of multiple sclerosis grey and white matter pathology in the brain and spinal cord at 7 Tesla MRI', 'Deep Active Learning for Myelin Segmentation on Histology Data', 'Vertebral labeling on MRI using deep learning techniques', 'Approches en imagerie par resonance magnétique pour l’étude de l’impact de la rigidité artérielle sur la matière blanche du cerveau chez les personnes âgées', 'The qMRLab workflow: From acquisition to publication', 'Spatial distribution of multiple sclerosis lesions along the brain and spinal motor tracts and correlation with functional deficits', 'Arterial stiffness and white matter integrity in the elderly: a diffusion tensor and magnetization transfer imaging study', 'Investigation of DTI parameters in the corticospinal tract: from cervical cord to motor cortex', 'Stain-free histology to validate quantitative MRI', 'Construction of a quantifiable rat spinal cord atlas and tract delineation using agglomerative clustering', 'Application of Spinal Cord White Matter Tract Integrity Quantification with Atlas-based Analysis in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'Cervical spinal cord diffusion MRI and intraspinal space restriction at the occipito-cervical junction in mucopolysacharidoses patients', 'Deep learning for prognosis in Degenerative cervical myelopathy', 'Towards a Standard Pipeline for the Analysis of Human Spinal Cord fMRI Data Series', 'Integrated AC/DC coil and dipole Tx array for 7T MRI of the spinal cord', 'Novel HARDI-ZOOMit protocol detects changes in spinal cord microstructure in patients with asymptomatic non-myelopathic degenerative cervical spinal cord compression', 'Real-time shimming in the cervical spinal cord using an 8-channel AC/DC array and a capacitive respiratory sensor', 'Development of a Standardized Normative Pediatric Spinal Cord structural template: Demonstration of an automatic estimation of Spinal Cord Cross Sectional Area measurements (SCCSA)', 'The myelin-weighted connectome: a new look at multiple sclerosis', 'On the reproducibility of MRI-DTI based passive length changes and the added implications of quantitative MRI', 'qMRLab: An open source software project for streamlining quantitative magnetic resonance imaging', 'In vivo characterization of cortical lesion demyelination and remyelination in early multiple sclerosis by quantitative 7 Tesla MRI', 'Characterization of Cortico-striatal Myelination in the Context of Pathological Repetitive Behaviors', 'Development of a Standardized Normative Pediatric Spinal Cord Structural Template: Demonstration of an Automatic Estimation of Spinal Cord Cross Sectional Area Measurements (SCCSA)', 'Repeatability and reproducibility of quantitative synthetic MRI across vendors and field strengths', 'Automatic segmentation of spinal MS lesions: How to generalize across MR contrasts?', 'Real-Time Z-Shimming for Magnetic Resonance Imaging of the Spinal Cord', 'Neonatal functional connectivity MRI preprocessing toolbox', 'Spine inter vertebral disc labeling using a fully convolutional redundant counting model', 'Spinal cord tumor segmentation using multimodal deep learning approach', 'The Courtois project on neuronal modelling - first data release', 'Pediatric Spinal Cord DTI, integrated with atlas-based Analysis', 'Neural Networks For Nerve Analysis: Streamlining Axon Histomorphometry Using Machine Learning', 'Thinking outside the black box: A fully transparent T1 mapping pipeline', 'Spinal cord and brain DTI alterations in cervical spondylotic myelopathy (CSM)', 'Effect of non-protonated perfluorocarbon liquid-filled SatPads on spinal cord MR imaging', 'Ex vivo MRI template of the human cervical cord at 80μm isotropic resolution', 'Real-Time Z-Shimming for Magnetic Resonance Imaging of the Spinal Cord', 'Spinal Cord Evaluation by Double Diffusion Encoding with Atlas-based Analysis in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'Quantitative MRI of the spinal cord: reproducibility and normative values across 40 sites', 'Myelin-sensitive Quantitative Maps: Two’s Company, Three’s a Crowd?', 'Development of Pediatric Spinal Cord White Matter Atlas: Preliminary Analysis', 'A joint-community effort to standardize quantitative MRI data: Updates from the BIDS extension proposal', 'Atlas-based Quantication of DTI measures in Typically Developing Pediatric Spinal Cord', 'Variations of quantitative MRI metrics along the cervical spinal cord: multi-vendor, multi-center, multi-subject study', 'Shimming-Toolbox: An open-source software package for performing realtime B0 shimming experiments', 'Free Water Eliminated White Matter Tract Integrity of Spinal Cord in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'Spinal cord neurodegeneration rostral and caudal to a degenerative cervical myelopathy (DCM): a quantitative MRI study', 'Development of an optimized approach to spinal cord fMRI based on the combination of an ad hoc acquisition method and data analysis pipeline', 'Spinal cord imaging: some investigations', 'Diffusion MRI of the spinal cord ', 'Diffusion & functional MRI of the spinal cord', 'New advances in DTI of the spinal cord', 'Diffusion and functional MRI of the spinal cord', 'Diffusion Tensor Imaging: Principles and Applications', 'MRI of the spinal cord: from white matter organization to neuronal activity', 'DW-MRI and fMRI of the spinal cord', 'Diffusion Tensor Imaging and tractography of the spinal cord in animals and humans', 'Q-ball imaging of the spinal cord', 'Imaging spinal cord injury and white matter damage', 'How to detect BOLD responses in spinal cord fMRI? Acquisition, pre-processing and statistical issues', 'Improving HARDI Acquisition', 'IRM quantitative cérébrospinale à 3T et 7T', 'Susceptibility artifacts in DTI of the spinal cord', 'Multi-parametric MRI of the spinal cord', 'FMRI and DTI of the spinal cord: Methodological issues', '7T MRI of cortical and spinal cord pathology in MS', '7T MRI of the healthy and pathological cerebral cortex', 'What are strong magnets and strong gradients good for?', '7T MRI of the cerebral cortex', 'T2* mapping and B0 orientation-dependence of the in vivo human cortex at 7T', 'What are strong magnets and strong gradients good for?', 'Advanced image approaches to assess the spinal cord', 'High resolution diffusion MRI', '7T MRI of the spinal cord', 'Advanced spinal cord imaging', 'Multi-parametric MRI of the spinal cord', 'FMRI of the spinal cord', 'How to correct susceptibility artifacts in fMRI and DTI?', 'Frontier Neuroscientific applications of spinal MRI', 'Spinal Cord Imaging: Diffusion & Ultra-High Field', 'The Role of Diffusion Tensor Imaging in Assessment of the Spinal Cord Injury', 'Multi-parametric MRI of the spinal cord', 'IRM multi-paramétrique du système nerveux central.', 'Spinal Cord Toolbox. ', 'In vivo histology with MRI', 'Template-based analysis of multi-parametric MRI data using the Spinal Cord Toolbox', 'In vivo histology with MRI', 'Visualizing Spinal Cord Damage using MRI', 'Advanced Techniques in Imaging specific to degenerative myelopathy', 'Acquisition and image processing methods', 'Spinal MR: what multiparametric MR can add', 'Challenges of spinal cord imaging, and superior analysis techniques using the Spinal Cord Toolbox.', 'In vivo histology of the human spinal cord using MRI', 'Spinal Cord Toolbox for MRI: application to spinal cord injury', 'In vivo histology with MRI', 'In vivo histology with MRI', 'New Imaging Techniques for Spine and Plexus', 'Early Detection of Neurological Disorders with Imaging Biomarkers', 'New Imaging Techniques for Spinal Cord Microstructure', 'Advanced Techniques in Imaging Specific to Degenerative Myelopathy', 'Overview of myelin mapping and validation techniques', 'Advanced Tools for Spinal Cord Imaging in MS', 'Validation of Microstructural Modeling in Spinal Cord Imaging', 'In vivo histology with MRI', 'Imaging Spinal Cord Microstructure with MRI', 'Spinal cord imaging for ALS, MS, and spinal cord injury', 'In vivo histology with MRI', 'High-resolution spinal cord fMRI & DWI', 'In vivo histology with MRI', 'In vivo histology with MRI', 'In vivo histology with MRI', 'State of the art for spinal cord images acquisition and processing', 'In vivo histology of the spinal cord with MRI', 'Large-scale atlases of microstructure in the central nervous system: methodology and application to the spinal cord', 'Advances in acquisition and analysis of neuro MRI: Special focus to quantify microstructure in the spinal cord', 'Standardization of acquisition and data processing in spinal cord MRI: Application in degenerative cervical myelopathy.', 'Advances in acquisition and analysis of neuro MRI: Quantifying microstructure in the spinal cord', 'Connecting MRI physics and A.I. to advance neuroimaging', 'In vivo histology with MRI: Special focus on the spinal cord', 'Connecting MRI physics and A.I. to advance neuroimaging', 'Standardizing acquisition and processing of spinal cord MRI data', 'In vivo histology with MRI', 'In vivo histology with MRI and validation techniques: Application to create large-scale atlases of microstructure in the central nervous system', 'Standardizing acquisition and processing of spinal cord MRI data', 'Connecting MRI physics and A.I. to advance neuroimaging', 'Real time shimming with hybrid AC/DC coil technology', 'Challenges & Solutions for spinal cord imaging', 'Platforms, neuroinformatics and data solutions', 'Standardizing acquisition and processing of \u2028spinal cord quantitative MRI data', 'In vivo histology with ultra-high field MRI', 'High-resolution spinal cord fMRI & DWI', 'Standardizing acquisition and processing of spinal cord MRI data', 'Connecting physics and deep learning to generalize medical image analysis tasks', "Why isn't my 7T MRI showing 7T everywhere and why is that a problem? Real-time shimming with hybrid AC/DC coil technology", 'Artificial Intelligence for Multiple Sclerosis', 'MRI biomarkers for the spinal cord', 'How to fix magnetic field inhomogeneities in MRI?', 'Neuroimaging and AI: What do we need, what is out there, how can we do better', 'Neuroimaging and AI: What do we need, what is out there, how can we do better', 'Neuroimaging and AI: What do we need, what is out there, how can we do better', 'Spinal cord fMRI', 'Diffusion-weighted imaging', 'Coil arrays', 'Magnetic Resonance Imaging of the Injured Spinal Cord: The Present and the Future', 'Functional Magnetic Resonance Imaging', 'MRI coil apparatus and method', 'Les capacités d’apprentissage du système nerveux', 'AI Helps Doctors Detect MS In the Spinal Cord', 'MS: Distribution of Cervical Spine Lesion and Clinical Status', 'Giant leaps forward in spinal cord imaging', 'On the Accuracy of T1 Mapping: Searching for Common Ground.', 'Measuring within the Voxel: Brain Tissue Volume in Individual Subjects.', 'Practical Clinical Applications of MR relaxometry', 'Improving the Accuracy of Cross-relaxation Imaging', 'Steady-state MRI: Methods for Neuroimaging.', 'Bound Pool Fractions Complement Diffusion Measures in Characterizing White Matter Micro and Macrostructure', 'A Robust Methodology for T1 Mapping']

titlesB = ['Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation.', 'Cortico-spinal imaging to study pain', 'Associations between relative morning blood pressure, cerebral blood flow, and memory in older adults treated and controlled for hypertension', 'Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps', 'Spinal Cord Morphology in Degenerative Cervical Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools', 'Tracking White and Gray Matter Degeneration along the Spinal Cord Axis in Degenerative Cervical Myelopathy', 'Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning.', 'Diffusion magnetic resonance imaging reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression.', 'A simple and robust method for automating analysis of naïve and regenerating peripheral nerves.', 'Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers', 'Generic acquisition protocol for quantitative MRI of the spinal cord', 'The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure.', 'Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy.', 'Atlas-Based Quantification of DTI Measures in a Typically Developing Pediatric Spinal Cord.', 'Quantitative 7-Tesla Imaging of Cortical Myelin Changes in Early Multiple Sclerosis.', 'SoftSeg: Advantages of soft versus binary training for image segmentation', 'ivadomed: A Medical Imaging Deep Learning Toolbox', 'HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy', 'Machine learning and multi-parametric brain MRI to differentiate hereditary diffuse leukodystrophy with spheroids from multiple sclerosis', 'An interactive meta-analysis of MRI biomarkers of myelin', '7 T imaging reveals a gradient in spinal cord lesion distribution in multiple sclerosis', 'qMRLab: Quantitative MRI analysis, under one umbrella', 'Multi-parametric quantitative in vivo spinal cord MRI with unified signal readout and image denoising', 'Arterial stiffness cut-off value and white matter integrity in the elderly', 'Injury Volume Extracted from MRI Predicts Neurologic Outcome in Acute Spinal Cord Injury: A Prospective TRACK-SCI Pilot Study', "A Cross-Sectional Study on the Impact of Arterial Stiffness on the Corpus Callosum, a Key White Matter Tract Implicated in Alzheimer's Disease", 'Injury volume extracted from MRI predicts neurologic outcome in acute spinal cord injury: A prospective TRACK-SCI pilot study', 'Validation of Rapid Magnetic Resonance Myelin Imaging in Multiple Sclerosis', 'Multiple sclerosis lesions in motor tracts from the brain to the cervical cord: spatial distribution and correlation with disability', 'Signal Intensity within Cerebral Venous Sinuses on Synthetic MRI', 'Profiles of cortical inflammation in multiple sclerosis by 11C-PBR28 MR-PET and 7 Tesla imaging', 'Deep Semantic Segmentation of Natural and Medical Images: A Review', 'Resting-state brain and spinal cord networks in humans are functionally integrated', 'Imaging mechanisms of disease progression in multiple sclerosis: beyond brain atrophy', 'Construction of a rat spinal cord atlas of axon morphometry', 'Traumatic and nontraumatic spinal cord injury: pathological insights from neuroimaging', 'Brainstem and spinal cord MRI identifies altered sensorimotor pathways post-stroke', 'Promises and limitations of deep learning for medical image segmentation', 'Unsupervised domain adaptation for medical imaging segmentation with self-ensembling', 'Presymptomatic spinal cord pathology in c9orf72 mutation carriers: A longitudinal neuroimaging study', 'Deep Active Learning for Axon-Myelin Segmentation on Histology Data', 'Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks', 'Open-source pipeline for multi-class segmentation of the spinal cord with deep learning', 'The spinal and cerebral profile of adult spinal-muscular atrophy: A multimodal imaging study', 'Arterial stiffness and white matter integrity in the elderly: A diffusion tensor and magnetization transfer imaging study', 'Spatial distribution of multiple sclerosis lesions in the cervical spinal cord', 'Linearity, Bias, Intrascanner Repeatability, and Interscanner Reproducibility of Quantitative Multidynamic Multiecho Sequence for Rapid Simultaneous Relaxometry at 3 T: A Validation Study With a Standardized Phantom and Healthy Controls', 'Arterial stiffness and brain integrity: A review of MRI findings', 'Gray Matter Alterations in Early and Late Relapsing-Remitting Multiple Sclerosis Evaluated with Synthetic Quantitative Magnetic Resonance Imaging', 'Guidelines for the conduct of clinical trials in spinal cord injury: Neuroimaging biomarkers', 'Axons morphometry in the human spinal cord', 'Convolutional Neural Network-Based Automated Segmentation of the Spinal Cord and Contusion Injury: Deep Learning Biomarker Correlates of Motor Impairment in Acute Spinal Cord Injury', 'AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks', 'A pneumatic phantom for mimicking respiration-induced artifacts in spinal MRI', 'Spinal Cord Gray Matter Atrophy in Amyotrophic Lateral Sclerosis', 'Monitoring for myelopathic progression with multiparametric quantitative MRI', 'Effect of cardiac-related translational motion in diffusion MRI of the spinal cord', 'Promise and pitfalls of g-ratio estimation with MRI', 'Inter-Vendor Reproducibility of Myelin Water Imaging Using a 3D Gradient and Spin Echo Sequence', 'Real-time correction of respiration-induced distortions in the human spinal cord using a 24-channel shim array', 'Can microstructural MRI detect subclinical tissue injury in subjects with asymptomatic cervical spinal cord compression? A prospective cohort study', 'Spinal cord gray matter segmentation using deep dilated convolutions', 'Microstructural imaging in the spinal cord and validation strategies', 'Size-adaptable 13-channel receive array for brain MRI in human neonates at 3 T', 'Test-retest reliability of myelin imaging in the human spinal cord: Measurement errors versus region- and aging-induced variations', 'Changes in structural network are associated with cortical demyelination in early multiple sclerosis', 'PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space', 'Design and construction of an optimized transmit/receive hybrid birdcage resonator to improve full body images of medium-sized animals in 7T scanner', 'Scan-rescan of axcaliber, macromolecular tissue volume, and g-ratio in the spinal cord', 'Neuroinflammation of the spinal cord and nerve roots in chronic radicular pain patients', 'Automatic spinal cord localization, robust to MRI contrasts using global curve optimization', 'Postmortem diffusion MRI of the entire human spinal cord at microscopic resolution', 'What Has Been Learned from Magnetic Resonance Imaging Examination of the Injured Human Spinal Cord: A Canadian Perspective', 'Topologically preserving straightening of spinal cord MRI', 'AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter', 'In vivo characterization of cortical and white matter neuroaxonal pathology in early multiple sclerosis', 'Clinically Feasible Microstructural MRI to Quantify Cervical Spinal Cord Tissue Injury Using DTI, MT, and T2*-Weighted Imaging: Assessment of Normative Data and Reliability', 'MRI Atlas-Based Measurement of Spinal Cord Injury Predicts Outcome in Acute Flaccid Myelitis', 'Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter', 'Axon and Myelin Morphology in Animal and Human Spinal Cord', 'A Novel MRI Biomarker of Spinal Cord White Matter Injury: T2*-Weighted White Matter to Gray Matter Signal Intensity Ratio', 'Functional Magnetic Resonance Imaging of the Spinal Cord: Current Status and Future Developments', 'SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data', 'Brain processing of the temporal dimension of acute pain in short-term memory', 'Spinal cord grey matter segmentation challenge', 'g-Ratio weighted imaging of the human spinal cord in vivo', 'AxonSeg: open source software for axon and myelin segmentation and morphometric analysis', 'Brainhack: a collaborative workshop for the open neuroscience community', 'A 24-channel shim array for the human spinal cord: Design, evaluation, and application', 'ZOOM or Non-ZOOM? Assessing Spinal Cord Diffusion Tensor Imaging Protocols for Multi-Centre Studies', 'Is the Relationship between Cortical and White Matter Pathologic Changes in Multiple Sclerosis Spatially Specific? A Multimodal 7-T and 3-T MR Imaging Study with Surface and Tract-based Analysis', 'Translating state-of-the-art spinal cord MRI techniques to clinical use: A systematic review of clinical studies utilizing DTI, MT, MWF, MRS, and fMRI', 'Modeling white matter microstructure', 'Segmentation of the human spinal cord', 'Quantitative magnetization transfer imaging made easy with qMTLab: Software for data simulation, analysis, and visualization', 'Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe', 'White matter atlas of the human spinal cord with estimation of partial volume effect', 'In vivo mapping of human spinal cord microstructure at 300mT/m', 'Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling', 'Simultaneous Brain-Cervical Cord FMRI Reveals Intrinsic Spinal Cord Plasticity during Motor Sequence Learning', 'Spinal Cord Segmentation by One Dimensional Normalized Template Matching: A Novel, Quantitative Technique to Analyze Advanced Magnetic Resonance Imaging Data', 'Characterizing the location of spinal and vertebral levels in the human cervical spinal cord', 'In vivo histology of the myelin g-ratio with magnetic resonance imaging', 'Multivariate combination of magnetization transfer, T2* and B0 orientation to study the myelo-architecture of the in vivo human cortex', 'A reliable spatially normalized template of the human spinal cord--Applications to automated white matter/gray matter segmentation and tensor-based morphometry (TBM) mapping of gray matter alterations occurring with age', 'Real diffusion-weighted MRI enabling true signal averaging and increased diffusion contrast', 'The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter', 'Fully automated segmentation of the cervical cord from T1-weighted MRI using PropSeg: Application to multiple sclerosis', 'Reproducibility of T2* mapping in the human cerebral cortex in vivo at 7 Tesla MRI', 'A gradient in cortical pathology in multiple sclerosis by in vivo quantitative 7 T imaging', 'Quantitative analysis of the myelin g-ratio from electron microscopy images of the macaque corpus callosum', 'High resolution imaging of the central nervous system: how novel imaging methods combined with navigation strategies will advance patient care', 'Spinal diffusion tensor imaging: A comprehensive review with emphasis on spinal cord anatomy and clinical applications', 'Robust, accurate and fast automatic segmentation of the spinal cord', 'Multi-parametric spinal cord MRI as potential progression marker in amyotrophic lateral sclerosis', 'Nineteen-channel receive array and four-channel transmit array coil for cervical spinal cord imaging at 7T', 'What can we learn from T2* maps of the cortex?', 'The current state-of-the-art of spinal cord imaging: applications', 'Validation of a semiautomated spinal cord segmentation method', 'Automatic labeling of vertebral levels using a robust template-based approach', 'Framework for integrated MRI average of the spinal cord white and gray matter: the MNI-Poly-AMU template', 'The current state-of-the-art of spinal cord imaging: methods', 'Recovery of locomotion after partial spinal cord lesions in cats: assessment using behavioral, electrophysiological and imaging techniques', 'Effect of respiration on the B0 field in the human spinal cord at 3T', 'Identification of discrete functional subregions of the human periaqueductal gray', 'Fast diffusion tensor imaging and tractography of the whole cervical spinal cord using point spread function corrected echo planar imaging', 'Visualizing integrative functioning in the human brainstem and spinal cord with spinal functional magnetic resonance imaging', 'Involvement of spinal sensory pathway in ALS and specificity of cord atrophy to lower motor neuron degeneration', '7-T MRI of the spinal cord can detect lateral corticospinal tract abnormality in amyotrophic lateral sclerosis', 'Pushing the limits of in vivo diffusion MRI for the Human Connectome Project', 'The Human Connectome Project and beyond: initial applications of 300 mT/m gradients', '7T MRI of spinal cord injury', 'Cervical spinal cord injection of epidural corticosteroids: comprehensive longitudinal study including multiparametric magnetic resonance imaging', 'T2* mapping and B0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex', 'Focal cortical lesion detection in multiple sclerosis: 3 Tesla DIR versus 7 Tesla FLASH-T2', 'Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries', 'Reduction of physiological noise with independent component analysis improves the detection of nociceptive responses with fMRI of the human spinal cord', 'Improving diffusion MRI using simultaneous multi-slice echo planar imaging', 'Quality assessment of high angular resolution diffusion imaging data using bootstrap on Q-ball reconstruction', 'Demyelination and degeneration in the injured human spinal cord detected with diffusion and magnetization transfer MRI', '32-channel RF coil optimized for brain and cervical spinal cord at 3 T', 'Impact of outliers on diffusion tensor and Q-ball imaging: clinical implications and correction strategies', 'In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis', 'Wallerian degeneration after spinal cord lesions in cats detected with diffusion tensor imaging', 'BOLD signal responses to controlled hypercapnia in human spinal cord', 'Human cervical spinal cord funiculi: investigation with magnetic resonance diffusion tensor imaging', 'Characterization of the hemodynamic response in the vivo rat lumbar spinal cord by intrinsic optical imaging and laser speckle microscopy', 'Investigations on spinal cord fMRI of cats under ketamine', 'Characterization of cardiac-related noise in fMRI of the cervical spinal cord', 'Development of clinical diffusion tensor MRI of the spinal cord in a context of spinal cord injury', 'In vivo DTI of the healthy and injured cat spinal cord at high spatial and angular resolution', 'Detection of multiple pathways in the spinal cord using q-ball imaging', 'Activation detection in diffuse optical imaging by means of the general linear model', 'Quantitative MRI of the Spinal Cord', 'Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling', 'Benefits of Linear Conditioning with Metadata for Image Segmentation', 'Tract-specific diffusion MRI relates to the predictors of myelopathy in degenerative cervical spinal cord compression', 'Atlas-based Quantication of DTI measures in Typically Developing Pediatric Spinal Cord', 'Free Water Eliminated White Matter Tract Integrity of Spinal Cord in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'Spinal cord neurodegeneration rostral and caudal to a degenerative cervical myelopathy (DCM): a quantitative MRI study', 'Variations of quantitative MRI metrics along the cervical spinal cord: multi-vendor, multi-center, multi-subject study', 'Shimming-Toolbox: An open-source software package for performing realtime B0 shimming experiments', 'Development of an optimized approach to spinal cord fMRI based on the combination of an ad hoc acquisition method and data analysis pipeline', 'Neural Networks For Nerve Analysis: Streamlining Axon Histomorphometry Using Machine Learning', 'Effect of non-protonated perfluorocarbon liquid-filled SatPads on spinal cord MR imaging', 'Real-Time Z-Shimming for Magnetic Resonance Imaging of the Spinal Cord', 'Spinal Cord Evaluation by Double Diffusion Encoding with Atlas-based Analysis in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'A joint-community effort to standardize quantitative MRI data: Updates from the BIDS extension proposal', 'Thinking outside the black box: A fully transparent T1 mapping pipeline', 'Myelin-sensitive Quantitative Maps: Two’s Company, Three’s a Crowd?', 'Spinal cord and brain DTI alterations in cervical spondylotic myelopathy (CSM)', 'Ex vivo MRI template of the human cervical cord at 80μm isotropic resolution', 'Quantitative MRI of the spinal cord: reproducibility and normative values across 40 sites', 'Development of Pediatric Spinal Cord White Matter Atlas: Preliminary Analysis', 'Automatic segmentation of spinal MS lesions: How to generalize across MR contrasts?', 'Spinal cord tumor segmentation using multimodal deep learning approach', 'Repeatability and reproducibility of quantitative synthetic MRI across vendors and field strengths', 'Real-Time Z-Shimming for Magnetic Resonance Imaging of the Spinal Cord', 'Neonatal functional connectivity MRI preprocessing toolbox', 'The Courtois project on neuronal modelling - first data release', 'Spine inter vertebral disc labeling using a fully convolutional redundant counting model', 'Pediatric Spinal Cord DTI, integrated with atlas-based Analysis', 'Fixed-Point U-Net Quantization for Medical Image Segmentation', 'In vivo characterization of cortical lesion demyelination and remyelination in early multiple sclerosis by quantitative 7 Tesla MRI', 'On the reproducibility of MRI-DTI based passive length changes and the added implications of quantitative MRI', 'qMRLab: An open source software project for streamlining quantitative magnetic resonance imaging', 'Arterial stiffness and white matter integrity in the elderly: a diffusion tensor and magnetization transfer imaging study', 'Cervical spinal cord diffusion MRI and intraspinal space restriction at the occipito-cervical junction in mucopolysacharidoses patients', 'Investigation of DTI parameters in the corticospinal tract: from cervical cord to motor cortex', 'Integrated AC/DC coil and dipole Tx array for 7T MRI of the spinal cord', 'Novel HARDI-ZOOMit protocol detects changes in spinal cord microstructure in patients with asymptomatic non-myelopathic degenerative cervical spinal cord compression', 'The myelin-weighted connectome: a new look at multiple sclerosis', 'Deep learning for prognosis in Degenerative cervical myelopathy', 'Spatial distribution of multiple sclerosis lesions along the brain and spinal motor tracts and correlation with functional deficits', 'Development of a Standardized Normative Pediatric Spinal Cord structural template: Demonstration of an automatic estimation of Spinal Cord Cross Sectional Area measurements (SCCSA)', 'The qMRLab workflow: From acquisition to publication', 'Real-time shimming in the cervical spinal cord using an 8-channel AC/DC array and a capacitive respiratory sensor', 'Development of a Standardized Normative Pediatric Spinal Cord Structural Template: Demonstration of an Automatic Estimation of Spinal Cord Cross Sectional Area Measurements (SCCSA)', 'Towards a Standard Pipeline for the Analysis of Human Spinal Cord fMRI Data Series', 'Application of Spinal Cord White Matter Tract Integrity Quantification with Atlas-based Analysis in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder', 'Stain-free histology to validate quantitative MRI', 'Construction of a quantifiable rat spinal cord atlas and tract delineation using agglomerative clustering', 'Characterization of Cortico-striatal Myelination in the Context of Pathological Repetitive Behaviors', 'Geometric evaluation of distortion correction methods in diffusion MRI of the spinal cord', "Quel est le seuil de risque de la rigidité artérielle associé à l'intégrité de la substance blanche du cerveau des personnes âgées?", 'Approches en imagerie par résonance magnétique pour l’étude de l’impact de la rigidité artérielle sur la matière blanche du cerveau chez les personnes âgées', 'Corticospinal Tract Morphometry at the Cervical Spinal Cord in Chronic Hemiparetic Stroke', 'Characterization of multiple sclerosis grey and white matter pathology in the brain and spinal cord at 7 Tesla MRI', 'Clinical and histological validation of rapid magnetic resonance myelin imaging in multiple sclerosis', 'Deep semi-supervised segmentation with weight-averaged consistency targets', 'Development of a standardized normative pediatric spinal cord structural template: demonstration of an automatic estimation of spinal cord cross sectional area measurements (SCCSA)', 'A statistical framework for evaluating the reliability of myelin imaging', 'Comparison of cervical cord results from a quantitive 3D multi-parameter mapping (MPM) protocol of the whole brain with a dedicated cervical cord protocol', 'Spinal cord contribution to long-term motor skill learning', 'Spatial Distribution of Multiple Sclerosis lesions in the Cervical Cord', 'Accuracy and precision of Synthetic MRI', 'Quantitative MRI made easy with qMRLab', 'Volumetric Analysis of Pediatric Spinal Cord Structural MRI data using SCT', 'A unified signal readout improves denoising of multi-modal spinal cord MRI', 'Consensus acquisition protocol for quantitative MRI of the cervical spinal cord at 3T', 'Magnitude versus complex-valued images for spinal cord diffusion MRI: which one is best?', 'Rapid simultaneous acquisition of QSM and MTV', 'Integrated B0/Rx coil array for improved spinal cord imaging at 3T', 'Automatic MS lesion segmentation in the spinal cord using deep learning', 'Machine learning and rapid multi-parametric relaxometry can differentiate demyelinating disorders with high accuracy', 'Convolutional neural network based segmentation of the spinal cord and intramedullary injury in acute blunt spinal cor trauma', 'Fast multivariate relaxometry can differentiate neurodegenerative disease processes and phenotypes', 'Translating AxCaliber on a clinical system: 600mT/m versus optimized 80mT/m protocol', 'Evaluation of Axonal and Myelin Integrity with Advanced MRI Methods in Multiple Sclerosis', 'Toward Clinical Translation of Quantitative Spinal Cord MRI: Serial Monitoring to Identify Disease Progression in Patients with Degenerative Cervical Myelopathy', 'Fully automatic segmentation of spinal cord gray matter on patients with degenerative cervical myelopathy', 'Multi-Parametric Spinal Cord MRI Detects Subclinical Tissue Injury in Asymptomatic Cervical Spinal Cord Compression', 'Real-time shimming of the human spinal cord using a 24-channel shim array coil', 'Size-adaptable 13-channel receive array for brain imaging in human neonates at 3T', 'Scan-rescan of AxCaliber, macromolecular tissue volume and g-ratio in the spinal cord', 'Statistical combinations of T1, MTR, MTsat and Macromolecular Tissue Volume to improve myelin content estimation in the human spinal cord at 3T', 'Robust and automatic spinal cord detection on multiple MRI contrasts using machine learning', 'Making myelin water imaging mainstream: Multi-site and multi-vendor reproducibility', 'PAM50: Multimodal template of the brainstem and spinal cord compatible with the ICBM152 space', 'Repeatability and reproducibility of spinal cord atrophy measurements in a multiple sclerosis population using the Spinal Cord Toolbox', 'Partial volume effect correction for surface-based cortical mapping', 'On the Precision of Myelin Imaging: Characterizing Ex vivo Dog Spinal Cord with MRI and Histology', 'Histological validation of microstructural measures derived from the PICASO model', 'Changes in structural network connectivity in early-stage multiple sclerosis are associated with cortical demyelination', 'Exploring complementary in multi-modal imaging of cortex microstructure: a diffusion and relaxometry study', 'Bringing the T1 mapping sequences together: A study of the T2 effects in ex vivo pig hearts', 'A clinically feasible quantitative MRI protocol to assess tissue injury in the cervical spinal cord using DTI, MT, and T2*-weighted imaging: reliability and variations with confounding variables', 'Microstructural MRI Quantifies Tract-Specific Injury and Correlates With Global Disability and Focal Neurological Deficits in Degenerative Cervical Myelopathy', 'Very-high order shimming in the human spinal cord using a dedicated 24-channel array coil', 'Validation of quantitative MRI metrics using full slice histology with automatic axon segmentation', 'Fully-\xadintegrated T1,T2, T2*, white and gray matter atlases of the spinal cord', 'Quantitative Magnetization Transfer Imaging Made Easy with qMTLab: Software for Data Simulation, Analysis and Visualisation', 'Mapping the myelin g-ratio: promises and pitfalls', 'Fully-integrated framework for registration of spinal cord white and gray matter', 'Optimization of geometry for combined RF/shim coil arrays for the spinal cord', 'A Prospective Longitudinal Study in Degenerative Cervical Myelopathy Using Quantitative Microstructural MRI with Tract-Specific Metrics', 'A Temperature Phantom to Probe the Ensemble Average Propagator Asymmetry: an In-Silico Study', 'Multivariate combination of quantitative T2* and T1 at 7T MRI detects in vivo subpial demyelination in the early stages of MS', 'Next-Generation MRI of the Human Spinal Cord: Quantitative Imaging Biomarkers for Cervical Spondylotic Myelopathy (CSM)', 'A 24-channel shimarray for real-time shimming of the human spinal cord: Characterization and proof-of-conceptexperiment', 'Large-FOV Tractography of the Brain and Spinal Cord with Reduced Scan Time: A Study using Diffusion-Weighted, Readout-Segmented EPI and Simultaneous Multi-Slice Acceleration', 'Multivariate combination of magnetization transfer ratio and quantitative T2* to detectsubpial demyelination in multiple sclerosis', 'Spinal cord gray and white matter segmentation using atlas deformation', 'Slice-by-slice regularized registration for spinal cord MRI: SliceReg', 'Validation of MRI microstructure measurements with Coherent Anti-Stokes Raman Scattering (CARS)', 'Template-based analysis of multi-parametric MRI data with the Spinal Cord Toolbox', 'In vivo mapping of myelin g-ratio in the human spinal cord', 'Impact of noise bias with parallel imaging for axon diameter estimation with q-space MR', 'Spinal Cord Toolbox: Automated Software For Processing Quantitative MRI Data Of The Spinal Cord', 'Comparison of NOGSE and PGSE sequences for axon diameter estimation', 'T1 and T2 template of the human brainstem and spinal cord', 'Fully automated segmentation of the cervical spinal cord using PropSeg:application to multiple sclerosis', 'Next-generation MRI of the human spinal cord: Translating measures of microarchitecture and function to clinical utilization', 'Exploring the link between resting-state functional connectivity in the default mode network and subpial pathology in MS using multimodal 7 Tesla MRI', 'PropSeg: automatic spinal cord segmentation method for MR images using propagated deformable models', 'Atlas of white-matter tracts in the human spinal cord', 'Comparison between 7T T2* and 3T MTR in the in vivo human cortex', 'In vivo estimation of axon diameter in the human spinal cord using 300 mT/m gradients', 'Multisite DTI of the spinal cord with integrated template and white matter atlas processing pipeline', 'ZOOM and non-ZOOM Spinal Cord Diffusion Tensor Imaging protocols for multi-centre studies', 'Effect of spatial smoothing and cardiac gating on physiological noise in spinal cord fMRI', 'Validation of a 2D Spinal Cord probabilistic atlas. Application to FA measurement and VBM study of the GM atrophy occurring with age', 'Resolving the anatomic variability of the human cervical spinal cord: a solution to facilitate advanced neural imaging', 'MNI-Poly-AMU average anatomical template for automatic spinal cord measurements', 'Spinal Cord Toolbox: an open-source framework for processing spinal cord MRI data', 'The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter', 'Automatic 3D segmentation of spinal cord MRI using propagated deformable models', 'MTR and T2* analysis of subpial demyelination', 'A gradient in cortical T2* relaxation decay changes at 7 Tesla MRI in patients with multiple sclerosis', '7T MRI of the pathological spinal cord', 'Simultaneous Diffusion-Weighted MRI of Brain and Cervical Spinal Cord using a 64-Channel Head-Neck Array Coil at 3T', 'Low-Rank Basis Smoothing for the Denoising of Diffusion Weighted Images', 'Laminar-specific variations of T2* relaxation decay in the cortex at 7 Tesla MRI', 'Imaging the Grid Structure of the Brain with DSI and QBI with the 3T Connectom Instrument: Conditional Validation of in vivo MRI Tractography in Humans', 'Mechanism-Based Neuroimaging Using 7-T MRI in Amyotrophic Lateral Sclerosis (ALS)', 'Preliminary clinical utility of advanced spinal-cord MRI', '7T MRI of the human spinal cord', 'Reproducibility of surface-based laminar measures of T2* relaxation decay in the cortex at 7 Tesla MRI', 'In Vivo Human Brain Measurements of Axon Diameter Using 300 mT/m Maximum Gradient Strengths', 'Demonstration of a novel prospective motion correction technique for diffusion neuroimaging', '19-channel Rx array coil and 4-channel Tx loop array for cervical spinal cord imaging at 7T MRI', 'In vivo imaging of fiber pathways of the human brain with ultra-high gradients', 'Improved Q-Ball imaging using a 300 mT/m human gradient', 'In Vivo Human Brain Measurements of Axon Diameter Distributions in the Corpus Callosum using 300 mT/m Maximum Gradient Strengths', 'Improving SNR in high b-value diffusion imaging using Gmax=300mT/m human gradients', 'Spinal MRI atrophy study in amyotrophic lateral sclerosis and spinal muscular atrophy', 'B0-orientation dependence can characterize cortical and sub-cortical fibers in vivo at 7T', 'Characterization of cortical pathology using T2* mapping at 7T', 'Characterisation of cortical pathology using T2* mapping at 7T', 'Involvement of spinal sensory pathway in amyotrophic lateral sclerosis detected with DTI and magnetization transfer', 'Quantitative characterization of cortical pathology in multiple sclerosis using surface-based analysis of T2* relaxation at 7T', 'Diffusion and magnetization transfer imaging detects spinal cord lesions in amyotrophic lateral sclerosis', 'Evidence of Wallerian degeneration in the human spinal cord using in vivo high-resolution DTI and magnetization transfer', 'Demyelination in the injured human spinal cord detected with diffusion and magnetization transfer imaging', 'Subpial Pathology as a Substrate for Cortical Thinning in Multiple Sclerosis: a 7T MRI study', 'Assessing the quality of HARDI data using bootstrap on Q-Ball reconstruction', 'Improving diffusion and functional MRI of the brain and spinal cord using a new 32ch coil', 'Improving high-resolution Q-Ball imaging with a head insert gradient: Bootstrap and SNR analysis', 'A 32 Channel receive-only 3T array optimized for brain and cervical spine imaging', 'Surface-based analysis of subpial T2* signal changes at 7T in multiple sclerosis', 'Improving SNR per unit time in Diffusion Imaging using a blipped-CAIPIRINHA simultaneous multi-slice EPI acquisition', 'Improving Sensitivity in Low SNR Diffusion Imaging Using Optimal SNR Coil Combinations', 'Impact of Outliers in DTI and Q-Ball Imaging - Clinical Implications and Correction Strategies', 'Evidence of distributed subpial T2* signal changes at 7T in multiple sclerosis: an histogram based approach', 'High angular resolution diffusion MRI of spinal cord injured cats', 'Venous effect in spinal cord fMRI: insights from intrinsic optical imaging and laser speckle', 'H, Descoteaux M, Deriche R, Benali H, Rossignol S. Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury.', 'Optimizing locomotion after spinal lesions', 'Studying the sensorimotor pathways: brain - brainstem - spinal cord imaging', 'Comparison of hypercapnia-induced BOLD changes in the brain and spinal cord', 'Investigation of venous effects in spinal cord fMRI using hypercapnia', 'Evaluation of q-ball metrics for assessing the integrity of the injured spinal cord', 'Distortion correction in spinal cord DTI: What’s the best approach?', 'Point spread function mapping for distortion correction of spinal cord diffusion weighted MRI', 'Slice-by-slice motion correction in spinal cord fMRI: SliceCorr', 'The importance of the spinal CPG in the recovery of locomotion after partial spinal cord lesions', 'Characterization of the healthy and injured spinal cord using q-ball imaging', 'Locomotor recovery after spinal lesions in the cat using behavioral and imaging techniques', 'Diffusion Tensor Imaging and Tractography of the spinal cord in animals and humans', 'Q-ball imaging of the spinal cord', 'BOLD signal responses to controlled hypercapnia in human spinal cord', 'Characterizing and controlling for physiological noise in human cervical spinal fMRI in response to  noxious stimuli', 'In vivo assessment of spinal cord integrity by diffusion tensor imaging', 'In vivo diffusion MRI of the cat spinal cord following injury', 'A dual lesion paradigm to study spinal cord injury (SCI) in cats using electrophysiological and imaging methods', 'Spinal cord in vivo diffusion tensor imaging of healthy human and spinalized cats', 'In vivo diffusion tensor imaging of the spinal cord', 'A functional MRI methodology to map the neuronal activity in the spinal cord of cats', 'Methodology to study functional MRI of the cat lumbar spinal cord', 'Distribution and Management of Medical Videos in Clinical Routine']
fuzzy.py 
#!/usr/bin/env python3

"""

TODO:

- there should be some way to sync the threshold used by fuzzy_assign() to the threshold inside of
  real_real_quick_ratio
  the easy thing would be to change it from an implied keyword argument to just calling it directly in the functions
  then we can control

  but then these functions are less generic because they can only operate on single strings.
"""

import heapq
import itertools
import functools

try:

    import fuzzywuzzy.fuzz as difflib # speed hack
    # if you `pip install fuzzywuzzy python-levenshtein`,
    # then scoring strings is 10x times faster.
except ImportError:
    import difflib

import numpy as np
import scipy.optimize

import tqdm


#@functools.cache # python3.9
@functools.lru_cache(maxsize=None)
def real_real_quick_ratio(a,b, threshold=0.9):
    """
    Compute the similarity ratio(a,b) quickly.

    Inspired by difflib.get_close_matches(), which
    does basically the same thing but inline in a loop.
    This is more general.
    """
    #if a == b: return 1.0 # does this make it faster? # no, it doesn't

    # experimentally:
    # at threshold=0.9 this is about 10x faster than just calling m.ratio() directly
    # but at threshold=0.6 it is not noticeably faster

    m = difflib.SequenceMatcher(None, a, b)
    
    #return m.ratio() # DEBUG conclusion: fuzzy_assign is not sensitive to using this vs clamping to 0

    if m.real_quick_ratio() < threshold: return 0.0
    if m.quick_ratio() < threshold: return 0.0
    r=m.ratio() # now do the hard work
    if r < threshold: return 0.0 
    return r


def precompute_scores(A, B, score=real_real_quick_ratio):
    """
    precompute scores, with a status bar; this only usful if score is memoized
    """
    import tqdm
    for a,b in tqdm.tqdm(((a,b) for a in A for b in B), total=len(A)*len(B), desc="precomputing scores"):
        score(a,b)


def fuzzy_assign1(A, B, threshold=0.9, score=real_real_quick_ratio):
    """
    Fuzzily match elements in A to elements in B.

    This is the https://en.wikipedia.org/wiki/Assignment_problem.

    This uses a simple greedy algorithm, so it won't necessarily
    get the optimal result. In relatively clean and accurate data
    with obvious matches, it gives the optimal result; I'm not
    sure what conditions would cause it to diverge?

    :param A: list[T] - a list of items
    :param B: list[U] - a list of items
    :param score: score(a: T, b: U) -> float
      - return the socre
      - the default takes two strings (so A and B must be lists of strings)
      - provide a custom function to handle other types and adjust the way details are weighted

    :returns (pairs: list[tuple[T,U]], unmatched_A: list[T], unmatched_B: list[U]) 
     - pairs contains the best pairings, and the unmatched lists are the leftovers 
    
    This is sort of like computing (set(A).intersect(set(B)), set(A) - set(B), set(B) - set(A))
    except:
     - it handles duplicate elements (unlike set(), which throws them away),
     - there's a looser definition of equality between elements

    """


    # this is a simple greedy algorithm: score all pairs, then cross off the best pairs until no pairs are left.

    scores = {}
    for a,b in ((a,b) for a in A for b in B):
        scores[a,b] = score(a,b)

    A = list(A) # make copies, so we can edit them; by editing, we 
    B = list(B)
    pairs = []
    while True:
    #for i in tqdm.tqdm(itertools.count(), desc="Matching items - multiple sorts"): # note: this loop is unbounded and we don't know what its
        #upper limit is, but it does have one because each iteration it either terminates ('break') or it removes one item
        #from A and B, which will eventually cause L to be empty

        #print(len(A), len(B)) # DEBUG
        # this is still inefficient because it's constantly re-sorting the same sorted data
        # it would be simpler to
        L = heapq.nlargest(1, ((a,b) for a in A for b in B if scores[a,b] >= threshold), key=lambda pair: scores[pair])
        if not L:
            # no more matches
            break
        (a,b), = L # we told nlargest to give us at most 1 result; and we know it's not 0 because of the 'if not'
        A.remove(a) # cross these off the list
        B.remove(b)

        pairs.append((a,b))

    return pairs, A, B


def fuzzy_assign2(A, B, threshold=0.9, score=real_real_quick_ratio):
    scores = {}
    for a,b in ((a,b) for a in A for b in B):
        scores[a,b] = score(a,b)

    # this is a simple greedy algorithm: score all pairs, then cross off the best pairs until no pairs are left.

    # pay attention: a hidden assumption here is that score does thresholding`
    # this assumption greatly speeds things up
    # maybe we need to add a second threshold? kind of awkward

    # work with indexes instead of strings directly.
    # If we were using strings directly like fuzzy_assign1() it would not be safe to
    # do the filter in each step that crosses off all uses of each i or j, because
    # in the rare case where a string appears twice in A or B we couldn't tell
    # if we were crossing off its first or second sets of pairs; and that might be
    # bad if that second appearance was needed to match something later.
    # So we work with indexes.
    pairs = [(i,j) for i in range(len(A)) for j in range(len(B)) if scores[A[i], B[j]] >= threshold]

    # it would be nice if these were named better?
    # this one line is the bulk of the algorithm: sort by score.
    # the rest is just parsing through its result
    pairs = sorted(pairs, reverse=True, key=lambda pairi: scores[A[pairi[0]], B[pairi[1]]])

    # run down pairs from the top, picking off the best matches repeatedly
    matches = []
    while pairs:
        i,j = pairs[0]

        # cross off all pairs that involve i or j (including the one we just took off!)
        pairs = [(ii,jj) for ii,jj in pairs if not (i == ii or j == jj)]

        # record the successful match
        matches.append((i,j))

    # compute unmatched items
    Ai = set(range(len(A))) - set(i for i,j in matches)
    Bj = set(range(len(B))) - set(j for i,j in matches)

    # map indexes -> strings
    pairs = [(A[i], B[j]) for i,j in matches]
    A = [A[i] for i in Ai]
    B = [B[j] for j in Bj]

    return pairs, A, B


def fuzzy_assign3(A, B, threshold=0.9, score=real_real_quick_ratio):
    pairs = np.zeros((len(A), len(B)))
    for i,a in enumerate(A):
        for j,b in enumerate(B):
            pairs[i,j] = score(a,b)

    pairs_i, pairs_j = scipy.optimize.linear_sum_assignment(pairs, maximize=True)

    # linear_sum_assignment() assigns as many items given to it as it can:
    # it's always true that len(pairs_i) == len(pairs_j) == min(len(A), len(B))
    # but some of these will be junk: pairs below our threshold. So toss them out.
    q = pairs[pairs_i, pairs_j] >= threshold
    pairs_i, pairs_j = pairs_i[q], pairs_j[q]

    # the unmatched sets are
    Ai = set(range(len(A))) - set(pairs_i)
    Bj = set(range(len(B))) - set(pairs_j)

    # map numpy.array -> tuples
    pairs = zip(pairs_i, pairs_j)

    # map indexes -> strings
    pairs = [(A[i], B[j]) for i,j in pairs]
    A = [A[i] for i in Ai]
    B = [B[j] for j in Bj]

    # done
    return pairs, A, B 


if __name__ == '__main__':

    from data import titlesA, titlesB

    precompute_scores(titlesA,titlesB) # DEBUG: cache the scores first, so their time doesn't count towards the matching algorithm


    # compare implementations

    import timeit

    t0 = timeit.default_timer()
    pairs1, A1, B1 = fuzzy_assign1(titlesA,titlesB, threshold=0.6)
    t1 = timeit.default_timer()
    print('assign1:', t1 - t0)

    t0 = timeit.default_timer()
    pairs2, A2, B2 = fuzzy_assign2(titlesA,titlesB, threshold=0.6)
    t1 = timeit.default_timer()
    print('assign2:', t1 - t0)

    t0 = timeit.default_timer()
    pairs3, A3, B3 = fuzzy_assign3(titlesA,titlesB, threshold=0.6)
    t1 = timeit.default_timer()
    print('assign3:', t1 - t0)

    # the results aren't guaranteed to be ordered...
    # maybe they should be?
    pairs1 = sorted(pairs1)
    pairs2 = sorted(pairs2)
    pairs3 = sorted(pairs3)

    A1 = sorted(A1)
    A2 = sorted(A2)
    A3 = sorted(A3)

    B1 = sorted(B1)
    B2 = sorted(B2)
    B3 = sorted(B3)

    print(len(pairs1), len(A1), len(B1))
    print(len(pairs2), len(A2), len(B2))
    print(len(pairs3), len(A3), len(B3))

    assert pairs1 == pairs2 == pairs3
    assert A1 == A2 == A3
    assert B1 == B2 == B3

    # try to extend results by recomputing at lower thresholds
    # hopefully, all the obvious matches have been taken out already
    # and now A3 and B3 are short.
    # 
    # XXX actually this doesn't do much.
    # fuzzy_assign3 isn't as sensitive to threshold as fuzzy_assign2 is
    # because the main processing loop in the latter depends on how many items pass the threshold
    # but the main processing in scipy.optimize.linear_sum_assign() depends rather on len(A)*len(B); it doesn't win
    # anything from sparseness; but even so, it's in C so it's much faster than the python.
    for t in [0.8, 0.7, 0.6]: # don't go below .6, results are pretty unreliable down there
        t0 = timeit.default_timer()
        pairs3_b, A3_b, B3_b = fuzzy_assign3(A3, B3, threshold=t)
        pairs3, A3, B3 = sorted(pairs3 + pairs3_b), A3_b, B3_b
        t1 = timeit.default_timer()
        print(f'extending assign3 @ {t}:', t1 - t0)
        print(len(pairs3), len(A3), len(B3))


    # inspect results

    pairs = pairs3
    A = A3
    B = B3

    score = real_real_quick_ratio
    for a,b in sorted(pairs, key=lambda p: score(*p), reverse=True):
        if score(a,b) == 1.0:
            # quiet noise
            assert a == b
            continue
        print(score(a,b), "\n\t", repr(a),'=>\n\t',repr(b))
    for a in A:
        print('A unmatched:', repr(a))
    for b in B:
        print('B unmatched:', repr(b))

    print(len(pairs), len(A), len(B))

This gets me:

kousu@ail:~/src/neuropoly/bibeasy$ python3 fuzzy.py
precomputing scores:   0%|          | 0/168350 [00:00<?, ?it/s]
precomputing scores:   3%|▎         | 4214/168350 [00:00<00:03, 42135.62it/s]
precomputing scores:   5%|▍         | 8344/168350 [00:00<00:03, 41881.39it/s]
precomputing scores:   8%|▊         | 12812/168350 [00:00<00:03, 42679.94it/s]
precomputing scores:  10%|█         | 16998/168350 [00:00<00:03, 42420.40it/s]
precomputing scores:  12%|█▏        | 20342/168350 [00:00<00:03, 39256.81it/s]
precomputing scores:  15%|█▍        | 24975/168350 [00:00<00:03, 41138.56it/s]
precomputing scores:  18%|█▊        | 29822/168350 [00:00<00:03, 43090.90it/s]
precomputing scores:  20%|██        | 34099/168350 [00:00<00:03, 42991.45it/s]
precomputing scores:  23%|██▎       | 38723/168350 [00:00<00:02, 43913.76it/s]
precomputing scores:  26%|██▌       | 42982/168350 [00:01<00:02, 43046.42it/s]
precomputing scores:  28%|██▊       | 47198/168350 [00:01<00:02, 42114.70it/s]
precomputing scores:  31%|███       | 51352/168350 [00:01<00:02, 40921.44it/s]
precomputing scores:  33%|███▎      | 55411/168350 [00:01<00:03, 37287.28it/s]
precomputing scores:  35%|███▌      | 59179/168350 [00:01<00:03, 35686.66it/s]
precomputing scores:  37%|███▋      | 62790/168350 [00:01<00:03, 33859.63it/s]
precomputing scores:  40%|████      | 67686/168350 [00:01<00:02, 37310.90it/s]
precomputing scores:  43%|████▎     | 72159/168350 [00:01<00:02, 39263.31it/s]
precomputing scores:  45%|████▌     | 76461/168350 [00:01<00:02, 40312.85it/s]
precomputing scores:  48%|████▊     | 80770/168350 [00:01<00:02, 41107.34it/s]
precomputing scores:  51%|█████     | 85687/168350 [00:02<00:01, 43231.79it/s]
precomputing scores:  54%|█████▎    | 90089/168350 [00:02<00:01, 42660.10it/s]
precomputing scores:  56%|█████▌    | 94412/168350 [00:02<00:01, 40598.04it/s]
precomputing scores:  59%|█████▊    | 98533/168350 [00:02<00:01, 40233.82it/s]
precomputing scores:  61%|██████    | 102600/168350 [00:02<00:01, 40116.68it/s]
precomputing scores:  63%|██████▎   | 106642/168350 [00:02<00:01, 39504.59it/s]
precomputing scores:  66%|██████▌   | 111487/168350 [00:02<00:01, 41816.61it/s]
precomputing scores:  69%|██████▉   | 116242/168350 [00:02<00:01, 43379.39it/s]
precomputing scores:  72%|███████▏  | 120632/168350 [00:02<00:01, 43199.89it/s]
precomputing scores:  74%|███████▍  | 125207/168350 [00:03<00:00, 43931.47it/s]
precomputing scores:  77%|███████▋  | 129629/168350 [00:03<00:00, 42810.35it/s]
precomputing scores:  81%|████████  | 135801/168350 [00:03<00:00, 47143.12it/s]
precomputing scores:  85%|████████▌ | 143413/168350 [00:03<00:00, 53219.47it/s]
precomputing scores:  91%|█████████ | 152873/168350 [00:03<00:00, 61258.19it/s]
precomputing scores:  95%|█████████▍| 159694/168350 [00:03<00:00, 62467.31it/s]
precomputing scores:  99%|█████████▉| 166675/168350 [00:03<00:00, 64502.33it/s]
precomputing scores: 100%|██████████| 168350/168350 [00:03<00:00, 45922.91it/s]assign1: 11.565089895999336
assign2: 0.38203748100022494
assign3: 0.20900208400053089
344 137 6
344 137 6
344 137 6
extending assign3 @ 0.8: 0.0023871119992691092
344 137 6
extending assign3 @ 0.7: 0.0019260959998064209
344 137 6
extending assign3 @ 0.6: 0.0018989520012837602
344 137 6
0.9963898916967509 
	 'Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation' =>
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	 'Multivariate combination of magnetization transfer ratio and quantitative T2* to detect subpial demyelination in multiple sclerosis' =>
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0.9943502824858758 
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0.9940828402366864 
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0.9932885906040269 
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0.9924242424242424 
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0.98989898989899 
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0.975 
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	 'Fully-\xadintegrated T1,T2, T2*, white and gray matter atlases of the spinal cord'
0.966542750929368 
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0.964824120603015 
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0.9608938547486033 
	 'Atlas-based Quantification of DTI measures in Typically Developing Pediatric Spinal Cord' =>
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0.9285714285714286 
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0.9101796407185628 
	 'Quantitative 7-Tesla imaging of cortical myelin changes in early multiple sclerosis' =>
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A unmatched: 'Spinal MR: what multiparametric MR can add'
A unmatched: 'Spinal cord fMRI'
A unmatched: 'Spinal cord imaging for ALS, MS, and spinal cord injury'
A unmatched: 'Spinal cord imaging: some investigations'
A unmatched: 'Spine intervertebral disc labeling using a fully convolutional redundant counting model'
A unmatched: 'Standardization of acquisition and data processing in spinal cord MRI: Application in degenerative cervical myelopathy.'
A unmatched: 'Standardizing acquisition and processing of spinal cord MRI data'
A unmatched: 'Standardizing acquisition and processing of spinal cord MRI data'
A unmatched: 'Standardizing acquisition and processing of spinal cord MRI data'
A unmatched: 'Standardizing acquisition and processing of \u2028spinal cord quantitative MRI data'
A unmatched: 'State of the art for spinal cord images acquisition and processing'
A unmatched: 'Steady-state MRI: Methods for Neuroimaging.'
A unmatched: 'Straightening the spinal cord using fiber tractography'
A unmatched: 'Susceptibility artifacts in DTI of the spinal cord'
A unmatched: 'T2* mapping and B0 orientation-dependence of the in vivo human cortex at 7T'
A unmatched: 'Template-based analysis of multi-parametric MRI data using the Spinal Cord Toolbox'
A unmatched: 'The Role of Diffusion Tensor Imaging in Assessment of the Spinal Cord Injury'
A unmatched: 'Translating State-Of-The-Art Spinal Cord MRI Techniques To Clinical Use: A Systematic Review Of Clinical Studies Utilizing DTI, MT, MWF, MRS, and fMRI'
A unmatched: 'Validation of Microstructural Modeling in Spinal Cord Imaging'
A unmatched: 'Validation of a cord atrophy measurements method in motor neuron diseases'
A unmatched: 'Vertebral labeling on MRI using deep learning techniques'
A unmatched: 'Visualizing Spinal Cord Damage using MRI'
A unmatched: 'What are strong magnets and strong gradients good for?'
A unmatched: 'What are strong magnets and strong gradients good for?'
A unmatched: "Why isn't my 7T MRI showing 7T everywhere and why is that a problem? Real-time shimming with hybrid AC/DC coil technology"
A unmatched: 'ivadomed: A Medical Imaging Deep Learning Toolbox'
B unmatched: "A Cross-Sectional Study on the Impact of Arterial Stiffness on the Corpus Callosum, a Key White Matter Tract Implicated in Alzheimer's Disease"
B unmatched: 'H, Descoteaux M, Deriche R, Benali H, Rossignol S. Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury.'

B unmatched: 'Injury volume extracted from MRI predicts neurologic outcome in acute spinal cord injury: A prospective TRACK-SCI pilot study'
B unmatched: 'Quantitative MRI of the Spinal Cord'
B unmatched: "Quel est le seuil de risque de la rigidité artérielle associé à l'intégrité de la substance blanche du cerveau des personnes âgées?"
B unmatched: 'Tract-specific diffusion MRI relates to the predictors of myelopathy in degenerative cervical spinal cord compression'
344 137 6

It's already pretty accurate. It only missed 6, and of those I'm pretty sure 2 are genuine misses (and can be found by turning the threshold down from .9 to .7) and the rest are genuine mismatches.

the two genuine but more ambiguous matches

Here's the result if I turn the threshold down more:

0.7570093457943925 
	 'Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury' =>
	 'H, Descoteaux M, Deriche R, Benali H, Rossignol S. Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury.'
0.7297297297297297 
	 'Multi-parametric MRI of the spinal cord' =>
	 'Quantitative MRI of the Spinal Cord'

When I work in the idea of a multi-field score() I'm sure it will be even more reliable; maybe not any more accurate though, I think it's already at 100% accuracy for this dataset.

This was referenced May 31, 2023
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@jcohenadad jcohenadad transferred this issue from another repository May 31, 2023
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@kousu @jcohenadad