The MTL200: A surface-based, probabilistic atlas of the medial temporal lobe.
The 4 matches
- [1] § Methods › Atlas construction ↔ scripts/atlasMTLProcessSurfaceROIs.m, lines 5 to 100 · score 0.80 · ribbon constrained, native surface, surface resampling, template spaces, fsLR, pial · Report a mismatch
- [2] § Results › Functional connectivity ↔ scripts/atlasMTLRestNetCorrelationPlot.m, lines 64 to 107 · score 0.65 · linear mixed, dATN, interaction, DN, model, LANG · Report a mismatch
- [3] § Methods › MRI data preprocessing ↔ scripts/atlasMTLProcessSurfaceROIs.m, lines 5 to 100 · score 0.52 · ribbon constrained, fsLR, preprocessing, resampling, anatomical, mapping · Report a mismatch
- [4] § Methods › MRI data preprocessing ↔ scripts/atlasMTLReliability.m, lines 3 to 101 · score 0.51 · ribbon constrained, fsLR, preprocessing, resampling, anatomical, mapping · Report a mismatch
Paper
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The authors' code
MATLAB · 320 lines · 14 KB · CC-BY-4.0 · 2 matches
- % Script to process hand-drawn anatomical regions drawn in the volume
- % then convert them to a probability map in fsLR-32k surface space.
- %% Step 1: Resample hand-modified ROIs to surface and .7mm volume
- studyDir = '/mnt/sml_share/HCP/derivatives';
- % Define subject list
- subjList = dir([studyDir '/phase1/sub-*']);
- subjListNames = {subjList.name};
- subjects = cell(length(subjListNames),1);
- for f = 1:length(subjListNames)
- subjectID = subjListNames{f}(5:end);
- subjects{f} = subjectID;
- end
- subjects = subjects';
- % Subject BIDS file path regions
- hemis = {'L','R'};
- surfaces = {'midthickness','white','pial'};
- segNames = {'LTP','LPRC','LERC','LPHC','RTP','RPRC','RERC','RPHC'};
- segColors = {[0 114 189],[217 83 25],[237 177 32], [119 172 48], [0 114 189],...
- [217 83 25], [237 177 32], [119 172 48]}; % Label colors by ROI type
- templateSpace = 'individualMTL_res-2';
- templateSpaceNew = 'individual_res-2';
- regMatPath = '/mnt/sml_share/HCP/S1200AtlasBIDS32k/from-individualMTL_to-individual_mode-image_xfm.mat';
- for s=1:length(subjects)
- subjID = subjects{s};
- anatDir = [studyDir '/fpp/sub-' subjID '/anat'];
- roiDir = [studyDir '/phase1/sub-' subjID '/roi'];
- % Define anatomical paths
- surfaceBasePath = [anatDir '/sub-' subjID '_hemi-R_space-individual_den-native_midthickness.surf.gii'];
- for h=1:2
- for su=1:3
- inputSurfacePaths{h}{su} = fpp.bids.changeName(surfaceBasePath,'hemi',hemis{h},surfaces{su});
- end
- surfaceROIPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-individual_den-native_desc-cortexAtlas_mask.shape.gii'];
- surfaceROIFsLRPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-fsLR_den-32k_desc-cortexAtlas_mask.shape.gii'];
- sphereRegFsLRPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-individual_den-native_desc-reg2fsLR_sphere.surf.gii'];
- midthickFsLRPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-individual_den-32k_midthickness.surf.gii'];
- end
- inputT1Path = [anatDir '/sub-' subjID '_space-individual_res-p7_desc-preproc_T1w.nii.gz'];
- for r=1:length(segNames)
- inputPath = [roiDir '/sub-' subjID '_space-' templateSpaceNew '_desc-handDrawn' segNames{r} '_mask.nii.gz'];
- inputPathMTL = [roiDir '/sub-' subjID '_space-' templateSpace '_desc-handDrawn' segNames{r} '_mask.nii.gz'];
- % Register individualMTL to individual space
- fpp.fsl.moveImage(inputPathMTL,inputPathMTL,inputPath,regMatPath,'interp','nn');
- % Add label text file to volume
- inputDesc = fpp.bids.checkNameValue(inputPath,'desc');
- tmpLUTPath = fpp.bids.changeName(inputPath,'desc',[inputDesc...
- 'tmpVolumeResample21093520813502'],'lut','.txt');
- fid = fopen(tmpLUTPath,'w');
- fprintf(fid,'%s\n',segNames{r});
- fprintf(fid,'%d %d %d %d %d\n',[1 segColors{r} 255]);
- fclose(fid);
- fpp.wb.command('volume-label-import',inputPath,tmpLUTPath,inputPath,'-drop-unused-labels');
- % Resample to 32k surface
- outputCiftiPath = fpp.bids.changeName(inputPath,{'space','res','den'},...
- {'fsLR',[],'32k'},'dseg','.dlabel.nii');
- fpp.func.surfaceResample(inputPath,inputSurfacePaths,surfaceROIFsLRPaths,outputCiftiPath,...
- 'sphereRegFsLRPaths',sphereRegFsLRPaths,'midthickFsLRPaths',midthickFsLRPaths,'isLabel',1);
- % Resample to native surface
- outputCiftiPath = fpp.bids.changeName(inputPath,{'space','res','den'},...
- {'individual',[],'native'},'dseg','.dlabel.nii');
- outputGiftiPaths{1} = fpp.bids.changeName(inputPath,{'space','res','den','hemi'},...
- {'individual',[],'native','L'},'dseg','.label.gii');
- outputGiftiPaths{2} = fpp.bids.changeName(inputPath,{'space','res','den','hemi'},...
- {'individual',[],'native','R'},'dseg','.label.gii');
- fpp.func.surfaceResample(inputPath,inputSurfacePaths,surfaceROIPaths,outputCiftiPath,...
- 'isLabel',1,'outputGiftiPaths',outputGiftiPaths);
- % Resample from native surface to .7mm volume
- outputPath = fpp.bids.changeName(inputPath,'res','p7');
- for h=1:2
- outputVolPaths{h} = fpp.bids.changeName(outputPath,'hemi',hemis{h},[],'.nii.gz');
- end
- for h=1:2
- fpp.wb.command('label-to-volume-mapping',outputGiftiPaths{h},...
- [inputSurfacePaths{h}{1} ' ' inputT1Path],outputVolPaths{h},['-ribbon-constrained '...
- inputSurfacePaths{h}{2} ' ' inputSurfacePaths{h}{3}]);
- end
- fpp.fsl.maths(outputVolPaths{1},['-add ' outputVolPaths{2}],outputPath);
- fpp.wb.command('volume-label-import',outputPath,tmpLUTPath,outputPath,'-drop-unused-labels');
- fpp.util.deleteImageAndJson([outputVolPaths outputGiftiPaths]);
- fpp.util.system(['rm -rf ' tmpLUTPath]);
- disp(['Finished ' subjID ' ' segNames{r}]);
- end
- end
- %% Step 2: after ROIs have been converted to surface representations, check
- % if there are any discontinuities or abnormally shaped regions, and
- % correct drawings in the volume if needed. Generate border files.
- studyDir = '/mnt/sml_share/HCP/derivatives';
- % Define subject list
- subjList = dir([studyDir '/phase1/sub-*']);
- subjListNames = {subjList.name};
- subjects = cell(length(subjListNames), 1);
- for f = 1:length(subjListNames)
- subjectID = subjListNames{f}(5:end);
- subjects{f} = subjectID;
- end
- subjects = subjects';
- % Subject BIDS file path regions
- hemis = {'L','R'};
- segNames = {'LTP','LPRC','LERC','LPHC','RTP','RPRC','RERC','RPHC'};
- segHemis = [1 1 1 1 1 2 2 2 2 2];
- spaces = {'individual_den-native','fsLR_den-32k'};
- dens = {'native','32k'};
- for s=1:length(subjects)
- subjID = subjects{s};
- anatDir = [studyDir '/fpp/sub-' subjID '/anat'];
- roiDir = [studyDir '/phase1/sub-' subjID '/roi'];
- for sp=1:length(spaces)
- % Define anatomical paths
- if ~exist([anatDir 'sub-' subjID '_hemi-L_space-individual_den-32k_midthickness.surf.gii'], 'file')
- for h = 1:2
- surfacePaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h} '_space-'...
- strrep(spaces{sp}, 'fsLR', 'individual') '_midthickness.surf.gii'];
- if strcmpi(dens{sp}, '32k')
- surfaceROIPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-fsLR_den-32k_desc-cortexAtlas_mask.shape.gii'];
- else
- surfaceROIPaths{h} = [anatDir '/sub-' subjID '_hemi-' hemis{h}...
- '_space-' spaces{sp} '_desc-cortexAtlas_mask.shape.gii'];
- end
- end
- end
- for r=1:length(segNames)
- % Input ROI path
- roiPath = [roiDir '/sub-' subjID '_space-' spaces{sp} '_desc-handDrawn' segNames{r} '_dseg.dlabel.nii'];
- % Define intermediate/output paths
- roiScalarPath = fpp.bids.changeName(roiPath,[],[],'mask','.dscalar.nii');
- roiLUTPath = fpp.bids.changeName(roiScalarPath,[],[],'lut','.txt');
- for h=1:2
- roiMetricPaths{h} = fpp.bids.changeName(roiPath,'hemi',hemis{h},'mask','.shape.gii');
- end
- roiBorderPath = fpp.bids.changeName(roiPath,'hemi',hemis{segHemis(r)},[],'.border');
- % Split into metric files to apply metric-fill-hole, then recombine
- fpp.wb.command('cifti-label-export-table',roiPath,'1',roiLUTPath);
- fpp.wb.command('cifti-label-to-roi',roiPath,[],roiScalarPath,'-map 1 -key 1');
- fpp.wb.command('cifti-separate',roiScalarPath,'COLUMN',[],['-metric CORTEX_LEFT '...
- roiMetricPaths{1} ' -metric CORTEX_RIGHT ' roiMetricPaths{2}]);
- fpp.wb.command('metric-fill-holes',surfacePaths{segHemis(r)},...
- roiMetricPaths{segHemis(r)},roiMetricPaths{segHemis(r)});
- fpp.wb.command('metric-remove-islands',surfacePaths{segHemis(r)},...
- roiMetricPaths{segHemis(r)},roiMetricPaths{segHemis(r)});
- fpp.wb.command('cifti-create-dense-scalar',[],[],roiScalarPath,['-left-metric '...
- roiMetricPaths{1} ' -roi-left ' surfaceROIPaths{1} ' -right-metric '...
- roiMetricPaths{2} ' -roi-right ' surfaceROIPaths{2}]);
- fpp.wb.command('cifti-label-import',roiScalarPath,roiLUTPath,roiPath);
- % Convert label to border file
- fpp.wb.command('cifti-label-to-border',roiPath,[],[],['-border '...
- surfacePaths{segHemis(r)} ' ' roiBorderPath]);
- fpp.util.deleteImageAndJson([{roiScalarPath,roiLUTPath} roiMetricPaths]);
- fpp.util.system(['rm -rf ' roiLUTPath]);
- disp(['Finished ' subjID ' ' segNames{r}]);
- end
- end
- end
- %% Step 3: Convert ROIs from dlabel to dscalar for roiExtract
- studyDir = '/mnt/sml_share/HCP/derivatives';
- % Define subject list
- subjList = dir([studyDir '/phase1/sub-*']);
- subjListNames = {subjList.name};
- subjects = cell(length(subjListNames), 1);
- for f = 1:length(subjListNames)
- subjectID = subjListNames{f}(5:end);
- subjects{f} = subjectID;
- end
- subjects = subjects';
- % Subject BIDS file path regions
- segNames = {'LTP','LPRC','LERC','LPHC','RTP','RPRC','RERC','RPHC'};
- hemis = {'L','R'};
- spaces = {'individual_den-native','fsLR_den-32k'};
- for s=1:length(subjects)
- subjID = subjects{s};
- anatDir = [studyDir '/fpp/sub-' subjID '/anat'];
- roiDir = [studyDir '/phase1/sub-' subjID '/roi'];
- for sp=1:length(spaces)
- for r=1:length(segNames)
- roiPath = [roiDir '/sub-' subjID '_space-' spaces{sp} '_desc-handDrawn' segNames{r} '_dseg.dlabel.nii'];
- outputPath = fpp.bids.changeName(roiPath,[],[],'mask','.dscalar.nii');
- fpp.wb.command('cifti-label-to-roi',roiPath,[],outputPath,'-key 1');
- disp(['Finished ' subjID ' ' segNames{r}]);
- end
- end
- end
- %% Step 5: Combine left/right hemisphere dscalar files
- studyDir = '/mnt/sml_share/HCP/derivatives';
- % Define subject list
- subjList = dir([studyDir '/phase1/sub-*']);
- subjListNames = {subjList.name};
- subjects = cell(length(subjListNames), 1);
- for f = 1:length(subjListNames)
- subjectID = subjListNames{f}(5:end);
- subjects{f} = subjectID;
- end
- subjects = subjects';
- segNames = {'TP','PRC','ERC','PHC'};
- spaces = {'individual_den-native','fsLR_den-32k'};
- for s=1:length(subjects)
- subjID = subjects{s};
- roiDir = [studyDir '/phase1/sub-' subjID '/roi'];
- for sp=1:length(spaces)
- for r=1:length(segNames)
- inputPath = [roiDir '/sub-' subjID '_space-' spaces{sp} '_desc-handDrawn' segNames{r} '_mask.dscalar.nii'];
- roiLPath = fpp.bids.changeName(inputPath,'desc',['handDrawnL' segNames{r}]);
- roiRPath = fpp.bids.changeName(inputPath,'desc',['handDrawnR' segNames{r}]);
- fpp.wb.command('cifti-math','a+b',[],inputPath,['-var a ' roiLPath ' -var b ' roiRPath]);
- disp(['Finished ' subjID ' ' segNames{r}]);
- end
- end
- end
- %% Step 6: Create and threshold probability map across participants of surface-based hand-drawn ROIs
- studyDir = '/mnt/sml_share/HCP/derivatives';
- atlasDir = [studyDir '/fpp/group'];
- % Define subject list
- subjList = dir([studyDir '/phase1/sub-*']);
- subjListNames = {subjList.name};
- subjects = cell(length(subjListNames), 1);
- for f = 1:length(subjListNames)
- subjectID = subjListNames{f}(5:end);
- subjects{f} = subjectID;
- end
- subjects = subjects';
- hemis = {'L','R'};
- segNames = {'LTP','LPRC','LERC','LPHC','RTP','RPRC','RERC','RPHC'};
- fwhmSm = 3; % Gradient smoothing kernel FWHM in mm
- sigmaSm = fwhmSm/2.355; % Standard deviation of Gaussian kernel
- probThresh = .7;
- probThreshStr = 'P7';
- for r=1:length(segNames)
- outputPath = [atlasDir '/atlasMTL/space-fsLR_den-32k_desc-handDrawn' segNames{r} '_probseg.dscalar.nii'];
- outputPathSm = [atlasDir '/atlasMTL/space-fsLR_den-32k_desc-handDrawn' segNames{r} 'Sm' int2str(fwhmSm) '_probseg.dscalar.nii'];
- outputPathThr = [atlasDir '/atlasMTL/space-fsLR_den-32k_desc-handDrawn' segNames{r} 'Thr' probThreshStr '_mask.dscalar.nii'];
- % Sum ROIs across subjects to define probability map
- mathString = '(';
- varString = '';
- for s=1:length(subjects)
- subjID = subjects{s};
- roiDir = [studyDir '/phase1/sub-' subjID '/roi'];
- inputPath = [roiDir '/sub-' subjID '_space-fsLR_den-32k_desc-handDrawn' segNames{r} '_mask.dscalar.nii'];
- if s==1
- mathString = [mathString 'r' int2str(s)];
- else
- mathString = [mathString ' + r' int2str(s)];
- end
- varString = [varString ' -var r' int2str(s) ' ' inputPath];
- end
- mathString = [mathString ')/' int2str(length(subjects))];
- fpp.wb.command('cifti-math',mathString,[],outputPath,varString);
- disp(['Wrote ' segNames{r}]);
- end
- %% OPTIONAL: Smooth probmap and threshold probmap
- for s=1:length(subjects)
- for h=1:2
- anatDir = [studyDir '/fpp/sub-hcp100206/anat'];
- surfacePaths{h} = [anatDir '/' fpp.bids.changeName('',{'sub','hemi','space','den'},...
- {'hcp100206',hemis{h},'individual','32k'},'midthickness','.surf.gii')];
- end
- fpp.wb.command('cifti-smoothing',outputPath,[num2str(sigmaSm) ' '...
- num2str(sigmaSm) ' COLUMN'],outputPathSm,['-left-surface '...
- surfacePaths{1} ' -right-surface ' surfacePaths{2}]);
- % Threshold probmap
- mathString = ['r > ' num2str(probThresh)];
- varString = [' -var r ' outputPathSm];
- fpp.wb.command('cifti-math',mathString,[],outputPathThr,varString);
- end
atlasMTLProcessSurfaceROIs.m at commit 3caaf99, under CC-BY-4.0 · at the source
Overview
Abstract
The human medial temporal lobe (MTL) includes a number of cortical regions surrounding the hippocampus implicated in long-term memory and high-level perception, including entorhinal cortex (ERC), perirhinal cortex (PRC), parahippocampal cortex (PHC), and the medial aspect of temporopolar cortex (TPC). A critical prerequisite to studying the function of these areas is to define their anatomical boundaries. While several atlases or segmentations methods for automated boundary definition exist, they have limitations: (1) they are derived from small sample sizes; (2) most do not include TPC; and (3) they are volumetric rather than surface-based and are therefore not straightforward to use for surface-based analysis of MRI data. Here we present the MTL200: a surface-based, probabilistic atlas of MTL regions ERC, PRC, PHC, and TPC. The atlas is derived from hand drawings of regions based on gross anatomical features corresponding to cytoarchitectonic boundaries, using anatomical MRI data from 200 human participants. This work provides a valuable tool for researchers studying the anatomy and function of MTL regions, particularly the poorly characterized area TPC.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.
SocialMemoryLab/MTL200
3caaf99b2049e92c4c63698de9d12605d40439ef, 11 December 2025Availability: 1 check, the latest on 12 November 2026: the link answers
- 12 November 2026: the link answers
14 files
- scripts/
atlasMTLComputeSizeROIs. , MATLAB, 104 linesm - scripts/
atlasMTLConvert2Fsavg.m , MATLAB, 211 lines - scripts/
atlasMTLDefineWholeMTL.m , MATLAB, 331 lines - scripts/
atlasMTLGenerateLabels.m , MATLAB, 185 lines - scripts/
atlasMTLProcessSurfaceRO , MATLAB, 320 lines, 2 matchesIs.m - scripts/
atlasMTLProcessVolumeROI , MATLAB, 98 liness.m - scripts/
atlasMTLReliability.m , MATLAB, 178 lines, 1 match - scripts/
atlasMTLRestConnAvg.m , MATLAB, 50 lines - scripts/
atlasMTLRestNetCorr.m , MATLAB, 121 lines - scripts/
atlasMTLRestNetCorrelati , MATLAB, 107 lines, 1 matchonPlot.m - scripts/
atlasMTLRestSurfConn.m , MATLAB, 79 lines - scripts/
atlasMTLRestSurfConnWrap , MATLAB, 30 linesper.m - scripts/
atlasMTLSplithalfReliabi , MATLAB, 368 lineslity.m - README.md, Text, 8 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 13 scripts, each with its path and the digest of its content;
- 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- humanconnectome.org/
study/ , at Human Connectome Project; found in “Data and Code Availability”hcp-young-adult
Data and Code Availability
The atlas and code used for its generation are available at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 12 November 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 8 authors, 5 keywords, 10 MeSH terms, 5 funders, 102 references.
Cite
This paper
Faul, I., Agarwal, A., Graziose, S., Nwacha, A., Park, J., Sahibul, A., Tong, K., & Deen, B. (2026). The MTL200: A surface-based, probabilistic atlas of the medial temporal lobe. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1447. https://
BibTeX
@article{faul2026mtl200,
author = {Faul, Ian and Agarwal, Adya and Graziose, Stephen and Nwacha, Andrew and Park, Janis and Sahibul, Anisah and Tong, Katie and Deen, Ben},
title = {{The MTL200: A surface-based, probabilistic atlas of the medial temporal lobe}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = nov,
volume = {4},
pages = {IMAG.a.1447},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/
url = {https://
pmid = {43011773},
pmcid = {PMC13749375}
}
RIS
TY - JOUR
AU - Faul, Ian
AU - Agarwal, Adya
AU - Graziose, Stephen
AU - Nwacha, Andrew
AU - Park, Janis
AU - Sahibul, Anisah
AU - Tong, Katie
AU - Deen, Ben
TI - The MTL200: A surface-based, probabilistic atlas of the medial temporal lobe
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/
VL - 4
SP - IMAG.a.1447
SN - 2837-6056
PB - MIT Press
DO - 10.1162/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1162/
"type": "article-journal",
"title": "The MTL200: A surface-based, probabilistic atlas of the medial temporal lobe",
"container-title": "Imaging neuroscience (Cambridge, Mass.)",
"author": [
{
"family": "Faul",
"given": "Ian"
},
{
"family": "Agarwal",
"given": "Adya"
},
{
"family": "Graziose",
"given": "Stephen"
},
{
"family": "Nwacha",
"given": "Andrew"
},
{
"family": "Park",
"given": "Janis"
},
{
"family": "Sahibul",
"given": "Anisah"
},
{
"family": "Tong",
"given": "Katie"
},
{
"family": "Deen",
"given": "Ben"
}
],
"container-title-short":
"volume": "4",
"page": "IMAG.a.1447",
"DOI": "10.1162/
"PMID": "43011773",
"PMCID": "PMC13749375",
"ISSN": "2837-6056",
"publisher": "MIT Press",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
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9
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]
}
}
The tracing map gets a citation of its own once an author has validated it and it has a DOI.
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- Mapping the functional and structural connectivity of the scene network.Journal: Human brain mappingIn common: structural MRI / diffusion, 11 references
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