-
Notifications
You must be signed in to change notification settings - Fork 159
/
process_segment_cat12.m
453 lines (431 loc) · 21.5 KB
/
process_segment_cat12.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
function varargout = process_segment_cat12( varargin )
% PROCESS_SEGMENT_CAT12: Run the segmentation of a T1 MRI with SPM12/CAT12.
%
% USAGE: OutputFiles = process_segment_cat12('Run', sProcess, sInputs)
% [isOk, errMsg] = process_segment_cat12('Compute', iSubject, iAnatomy=[default], nVertices, isSphReg, isExtraMaps, isInteractive)
% process_segment_cat12('ComputeInteractive', iSubject, iAnatomy)
% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Francois Tadel, 2019-2023
eval(macro_method);
end
%% ===== GET DESCRIPTION =====
function sProcess = GetDescription() %#ok<DEFNU>
% Description the process
sProcess.Comment = 'Segment MRI with CAT12';
sProcess.Category = 'Custom';
sProcess.SubGroup = {'Import', 'Import anatomy'};
sProcess.Index = 31;
sProcess.Description = 'https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12';
% Definition of the input accepted by this process
sProcess.InputTypes = {'import'};
sProcess.OutputTypes = {'import'};
sProcess.nInputs = 1;
sProcess.nMinFiles = 0;
% Option: Subject name
sProcess.options.subjectname.Comment = 'Subject name:';
sProcess.options.subjectname.Type = 'subjectname';
sProcess.options.subjectname.Value = '';
% Option: Number of vertices
sProcess.options.nvertices.Comment = 'Number of vertices (cortex): ';
sProcess.options.nvertices.Type = 'value';
sProcess.options.nvertices.Value = {15000, '', 0};
% Option: TPM atlas
SelectOptions = {...
'', ... % Filename
'Nifti1', ... % FileFormat
'open', ... % Dialog type: {open,save}
'Select TPM atlas...', ... % Window title
'ImportAnat', ... % LastUsedDir: {ImportData,ImportChannel,ImportAnat,ExportChannel,ExportData,ExportAnat,ExportProtocol,ExportImage,ExportScript}
'single', ... % Selection mode: {single,multiple}
'files', ... % Selection mode: {files,dirs,files_and_dirs}
{{'.nii','.gz'}, 'MRI: NIfTI-1 (*.nii;*.nii.gz)', 'Nifti1'}, ... % Get all the available file formats
'MriIn'}; % DefaultFormats: {ChannelIn,DataIn,DipolesIn,EventsIn,MriIn,NoiseCovIn,ResultsIn,SspIn,SurfaceIn,TimefreqIn
sProcess.options.tpmnii.Comment = 'TPM atlas: ';
sProcess.options.tpmnii.Type = 'filename';
sProcess.options.tpmnii.Value = SelectOptions;
% Option: Spherical registration
sProcess.options.sphreg.Comment = 'Use spherical registration<BR><I><FONT color="#777777">Required for atlases, group analysis and thickness maps</FONT></I>';
sProcess.options.sphreg.Type = 'checkbox';
sProcess.options.sphreg.Value = 1;
% Option: Volume atlases
sProcess.options.vol.Comment = 'Compute volume parcellations';
sProcess.options.vol.Type = 'checkbox';
sProcess.options.vol.Value = 1;
% Option: Import extra map
sProcess.options.extramaps.Comment = 'Import additional cortical maps<BR><I><FONT color="#777777">Cortical thickness, gyrification index, sulcal depth</FONT></I>';
sProcess.options.extramaps.Type = 'checkbox';
sProcess.options.extramaps.Value = 0;
% Option: Compute cerebellum surfaces
sProcess.options.cerebellum.Comment = '<FONT color="#777777">Compute cerebellum surfaces [Experimental]</FONT>';
sProcess.options.cerebellum.Type = 'checkbox';
sProcess.options.cerebellum.Value = 0;
sProcess.options.cerebellum.Hidden = 1;
end
%% ===== FORMAT COMMENT =====
function Comment = FormatComment(sProcess) %#ok<DEFNU>
Comment = sProcess.Comment;
end
%% ===== RUN =====
function OutputFiles = Run(sProcess, sInputs) %#ok<DEFNU>
OutputFiles = {};
% Number of vertices
nVertices = sProcess.options.nvertices.Value{1};
if isempty(nVertices) || (nVertices < 50)
bst_report('Error', sProcess, [], 'Invalid number of vertices.');
return
end
% Spherical registration?
if isfield(sProcess.options, 'sphreg') && isfield(sProcess.options.sphreg, 'Value') && ~isempty(sProcess.options.sphreg.Value)
isSphReg = sProcess.options.sphreg.Value;
else
isSphReg = 1;
end
% Volume atlases?
if isfield(sProcess.options, 'vol') && isfield(sProcess.options.vol, 'Value') && ~isempty(sProcess.options.vol.Value)
isVolumeAtlases = sProcess.options.vol.Value;
else
isVolumeAtlases = 0;
end
% Cerebellum?
if isfield(sProcess.options, 'cerebellum') && isfield(sProcess.options.cerebellum, 'Value') && ~isempty(sProcess.options.cerebellum.Value)
isCerebellum = sProcess.options.cerebellum.Value;
else
isCerebellum = 1;
end
% TPM atlas
if isfield(sProcess.options, 'tpmnii') && isfield(sProcess.options.tpmnii, 'Value') && ~isempty(sProcess.options.tpmnii.Value) && ~isempty(sProcess.options.tpmnii.Value{1})
TpmNii = sProcess.options.tpmnii.Value{1};
else
TpmNii = bst_get('SpmTpmAtlas');
end
% Thickness maps
if isfield(sProcess.options, 'extramaps') && isfield(sProcess.options.extramaps, 'Value') && ~isempty(sProcess.options.extramaps.Value)
isExtraMaps = sProcess.options.extramaps.Value;
else
isExtraMaps = 0;
end
% Get subject name
SubjectName = file_standardize(sProcess.options.subjectname.Value);
if isempty(SubjectName)
bst_report('Error', sProcess, [], 'Subject name is empty.');
return;
end
% Get subject
[sSubject, iSubject] = bst_get('Subject', SubjectName);
if isempty(iSubject)
bst_report('Error', sProcess, [], ['Subject "' SubjectName '" does not exist.']);
return
end
% Call processing function
[isOk, errMsg] = Compute(iSubject, [], nVertices, 0, TpmNii, isSphReg, isVolumeAtlases, isExtraMaps, isCerebellum);
% Handling errors
if ~isOk
bst_report('Error', sProcess, [], errMsg);
elseif ~isempty(errMsg)
bst_report('Warning', sProcess, [], errMsg);
end
% Return an empty structure
OutputFiles = {'import'};
end
%% ===== COMPUTE CAT12 SEGMENTATION =====
function [isOk, errMsg] = Compute(iSubject, iAnatomy, nVertices, isInteractive, TpmNii, isSphReg, isVolumeAtlases, isExtraMaps, isCerebellum)
errMsg = '';
isOk = 0;
% Initialize SPM12+CAT12
[isInstalled, errMsg, PlugCat] = bst_plugin('Install', 'cat12', isInteractive, 1728);
if ~isInstalled
return;
end
bst_plugin('SetProgressLogo', 'cat12');
% Check if SPM is in the path
if ~exist('spm_jobman', 'file')
errMsg = 'SPM must be in the Matlab path to use this feature.';
return;
end
% Check if CAT12 is in the path
if ~exist('cat12', 'file')
errMsg = 'SPM subfolders must be in the Matlab path to use this feature (missing: spm12/toolbox/cat12).';
return;
end
% Check CAT version
[catName, catVer] = cat_version;
if isempty(catVer)
errMsg = 'Cannot identify CAT12 version: please re-install it.';
return;
end
catVer = str2num(catVer);
if (catVer < 1728)
errMsg = [...
'Please update CAT12.' 10 ...
' - Version of CAT installed on this computer: ' num2str(catVer) 10 ...
' - Minimum version of CAT supported by Brainstorm: 1728' 10 ...
' - http://www.neuro.uni-jena.de/cat/index.html#DOWNLOAD'];
return;
end
% Get default TPM.nii template
if isempty(TpmNii)
TpmNii = bst_get('SpmTpmAtlas');
end
if isempty(TpmNii) || ~file_exist(TpmNii)
error('Missing file TPM.nii');
end
% ===== GET SUBJECT =====
% Get subject
[sSubject, iSubject] = bst_get('Subject', iSubject);
if isempty(sSubject)
errMsg = 'Subject does not exist.';
return
end
% Check if a MRI is available for the subject
if isempty(sSubject.Anatomy)
errMsg = ['No MRI available for subject "' sSubject.Name '".'];
return
end
% Get default MRI if not specified
if isempty(iAnatomy)
iAnatomy = sSubject.iAnatomy;
end
% ===== DELETE EXISTING SURFACES =====
% Confirm with user that the existing surfaces will be removed
if isInteractive && ~isempty(sSubject.Surface)
isDel = java_dialog('confirm', ['Warning: There are already surfaces in this subject.' 10 ...
'Running CAT12 will remove all the existing surfaces.' 10 10 ...
'Delete the existing files?' 10 10], 'CAT12 segmentation');
if ~isDel
errMsg = 'Process aborted by user.';
return;
end
end
% ===== VERIFY FIDUCIALS IN MRI =====
% Load MRI file
T1FileBst = sSubject.Anatomy(iAnatomy).FileName;
sMri = in_mri_bst(T1FileBst);
% If the SCS transformation is not defined: compute MNI transformation to get a default one
if isempty(sMri) || ~isfield(sMri, 'SCS') || ~isfield(sMri.SCS, 'NAS') || ~isfield(sMri.SCS, 'LPA') || ~isfield(sMri.SCS, 'RPA') || (length(sMri.SCS.NAS)~=3) || (length(sMri.SCS.LPA)~=3) || (length(sMri.SCS.RPA)~=3) || ~isfield(sMri.SCS, 'R') || isempty(sMri.SCS.R) || ~isfield(sMri.SCS, 'T') || isempty(sMri.SCS.T)
% Issue warning
errMsg = 'Missing NAS/LPA/RPA: Computing the MNI normalization to get default positions.';
% Compute MNI normalization
[sMri, errNorm] = bst_normalize_mni(T1FileBst);
% Handle errors
if ~isempty(errNorm)
errMsg = [errMsg 10 'Error trying to compute the MNI normalization: ' 10 errNorm 10 ...
'Missing fiducials: the surfaces cannot be aligned with the MRI.'];
end
end
% A vox2ras matrix must be present in the MRI for running CAT12
sMri = mri_add_world(T1FileBst, sMri);
% ===== SAVE MRI AS NII =====
bst_progress('text', 'Saving temporary files...');
% Empty temporary folder, otherwise it reuses previous files in the folder
gui_brainstorm('EmptyTempFolder');
% Create temporay folder for CAT12 output
catDir = bst_fullfile(bst_get('BrainstormTmpDir'), 'cat12');
mkdir(catDir);
% Save MRI in .nii format
subjid = strrep(sSubject.Name, '@', '');
NiiFile = bst_fullfile(catDir, [subjid, '.nii']);
out_mri_nii(sMri, NiiFile);
% If a "world transformation" was not available in the MRI in the database, it was set to a default when saving to .nii
% Let's reload this file to get the transformation matrix, it will be used when importing the results
if ~isfield(sMri, 'InitTransf') || isempty(sMri.InitTransf) || isempty(find(strcmpi(sMri.InitTransf(:,1), 'vox2ras')))
% Load again the file, with the default vox2ras transformation
[tmp, vox2ras] = in_mri_nii(NiiFile, 0, 0, 0);
% Prepare the history of transformations
if ~isfield(sMri, 'InitTransf') || isempty(sMri.InitTransf)
sMri.InitTransf = cell(0,2);
end
% Add this transformation in the MRI
sMri.InitTransf(end+1,[1 2]) = {'vox2ras', vox2ras};
% Save modification on hard drive
bst_save(file_fullpath(T1FileBst), sMri, 'v7');
end
% ===== INITIALIZE SPM+CAT =====
% Switch to CAT12 expert mode
cat12('expert');
% Hide CAT12 figures
set([findall(0, 'Type', 'Figure', 'Tag', 'Interactive'), ...
findall(0, 'Type', 'Figure', 'Tag', 'CAT'), ...
findall(0, 'Type', 'Figure', 'Tag', 'Graphics')], 'Visible', 'off');
% Initialize SPM job manager
spm_jobman('initcfg');
% ===== CALL CAT12 SEGMENTATION =====
bst_progress('text', '<HTML>Starting SPM batch... <FONT COLOR="#707070"><I>(see command window)</I></FONT>');
% Create SPM batch
matlabbatch{1}.spm.tools.cat.estwrite.data = {NiiFile};
matlabbatch{1}.spm.tools.cat.estwrite.nproc = 0; % Blocking call to CAT12
matlabbatch{1}.spm.tools.cat.estwrite.opts.tpm = {TpmNii}; % User-defined TPM atlas
matlabbatch{1}.spm.tools.cat.estwrite.output.bias.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.GM.native = 1; % GM tissue maps
matlabbatch{1}.spm.tools.cat.estwrite.output.GM.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.GM.mod = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.GM.dartel = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.WM.native = 1; % WM tissue maps
matlabbatch{1}.spm.tools.cat.estwrite.output.WM.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.WM.mod = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.WM.dartel = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.native = 1; % Tissue classes 4-6 to create own TPMs
matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.mod = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.TPMC.dartel = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.native = 1; % CSF tissue maps
matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.mod = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.CSF.dartel = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.label.native = 1; % Label: background=0, CSF=1, GM=2, WM=3, WMH=4
matlabbatch{1}.spm.tools.cat.estwrite.output.label.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.label.dartel = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.labelnative = 1; % Confirmed useful by CGaser in CAT12.8
% CAT12.8 now saves everything in ICBM152NLinAsym09 space: we can use directly the MNI deformation fields
matlabbatch{1}.spm.tools.cat.estwrite.output.warps = [1 1]; % Non-linear MNI normalization deformation fields: [forward inverse]
% Volume atlases
if isVolumeAtlases
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.aal3 = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.anatomy3 = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.ibsr = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.julichbrain = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.mori = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.thalamus = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.Schaefer2018_100Parcels_17Networks_order = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.Schaefer2018_200Parcels_17Networks_order = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.Schaefer2018_400Parcels_17Networks_order = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.Schaefer2018_600Parcels_17Networks_order = 1;
matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.native = 1; % Save atlases in native space
matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.warped = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.atlas.dartel = 0;
else
% No ROIs
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.noROI = struct([]); % CGaser comment: Correct syntax to disable ROI processing for volumes
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 0;
matlabbatch{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 0;
end
% Spherical registration (much slower)
if isSphReg && ~isCerebellum % CGaser comment: Cerebellum extraction is experimental, not to be used routinely
matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 1; % 1: lh+rh
elseif isSphReg && isCerebellum
matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 2; % 2: lh+rh+cerebellum
elseif ~isSphReg && ~isCerebellum
matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 5; % 5: lh+rh (fast, no registration, quick review only)
elseif ~isSphReg && isCerebellum
matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 6; % 6: lh+rh+cerebellum (fast, no registration, quick review only)
end
% Extract additional surface parameters: Cortical thickness, Gyrification index, Sulcal depth (can't be imported for default anatomy)
if isExtraMaps && (iSubject > 0)
matlabbatch{1}.spm.tools.cat.estwrite.output.surf_measures = 1; % Thickness maps
% Separate SPM process (second element in the batch)
matlabbatch{2}.spm.tools.cat.stools.surfextract.data_surf(1) = cfg_dep('CAT12: Segmentation (current release): Left Central Surface', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','lhcentral', '()',{':'}));
matlabbatch{2}.spm.tools.cat.stools.surfextract.GI = 1; % Gyrification index
matlabbatch{2}.spm.tools.cat.stools.surfextract.SD = 1; % Sulcal depth
matlabbatch{2}.spm.tools.cat.stools.surfextract.nproc = 0; % Blocking call to CAT12
end
% Run batch
spm_jobman('run',matlabbatch);
% Close CAT12 figures
close([findall(0, 'Type', 'Figure', 'Tag', 'Interactive'), ...
findall(0, 'Type', 'Figure', 'Tag', 'CAT')]);
% ===== PROJECT ATLASES =====
TessLhFile = file_find(catDir, 'lh.central.*.gii', 2);
if exist('cat_surf_map_atlas', 'file') && file_exist(TessLhFile)
% Get CAT12 dir
CatDir = bst_fullfile(PlugCat.Path, PlugCat.SubFolder);
% List of parcellations to project
AnnotLhFiles = file_find(bst_fullfile(CatDir, 'atlases_surfaces'), 'lh.*.annot', 2, 0);
% Import atlases (cat_surf_map_atlas calls both hemispheres at once)
for iAnnot = 1:length(AnnotLhFiles)
[fAnnotPath, fAnnotName] = bst_fileparts(AnnotLhFiles{iAnnot});
bst_progress('text', ['Interpolating atlas: ' fAnnotName '...']);
cat_surf_map_atlas(TessLhFile, AnnotLhFiles{iAnnot});
end
end
% ===== IMPORT OUTPUT FOLDER =====
% Import CAT12 anatomy folder
isKeepMri = 1;
errMsg = import_anatomy_cat(iSubject, catDir, nVertices, 0, [], isExtraMaps, isKeepMri);
if ~isempty(errMsg)
return;
end
% Delete temporary folder
% file_delete(catDir, 1, 3);
% Remove logo
bst_plugin('SetProgressLogo', []);
% Return success
isOk = 1;
end
%% ===== COMPUTE/INTERACTIVE =====
function ComputeInteractive(iSubject, iAnatomy) %#ok<DEFNU>
% Get inputs
if (nargin < 2) || isempty(iAnatomy)
iAnatomy = [];
end
% Ask for number of vertices
nVertices = java_dialog('input', 'Number of vertices on the cortex surface:', 'CAT12 segmentation', [], '15000');
if isempty(nVertices)
return
end
nVertices = str2double(nVertices);
% Ask for volume atlases
[isVolumeAtlases, isCancel] = java_dialog('confirm', ['Compute anatomical parcellations?' 10 10 ...
' - AAL3', 10 ...
' - Anatomy v3', 10 ...
' - CoBrALab' 10 ...
' - Hammers' 10 ...
' - IBSR', 10 ...
' - JulichBrain v2', 10 ...
' - LPBA40' 10 ...
' - Mori', 10 ...
' - Neuromorphometrics' 10 ...
' - Schaefer2018', 10 10], 'CAT12 MRI segmentation');
if isCancel
return
end
% Ask for cortical maps (not for default anatomy)
if (iSubject > 0)
[isExtraMaps, isCancel] = java_dialog('confirm', ['Compute cortical maps?' 10 10 ...
' - Cortical thickness', 10 ...
' - Gyrification index', 10 ...
' - Sulcal depth', 10 10], 'CAT12 MRI segmentation');
if isCancel
return
end
else
isExtraMaps = 0;
end
% Open progress bar
bst_progress('start', 'CAT12', 'CAT12 MRI segmentation...');
% Run CAT12
TpmNii = bst_get('SpmTpmAtlas');
isInteractive = 1;
isSphReg = 1;
isCerebellum = 0;
[isOk, errMsg] = Compute(iSubject, iAnatomy, nVertices, isInteractive, TpmNii, isSphReg, isVolumeAtlases, isExtraMaps, isCerebellum);
% Error handling
if ~isOk
bst_error(errMsg, 'CAT12 MRI segmentation', 0);
elseif ~isempty(errMsg)
java_dialog('msgbox', ['Warning: ' errMsg]);
end
% Close progress bar
bst_progress('stop');
end