Merge pull request #728 from cpp-lln-lab/dev

[REL] v2.1.0

Author: Remi-Gau

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "CPP SPM"
 
-version: 2.0.0
+version: 2.1.0
 
 abstract: CPP_SPM is a set pipelines and tools for Octave/MATLAB to process and analyze BIDS data sets using SPM.
 

demos/MoAE/moae_01_bids_app.m

@@ -98,6 +98,14 @@
 opt.results(1).montage.slices = -4:2:16;
 opt.results(1).nidm = true();
 
+opt.results(2).nodeName = 'run_level';
+opt.results(2).name = {'listening_inf_baseline'};
+opt.results(2).p = 0.01;
+opt.results(2).k = 10;
+opt.results(2).MC = 'none';
+opt.results(2).csv = true;
+opt.results(2).atlas = 'AAL';
+
 cpp_spm(bids_dir, output_dir, 'subject', ...
         'participant_label', {subject_label}, ...
         'action', 'stats', ...

demos/lesion_detection/run_lesion.m

@@ -22,10 +22,10 @@
 
 bidsCopyInputFolder(opt);
 
-% Step 1: segmentation
+%% Step 1: segmentation
 bidsLesionSegmentation(opt);
 
-% % Step 2: lesion abnormalities
+%% Step 2: lesion abnormalities
 bidsLesionAbnormalitiesDetection(opt);
 
 % % Step 3: overlap map

docs/cpp_spm-manual.pdf

@@ -8,19 +8,17 @@ function renameSegmentParameter(BIDS, subLabel, opt)
   %
   % (C) Copyright 2020 CPP_SPM developers
 
+  opt = set_spm_2_bids_defaults(opt);
+
   [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel);
 
   segmentParam = spm_select('FPList', anatDataDir, ['^.*', ...
                                                     spm_file(anatImage, 'basename'), ...
                                                     '_seg8.mat$']);
 
-  bf = bids.File(anatImage);
-  bf.entities.label = bf.suffix;
-
-  bf.suffix = 'segparam';
-  bf.extension = '.mat';
+  newFilename = spm_2_bids(segmentParam, opt.spm_2_bids);
 
-  newName = spm_file(segmentParam, 'filename',  bf.filename);
+  newName = spm_file(segmentParam, 'filename',  newFilename);
 
   if ~isempty(segmentParam)
     movefile(segmentParam, newName);

lib/CPP_ROI

@@ -12,24 +12,21 @@ function renameUnwarpParameter(BIDS, subLabel, opt)
     return
   end
 
+  opt = set_spm_2_bids_defaults(opt);
+
   for iTask = 1:numel(opt.taskName)
 
     unwarpParam = spm_select('FPListRec', BIDS.pth, ...
                              ['^.*sub-' subLabel '.*_task-' opt.taskName{iTask} '.*_bold_uw.mat$']);
 
     for iFile = 1:size(unwarpParam, 1)
 
-      inputFilename = strrep(unwarpParam(iFile, :), '_uw.', '.');
-
-      bf = bids.File(inputFilename);
-      bf.entities.label = bf.suffix;
-      bf.suffix = 'unwarpparam';
-      bf.extension = '.mat';
+      newFilename = spm_2_bids(unwarpParam(iFile, :), opt.spm_2_bids);
 
-      newName = spm_file(unwarpParam(iFile, :), 'filename',  bf.filename);
+      outputFile = spm_file(unwarpParam(iFile, :), 'filename', newFilename);
 
       if ~isempty(unwarpParam(iFile, :))
-        movefile(unwarpParam(iFile, :), newName);
+        movefile(unwarpParam(iFile, :), outputFile);
       end
 
     end

lib/spm_2_bids

@@ -21,6 +21,8 @@
 
   outliers_detection = opt.toolbox.ALI.outliers_detection;
 
+  outliers_detection.step3mask{1} = resizeAliMask(opt);
+
   for i = 1:size(images, 1)
 
     % 1. Define smoothed segmented tissue images of patients

src/IO/renameSegmentParameter.m

@@ -21,10 +21,16 @@
 
   [anatImage, anatDataDir] = getAnatFilename(BIDS, opt, subLabel);
 
-  hdr = spm_vol(fullfile(anatDataDir, anatImage));
-  voxRes = diag(hdr.mat);
-  voxRes = min(voxRes(1:3));
-  unified_segmentation.step1vox = abs(voxRes);
+  % TODO
+  % this needs to be changed
+  % - to be consistent across subject
+  % - to reslice the size of the mask that is then used for lesion detection
+  %
+  %   hdr = spm_vol(fullfile(anatDataDir, anatImage));
+  %   voxRes = diag(hdr.mat);
+  %   voxRes = min(voxRes(1:3));
+  %   unified_segmentation.step1vox = abs(voxRes);
+
   unified_segmentation.step1data{1} = fullfile(anatDataDir, anatImage);
 
   matlabbatch{end + 1}.spm.tools.ali.unified_segmentation = unified_segmentation;