REF: Handle mixed cases of session label in rawdata folder.

netstim · Feb 14, 2024 · 677eb38 · 677eb38
1 parent 1ac5fab
commit 677eb38
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/helpers/BIDSFetcher.m b/helpers/BIDSFetcher.m
@@ -372,7 +372,8 @@
             end
 
             % Get images and modalities
-            images = fullfile(rawDataDir, 'ses-preop', 'anat', append(struct2cell(rawImages.preop.anat), obj.settings.niiFileExt));
+            preopRawDataDir = ea_regexpdir(rawDataDir, '^ses-preop$', 0, 'd');
+            images = fullfile(preopRawDataDir{1}, 'anat', append(struct2cell(rawImages.preop.anat), obj.settings.niiFileExt));
             modality = fieldnames(rawImages.preop.anat)';
 
             % Set pre-defined orders
@@ -427,7 +428,8 @@
             end
 
             % Get images and modalities
-            images = fullfile(rawDataDir, 'ses-postop', 'anat', append(struct2cell(rawImages.postop.anat), obj.settings.niiFileExt));
+            postopRawDataDir = ea_regexpdir(rawDataDir, '^ses-postop$', 0, 'd');
+            images = fullfile(postopRawDataDir, 'anat', append(struct2cell(rawImages.postop.anat), obj.settings.niiFileExt));
             modality = fieldnames(rawImages.postop.anat);
 
             % Check presence of CT and MR
@@ -477,7 +479,7 @@
             for i=1:length(fields)
                 modality = fields{i};
                 parsed = parseBIDSFilePath(preopAnat.(modality));
-                preprocAnat.preop.(modality) = strrep(preopAnat.(modality), [parsed.dir, filesep, 'sub-', subjId, '_ses-preop_'], [baseDir, filesep, baseName]);
+                preprocAnat.preop.(modality) = fullfile(baseDir, [baseName, 'acq-', parsed.acq, '_', parsed.suffix, parsed.ext]);
             end
 
             if ~exist('preferMRCT', 'var')

diff --git a/helpers/ea_genrawimagesjson.m b/helpers/ea_genrawimagesjson.m
@@ -4,15 +4,16 @@
 
 % Get all images
 rawdataFolder = fullfile(GetFullPath(BIDSRoot), 'rawdata', ['sub-', subjId]);
-preopNiftiFiles = ea_regexpdir([rawdataFolder, filesep, 'ses-preop'], '.*\.nii(\.gz)?$', 1, 'f');
-postopNiftiFiles = ea_regexpdir([rawdataFolder, filesep, 'ses-postop'], '.*\.nii(\.gz)?$', 1, 'f');
+niftiFiles = ea_regexpdir(rawdataFolder, '.*\.nii(\.gz)?$', 1, 'f');
+preopNiftiFiles = niftiFiles(contains(niftiFiles, [filesep, 'ses-preop', filesep], 'IgnoreCase', true));
+postopNiftiFiles = niftiFiles(contains(niftiFiles, [filesep, 'ses-postop', filesep], 'IgnoreCase', true));
 niftiFiles = [preopNiftiFiles; postopNiftiFiles];
 
 % Iterate all images
 rawImages = struct;
 for f = 1:length(niftiFiles)
     parsed = parseBIDSFilePath(niftiFiles{f});
-    session = parsed.ses; % preop, postop
+    session = lower(parsed.ses); % preop, postop
     [~, type] = fileparts(parsed.dir); % anat, func, dwi
     if isfield(parsed, 'acq')
         suffix = [parsed.acq, '_', parsed.suffix]; % e.g., ax_T1w