[ENH] Update bidspm path

.github/workflows/run_system_tests_octave.yml

@@ -82,5 +82,5 @@ jobs:
 
     - name: Run ${{ matrix.script }}
       run: |
-        cd /home/runner/work/CPP_SPM/CPP_SPM/.github/workflows
+        cd /home/runner/work/bidspm/bidspm/.github/workflows
         octave $OCTFLAGS --eval "run system_tests_${{ matrix.script }};"

demos/MoAE/moae_01_bids_app.m

@@ -73,7 +73,7 @@
 
 bids_dir = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
 output_dir = fullfile(bids_dir, '..', '..', 'outputs', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
 model_file = fullfile(pwd, 'models', 'model-MoAE_smdl.json');
 

demos/MoAE/moae_02_create_roi_extract_data.m

@@ -16,8 +16,8 @@
 subLabel = '01';
 
 opt.dir.derivatives = fullfile(fileparts(mfilename('fullpath')), 'outputs', 'derivatives');
-opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
-opt.dir.stats = fullfile(opt.dir.derivatives, 'outputs', 'cpp_spm-stats');
+opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
+opt.dir.stats = fullfile(opt.dir.derivatives, 'outputs', 'bidspm-stats');
 
 opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
                           'models', 'model-MoAE_smdl.json');

demos/MoAE/moae_03_slice_display.m

@@ -22,10 +22,10 @@
 
 opt.dir.raw = fullfile(this_dir, 'inputs', 'raw');
 opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
-opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
-opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
-opt.dir.stats = fullfile(opt.dir.derivatives, 'cpp_spm-stats');
+opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
+opt.dir.stats = fullfile(opt.dir.derivatives, 'bidspm-stats');
 
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 

demos/MoAE/moae_denoise_with_glm.m

@@ -13,7 +13,7 @@
 
 bids_dir = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
 output_dir = fullfile(bids_dir, '..', '..', 'outputs', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
 model_file = fullfile(pwd, 'models', 'model-denoiseOnly_smdl.json');
 

demos/MoAE/moae_fmriprep.m

@@ -41,7 +41,7 @@
 
 % we need to specify where the smoothed data will go
 opt.pipeline.type = 'preproc';
-opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
 opt.space = {'MNI152NLin6Asym'};
 
@@ -82,7 +82,7 @@
 
 bids_dir = fullfile(WD, 'inputs', 'raw');
 output_dir = fullfile(WD, 'outputs', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
 model_file = fullfile(pwd, 'models', 'model-MoAEfmriprep_smdl.json');
 

demos/MoAE/test_moae.m

@@ -64,7 +64,7 @@
          'options', optionsFile);
 
   %% stats
-  preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+  preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...

demos/face_repetition/face_rep_02_stats.m

@@ -40,7 +40,7 @@
 
 bids_dir = fullfile(this_dir, 'outputs', 'raw');
 output_dir = fullfile(this_dir, 'outputs', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
 model_file = fullfile(this_dir, 'models', 'model-faceRepetition_smdl.json');
 

demos/face_repetition/face_rep_02_stats_parametric.m

@@ -17,7 +17,7 @@
 
 bids_dir = fullfile(this_dir, 'outputs', 'raw');
 output_dir = fullfile(this_dir, 'outputs', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 
 model_file = fullfile(this_dir, 'models', 'model-faceRepetitionParametric_smdl.json');
 

demos/face_repetition/face_rep_03_roi_analysis.m

@@ -19,8 +19,8 @@
 %% Create roi
 
 opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
-opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
-opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
+opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
+opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
 
 opt.roi.atlas = 'wang';
 opt.roi.name = {'V1v', 'V1d'};
@@ -32,7 +32,7 @@
 
 bids_dir = fullfile(this_dir, 'outputs', 'raw');
 output_dir = fullfile(this_dir, 'outputs', 'derivatives');
-preproc_dir = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+preproc_dir = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
 opt.bidsFilterFile.roi.space = 'individual';
 

demos/face_repetition/test_face_rep.m

@@ -26,7 +26,7 @@
 
 for iResolution = 2:3
 
-  opt.pipeline.name = ['cpp_spm-res' num2str(iResolution)];
+  opt.pipeline.name = ['bidspm-res' num2str(iResolution)];
   opt.funcVoxelDims = repmat(iResolution, 1, 3);
 
   %% preproc
@@ -60,7 +60,7 @@
   % stats options
   opt = bids.util.jsondecode(optionsFile);
   % TODO put in a json file
-  opt.pipeline.name = ['cpp_spm-res' num2str(iResolution)];
+  opt.pipeline.name = ['bidspm-res' num2str(iResolution)];
 
   % specify underlay image
   BIDS = bids.layout([preproc_dir '-preproc'], 'use_schema', false);

demos/lesion_detection/lesion_get_option.m

@@ -26,7 +26,7 @@
   %%
   opt2.subjects = {'ctrl01'};
   opt2.dir.derivatives = '/home/remi/gin/Christine/olfaction_blind/derivatives/lesion/derivatives/';
-  opt2.dir.preproc = fullfile(opt2.dir.derivatives, 'cpp_spm-preproc');
+  opt2.dir.preproc = fullfile(opt2.dir.derivatives, 'bidspm-preproc');
   opt2.query.run = '';
   opt2.query.acq = '';
   opt2.toolbox.ALI.unified_segmentation.step1fwhm = 6;

demos/openneuro/ds000001_run.m

@@ -19,7 +19,7 @@
        'space', {'IXI549Space'});
 
 %% Stats
-preproc_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives', 'cpp_spm-preproc');
+preproc_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives', 'bidspm-preproc');
 
 model_file = fullfile(root_dir, 'models', 'model-defaultBalloonanalogrisktask_smdl.json');
 

demos/openneuro/ds000114_run.m

@@ -26,7 +26,7 @@
 
 %% Statistics
 
-preproc_dir = fullfile(root_dir, 'outputs', 'ds000114', 'derivatives', 'cpp_spm-preproc');
+preproc_dir = fullfile(root_dir, 'outputs', 'ds000114', 'derivatives', 'bidspm-preproc');
 model_file = fullfile(root_dir, 'models', 'model-ds000114_desc-linebisection_smdl.json');
 
 opt.results.nodeName = 'subject_level';

demos/openneuro/ds001168_run.m

@@ -48,7 +48,7 @@
 root_dir = fileparts(mfilename('fullpath'));
 bids_dir = fullfile(root_dir, 'inputs', 'ds001168');
 output_dir = fullfile(root_dir, 'outputs', 'ds001168', 'derivatives');
-preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
 model_file = fullfile(root_dir, 'models', 'model-ds001168_smdl.json');
 
 opt.glm.keepResiduals = true;

demos/openneuro/ds002799_run.m

@@ -33,7 +33,7 @@
 
 % we need to specify where the smoothed data will go
 opt.pipeline.type = 'preproc';
-opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
 opt = checkOptions(opt);
 
@@ -69,7 +69,7 @@
 % this use the "constant" Transformer
 % to add a column with all the same value in each row
 
-bm.Nodes{run_lvl_idx}.Transformations.Transformer = 'cpp_spm';
+bm.Nodes{run_lvl_idx}.Transformations.Transformer = 'bidspm';
 bm.Nodes{run_lvl_idx}.Transformations.Instructions = {struct('Name', 'Constant', ...
                                                              'Value', 'es', ...
                                                              'Output', 'trial_type')};

demos/tSNR/tsnr_03_compute.m

@@ -8,7 +8,7 @@
 
 [BIDS, opt] = getData(opt, opt.dir.preproc);
 
-opt.dir.roi = fullfile(opt.dir.preproc, '..', 'cpp_spm-roi');
+opt.dir.roi = fullfile(opt.dir.preproc, '..', 'bidspm-roi');
 opt = rmfield(opt, 'taskName');
 [BIDSroi, opt] = getData(opt, opt.dir.roi);
 

demos/vismotion/step_2_stats.m

@@ -11,7 +11,7 @@
 root_dir = fullfile(this_dir, '..', '..', '..', '..');
 bids_dir = fullfile(root_dir, 'inputs', 'raw');
 output_dir = fullfile(root_dir, 'outputs', 'derivatives');
-preproc_dir = fullfile(root_dir, 'outputs', 'derivatives', 'cpp_spm-preproc');
+preproc_dir = fullfile(root_dir, 'outputs', 'derivatives', 'bidspm-preproc');
 
 % TODO via BIDS api
 % bidsRFX('meananatandmask', opt);

docs/source/default_options.m

@@ -23,9 +23,9 @@
 opt.bidsFilterFile.t2w.modality = 'anat'  ;
 opt.bidsFilterFile.t2w.suffix = 'T2w'  ;
 opt.contrastList = {};
-opt.dir.derivatives = '/home/remi/gin/Christine/olfaction_blind/derivatives/bidspm/code/lib/CPP_SPM/docs/derivatives'  ;
+opt.dir.derivatives = '/home/remi/gin/Christine/olfaction_blind/derivatives/bidspm/code/lib/bidspm/docs/derivatives'  ;
 opt.dir.input = ''  ;
-opt.dir.jobs = '/home/remi/gin/Christine/olfaction_blind/derivatives/bidspm/code/lib/CPP_SPM/docs/jobs'  ;
+opt.dir.jobs = '/home/remi/gin/Christine/olfaction_blind/derivatives/bidspm/code/lib/bidspm/docs/jobs'  ;
 opt.dir.output = ''  ;
 opt.dir.preproc = ''  ;
 opt.dir.raw = ''  ;

scripts/group_rm_anova.m

@@ -53,7 +53,7 @@
                             1:numel(side_labels));
 
 %%
-opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'cpp_spm-groupStats');
+opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'bidspm-groupStats');
 opt.dir.jobs = fullfile(opt.dir.output, 'jobs',  strjoin(opt.taskName, ''));
 
 % collect con images

src/IO/getData.m

@@ -11,7 +11,7 @@
   %             See also: checkOptions
   %
   % :param bidsDir: the directory where the data is ; default is :
-  %                 ``fullfile(opt.dataDir, '..', 'derivatives', 'cpp_spm')``
+  %                 ``fullfile(opt.dataDir, '..', 'derivatives', 'bidspm')``
   % :type  bidsDir: char
   %
   % :returns:

src/defaults/checkOptions.m

@@ -167,8 +167,8 @@
 
   checkFields(opt);
 
-  if any(strcmp(opt.pipeline.name, {'cpp_spm-stats', 'cpp_spm-preproc'}))
-    opt.pipeline.name = 'cpp_spm';
+  if any(strcmp(opt.pipeline.name, {'bidspm-stats', 'bidspm-preproc'}))
+    opt.pipeline.name = 'bidspm';
   end
 
   % coerce query modality into a cell
@@ -278,7 +278,7 @@
                                       'roi',  struct('modality', 'roi', 'suffix', 'mask'));
 
   fieldsToSet.pipeline.type = '';
-  fieldsToSet.pipeline.name = 'cpp_spm';
+  fieldsToSet.pipeline.name = 'bidspm';
 
   fieldsToSet.useBidsSchema = false;
 

src/defaults/set_spm_2_bids_defaults.m

@@ -1,6 +1,6 @@
 function opt = set_spm_2_bids_defaults(opt)
   %
-  % set default map for renaming for cpp_spm
+  % set default map for renaming for bidspm
   %
   % USAGE::
   %

src/group_level/getRFXdir.m

@@ -23,7 +23,7 @@
   %
   % Typical output:
   %
-  % - ``opt.dir.derivatives/cpp_spm-stats/derivatives/cpp_spm-groupStats/cpp_spm-stats``
+  % - ``opt.dir.derivatives/bidspm-stats/derivatives/bidspm-groupStats/bidspm-stats``
   %
   % .. code-block:: matlab
   %
@@ -77,7 +77,7 @@
 
   rfxDir = fullfile(opt.dir.stats, ...
                     'derivatives', ...
-                    'cpp_spm-groupStats', ...
+                    'bidspm-groupStats', ...
                     glmDirName);
 
   spm_mkdir(rfxDir);

src/infra/returnRootDir.m

@@ -7,7 +7,7 @@
 
   % (C) Copyright 2022 bidspm developers
 
-  Mfile = 'cpp_spm.m';
+  Mfile = 'bidspm.m';
   rootDir = cellstr(which(Mfile, '-ALL'));
 
   % convert to absolute paths and keep unique ones

src/messages/errorHandling.m

@@ -31,7 +31,7 @@ function errorHandling(varargin)
 
   % (C) Copyright 2018 bidspm developers
 
-  defaultFunctionName = 'cpp_spm';
+  defaultFunctionName = 'bidspm';
   defaultId = 'unspecified';
   defaultMsg = 'unspecified';
   defaultTolerant = true;

src/workflows/bidsCopyInputFolder.m

@@ -69,7 +69,7 @@ function bidsCopyInputFolder(varargin)
     end
 
     % leave events files behind
-    if ismember(pipeline_name, {'preproc', 'cpp_spm-preproc'})
+    if ismember(pipeline_name, {'preproc', 'bidspm-preproc'})
       if ~isfield(filter, 'suffix')
         filter.suffix = {'^(?!(events)$).*$'};
       end

src/workflows/roi/bidsCreateROI.m

@@ -15,7 +15,7 @@ function bidsCreateROI(opt)
   %  opt.roi.atlas = 'wang';
   %  opt.roi.name = {'V1v', 'V1d'};
   %  opt.roi.space = {'IXI549Space', 'individual'};
-  %  opt.dir.stats = fullfile(opt.dir.raw, '..', 'derivatives', 'cpp_spm-stats');
+  %  opt.dir.stats = fullfile(opt.dir.raw, '..', 'derivatives', 'bidspm-stats');
   %
   %  bidsCreateROI(opt);
   %
@@ -28,7 +28,7 @@ function bidsCreateROI(opt)
   end
 
   if ~isfield(opt.dir, 'roi')
-    opt.dir.roi = spm_file(fullfile(opt.dir.derivatives, 'cpp_spm-roi'), 'cpath');
+    opt.dir.roi = spm_file(fullfile(opt.dir.derivatives, 'bidspm-roi'), 'cpath');
   end
   spm_mkdir(fullfile(opt.dir.roi, 'group'));
 

src/workflows/roi/bidsRoiBasedGLM.m

@@ -35,7 +35,7 @@
   description = 'ROI based GLMs';
 
   if ~isfield(opt.dir, 'roi')
-    opt.dir.roi = spm_file(fullfile(opt.dir.derivatives, 'cpp_spm-roi'), 'cpath');
+    opt.dir.roi = spm_file(fullfile(opt.dir.derivatives, 'bidspm-roi'), 'cpath');
   end
 
   [BIDS, opt] = setUpWorkflow(opt, description);

src/workflows/stats/bidsModelSelection.m

@@ -152,7 +152,7 @@
       opt.orderBatches.MACS_BMS_group_auto = 2;
   end
 
-  opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'cpp_spm-modelSelection');
+  opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'bidspm-modelSelection');
   opt.dir.jobs = fullfile(opt.dir.output, 'jobs');
 
   spm_mkdir(fullfile(opt.dir.output, 'group'));

src/workflows/stats/bidsRFX.m

@@ -67,7 +67,7 @@
   % - merge rfx and ffx into a single "stats" workflow
 
   if ismember(lower(action), {'meananatandmask', 'rfx', 'contrasts'})
-    opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'cpp_spm-groupStats');
+    opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'bidspm-groupStats');
     opt.dir.jobs = fullfile(opt.dir.output, 'jobs',  strjoin(opt.taskName, ''));
   end
 
@@ -153,7 +153,7 @@
   end
 
   if ismember(lower(action), {'meananatandmask', 'rfx'})
-    opt.pipeline.name = 'cpp_spm';
+    opt.pipeline.name = 'bidspm';
     opt.pipeline.type = 'groupStats';
     initBids(opt, 'description', description, 'force', false);
   end

src/workflows/stats/bidsResults.m

@@ -235,7 +235,7 @@
 
         batchName = 'compute_group_level_results';
 
-        tmp = fullfile(opt.dir.stats, 'derivatives', 'cpp_spm-groupStats');
+        tmp = fullfile(opt.dir.stats, 'derivatives', 'bidspm-groupStats');
         opt.dir.jobs = fullfile(tmp, 'jobs',  strjoin(opt.taskName, ''));
         status = saveAndRunWorkflow(matlabbatch, batchName, opt);