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Remi-GauRemi-Gau
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fix other demos
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11 files changed

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-47
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11 files changed

+73
-47
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‎demos/MoAE/moae_get_option.m‎

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@@ -14,7 +14,6 @@
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opt.dir.raw = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
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opt.dir.preproc = fullfile(opt.dir.raw, '..', '..', 'outputs', 'derivatives');
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opt.pipeline.type = 'preproc';
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opt.pipeline.name = 'cpp_spm-preproc';
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% Uncomment the lines below to run preprocessing

‎demos/openneuro/ds000001_get_option.m‎

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@@ -15,13 +15,15 @@
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% task to analyze
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opt.taskName = 'balloonanalogrisktask';
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opt.pipeline.type = 'preproc';
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opt.pipeline.name = 'cpp_spm-preproc';
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% The directory where the data are located
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opt.dir.raw = '/home/remi/openneuro/ds000001/raw';
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opt.dir.derivatives = spm_file(fullfile(opt.dir.raw, ...
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'..', ...
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'derivatives', ...
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'cpp_spm-preprocess'), ...
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'cpath');
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opt.dir.preproc = spm_file(fullfile(opt.dir.raw, ...
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'..', ...
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'derivatives'), ...
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'cpath');
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% Uncomment the lines below to run preprocessing
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% - don't use realign and unwarp

‎demos/openneuro/ds000001_run.m‎

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@@ -9,26 +9,28 @@
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FWHM = 6;
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conFWHM = 6;
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pipeline_name = 'cpp_spm-preprocess';
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run ../../initCppSpm.m;
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%% Set options
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opt = ds000001_get_option();
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reportBIDS(opt);
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% bidsCopyInputFolder(opt, pipeline_name);
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%
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% bidsSTC(opt);
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%
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% bidsSpatialPrepro(opt);
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%
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% anatomicalQA(opt);
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% bidsResliceTpmToFunc(opt);
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% functionalQA(opt);
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%
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% bidsSmoothing(FWHM, opt);
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bidsCopyInputFolder(opt);
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bidsSegmentSkullStrip(opt);
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bidsSTC(opt);
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bidsSpatialPrepro(opt);
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anatomicalQA(opt);
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bidsResliceTpmToFunc(opt);
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functionalQA(opt);
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bidsSmoothing(FWHM, opt);
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opt.pipeline.type = 'stats';
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bidsFFX('specifyAndEstimate', opt, FWHM);
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bidsFFX('contrasts', opt, FWHM);

‎demos/openneuro/ds000114_get_option.m‎

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@@ -8,6 +8,7 @@
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% The directory where the data are located
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opt.dir.raw = '/home/remi/openneuro/ds000114/raw';
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opt.pipeline.name = 'cpp_spm-preprocess';
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% suject to run in each group
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opt.subjects = {'01', '02'};

‎demos/openneuro/ds000114_run.m‎

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@@ -9,8 +9,6 @@
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FWHM = 6;
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conFWHM = 6;
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pipeline_name = 'cpp_spm-preprocess';
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run ../../initCppSpm.m;
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%% Set options
@@ -20,13 +18,7 @@
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reportBIDS(opt);
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opt.dir.derivatives = spm_file(fullfile(opt.dir.raw, ...
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'..', ...
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'derivatives', ...
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pipeline_name), ...
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'cpath');
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bidsCopyInputFolder(opt, pipeline_name);
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bidsCopyInputFolder(opt);
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bidsSTC(opt);
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bidsSpatialPrepro(opt);
@@ -38,29 +30,20 @@
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bidsSmoothing(FWHM, opt);
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%% Run level analysis: as for MVPA
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opt.pipeline.type = 'stats';
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bidsFFX('specifyAndEstimate', opt, FWHM);
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bidsFFX('contrasts', opt, FWHM);
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bidsConcatBetaTmaps(opt, FWHM, false, false);
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%% Subject level analysis: for regular univariate
48-
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opt.pipeline.type = 'stats';
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opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
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'models', ...
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'model-ds000114-linebisection_smdl.json');
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bidsFFX('specifyAndEstimate', opt, FWHM);
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opt.result.Steps(1) = struct( ...
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'Level', 'subject', ...
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'Contrasts', struct( ...
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'Name', 'Correct_Task', ... % has to match
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'Mask', false, ...
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'MC', 'FWE', ... FWE, none, FDR
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'p', 0.05, ...
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'k', 0));
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bidsFFX('contrasts', opt, FWHM);
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bidsResults(opt, FWHM);
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‎demos/openneuro/ds001168_get_option.m‎

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@@ -19,6 +19,8 @@
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% task to analyze
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opt.taskName = 'rest';
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opt.query.modality = {'anat', 'func', 'fmap'};
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opt.anatReference.type = 'T1w';
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opt.anatReference.session = '1';
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‎demos/openneuro/ds001168_run.m‎

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@@ -15,7 +15,7 @@
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%% Run batches
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reportBIDS(opt);
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% reportBIDS(opt);
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bidsCopyInputFolder(opt);
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‎demos/openneuro/openneuro.md‎

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@@ -1,4 +1,4 @@
1-
Download with datalad
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# Download with datalad
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In case you use the python package for datalad, activate your virtual
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environment (like conda).
@@ -7,6 +7,21 @@ environment (like conda).
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conda activate datalad
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```
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Datalad datasets can be accessed via their siblings on:
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https://github.com/OpenNeuroDatasets
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Otherwise you can also get them by using the Datalad superdataset. For example:
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```bash
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datalad clone ///
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cd datasets.datalad.org/
18+
datalad install openneuro datalad
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install openneuro/ds002790
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cd openneuro/ds002790
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# get rest data first subject
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datalad get /derivatives/fmriprep/sub-0001/func/sub-0001*task-restingstate_acq-seq*\*
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```
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## ds000114
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Multi-subject and multi-session dataset.
@@ -38,3 +53,25 @@ datalad get sub-0[12]/*/func/*linebisection*
3853
datalad get sub-0[12]/ses*/func/*fullbrain*
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```
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## frmriprep output from ds002790
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```bash
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datalad clone ///
61+
cd datasets.datalad.org/
62+
datalad install openneuro datalad
63+
install openneuro/ds002790
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cd openneuro/ds002790
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# get resting state data first 2 subjects from MNI space
66+
ls derivatives/fmriprep/sub-000[12]/func/sub-000[12]_task-restingstate_acq-seq_*space-*MNI*_*
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datalad get derivatives/fmriprep/sub-000[12]/func/sub-000[12]_task-restingstate_acq-seq_*space-*MNI*_*
68+
# get their realignment parameters and other confounds
69+
ls derivatives/fmriprep/sub-000[12]/func/sub-000[12]_task-restingstate_*confounds*
70+
datalad get derivatives/fmriprep/sub-000[12]/func/sub-000[12]_task-restingstate_*confounds*
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# get normalization parameters
72+
ls derivatives/fmriprep/sub-000[12]/anat/*.h5
73+
datalad get derivatives/fmriprep/sub-000[12]/anat/*.h5
74+
# get anat data from MNI space
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ls derivatives/fmriprep/sub-0001/anat/*MNI*desc*
76+
datalad get derivatives/fmriprep/sub-0001/anat/*MNI*desc*
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```

‎src/getData.m‎

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@@ -85,7 +85,7 @@
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'task', opt.taskName, ...
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'sub', subjects{1}, ...
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'suffix', suffix, ...
88-
'extension', '.nii');
88+
'extension', {'.nii', '.nii.gz'});
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case 'T1w'
9191
metadata = bids.query(BIDS, 'metadata', ...

‎src/workflows/bidsConcatBetaTmaps.m‎

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@@ -80,10 +80,10 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
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% tsv
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nameStructure = struct( ...
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'ext', '.tsv', ...
83-
'type', 'labelfold', ...
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'sub', subLabel, ...
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'task', opt.taskName, ...
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'space', opt.space);
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'suffix', 'labelfold', ...
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'entities', struct('sub', subLabel, ...
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'task', opt.taskName, ...
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'space', opt.space));
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tsvName = createFilename(nameStructure);
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tsvContent = struct('folds', runs, 'labels', {conditions});

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