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update notebooks
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‎examples/.gitignore‎ renamed to ‎notebooks/.gitignore‎

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‎examples/demo.ipynb‎ renamed to ‎notebooks/demo.ipynb‎

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"cells": [
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{
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"cell_type": "markdown",
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"id": "a4c07e0c-8673-4fa8-bc31-800409fb09c4",
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"metadata": {},
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"source": [
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"# SPM_2_BIDS DEMO\n",
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"\n",
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"**Helping you convert your SPM output into a BIDS compliant datasets.**\n"
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]
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"**Helping you convert your SPM output into a BIDS compliant datasets.**\n",
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"\n",
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"## BIDS filenames\n",
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"\n",
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"Ideally we would like to have the same pipeline for statistical analysis \n",
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"whether our data was preprocessed with SPM or with fmriprep (for example).\n",
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"\n",
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"This is possible under the condition that the input files for the statistical analysis are BIDS compliant: \n",
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"meaning that they follow the typical pattern of BIDS files:\n",
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"\n",
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"- pseudo \"regular expression\" : `entity-label(_entity-label)+_suffix.extension`\n",
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"\n",
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"\n",
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"- `entity`, `label`, `suffix`, `extension` are alphanumeric only (no special character): `([a-zA-Z0-9])+`\n",
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" - suffixes can be: `T1w` or `bold` but not `T1w_skullstripped` (no underscore allowed)\n",
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"\n",
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"\n",
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"- entity and label are separated by a dash: \n",
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" `entity-label --> ([a-zA-Z0-9])+-([a-zA-Z0-9])+`\n",
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" - you can have: `sub-01` but not `sub-01-blind`\n",
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" \n",
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"\n",
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"\n",
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"- entity-label pairs are separated by an underscore:\n",
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" `entity-label(_entity-label)+ --> ([a-zA-Z0-9])+-([a-zA-Z0-9])+(_([a-zA-Z0-9])+-([a-zA-Z0-9])+)+`\n",
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"\n",
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"\n",
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"- **prefixes are not a thing in official BIDS names**\n",
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"\n",
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"BIDS has a number of [officially recognised entities](https://bids-specification.readthedocs.io/en/stable/99-appendices/04-entity-table.html) (`sub`, `ses`, `task`...) \n",
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"that must come in a specific order for each data type.\n",
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"\n",
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"BIDS derivatives adds a few more entities (`desc`, `space`, `res`...) \n",
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"and suffixes (`pseg`, `dseg`, `mask`...) \n",
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"that can be used to name and describe preprocessed data.\n",
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"\n",
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"## Typical SPM filenames\n",
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"\n",
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"SPM typically adds prefixes to filenames and concatenates them.\n",
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"\n",
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"- `r` for realigned or resliced\n",
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"- `w` for warped (often means normalized in MNI space)\n",
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"- `a` for slice time corrected images\n",
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"- `u` for unwarped\n",
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"- `s` for smoothed\n",
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"- `c1` for grey matter tissue probability maps\n",
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"- ...\n",
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"\n",
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"## SPM to BIDS\n",
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"\n",
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"spm_2_bids offers a default mapping to rename the output of raw BIDS datasets preprocessed with SPM12\n",
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"into BIDS compliant derivatives datasets, by suggesting a name for each file by removing prefixes and \n",
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"adding the appropriate entities to be added.\n",
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"\n",
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"Files are not actually renamed by spm_2_bids (yet).\n"
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],
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"metadata": {}
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "68482373-0288-4920-99a6-68e7db8bac44",
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"metadata": {},
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"source": [
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"run ../init_spm_2_bids.m"
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],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"name": "stdout",
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"text": [
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"Correct matlab/octave verions and added to the path!\n"
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]
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}
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],
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"source": [
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"run ../init_spm_2_bids.m"
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]
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"metadata": {}
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"id": "0d1179df-bfa6-494c-a900-ab667d6bfa5d",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"sub-01_T1w_seg8.mat\t-->\tsub-01_label-T1w_segparam.mat\n",
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"sub-01_task-auditory_bold_uw.mat\t-->\tsub-01_task-auditory_label-bold_unwarpparam.mat\n",
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"y_sub-01_T1w.nii\t-->\tsub-01_from-T1w_to-IXI549Space_mode-image_xfm.nii\n",
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"iy_sub-01_T1w.nii\t-->\tsub-01_from-IXI549Space_to-T1w_mode-image_xfm.nii\n",
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"y_sub-01_T2w.nii\t-->\tsub-01_from-T2w_to-IXI549Space_mode-image_xfm.nii\n",
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"susub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"swuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"c1sub-01_T1w.nii\t-->\tsub-01_space-individual_label-GM_probseg.nii\n",
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"c2sub-01_T1w.nii\t-->\tsub-01_space-individual_label-WM_probseg.nii\n",
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"c3sub-01_T1w.nii\t-->\tsub-01_space-individual_label-CSF_probseg.nii\n",
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"msub-01_T1w.nii\t-->\tsub-01_space-individual_desc-biascor_T1w.nii\n",
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"wmsub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n",
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"wsub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n",
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"wc1sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-GM_probseg.nii\n",
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"wc2sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-WM_probseg.nii\n",
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"wc3sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-CSF_probseg.nii\n",
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"asub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-stc_bold.nii\n",
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"usub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii\n",
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"rp_sub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_desc-confounds_regressors.tsv\n",
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"rp_asub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_desc-confounds_regressors.tsv\n",
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"meansub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"meanusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"meanuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"wsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wrsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wrasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wmeanusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-mean_bold.nii\n",
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"swsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swrsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swrasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"ssub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"suasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"susub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"srsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"srasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n"
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]
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}
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],
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"source": [
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"input_files = { 'sub-01_T1w_seg8.mat'; ...\n",
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" 'sub-01_task-auditory_bold_uw.mat'; ...\n",
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" fprintf(1, '%s\\t-->\\t%s\\n', input_files{i, 1}, filename);\n",
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"\n",
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"end"
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]
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],
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"outputs": [
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{
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"output_type": "stream",
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"name": "stdout",
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"text": [
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"sub-01_T1w_seg8.mat\t-->\tsub-01_label-T1w_segparam.mat\n",
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"sub-01_task-auditory_bold_uw.mat\t-->\tsub-01_task-auditory_label-bold_unwarpparam.mat\n",
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"y_sub-01_T1w.nii\t-->\tsub-01_from-T1w_to-IXI549Space_mode-image_xfm.nii\n",
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"iy_sub-01_T1w.nii\t-->\tsub-01_from-IXI549Space_to-T1w_mode-image_xfm.nii\n",
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"y_sub-01_T2w.nii\t-->\tsub-01_from-T2w_to-IXI549Space_mode-image_xfm.nii\n",
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"susub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"swuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"c1sub-01_T1w.nii\t-->\tsub-01_space-individual_label-GM_probseg.nii\n",
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"c2sub-01_T1w.nii\t-->\tsub-01_space-individual_label-WM_probseg.nii\n",
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"c3sub-01_T1w.nii\t-->\tsub-01_space-individual_label-CSF_probseg.nii\n",
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"msub-01_T1w.nii\t-->\tsub-01_space-individual_desc-biascor_T1w.nii\n",
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"wmsub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n",
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"wsub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n",
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"wc1sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-GM_probseg.nii\n",
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"wc2sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-WM_probseg.nii\n",
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"wc3sub-01_T1w.nii\t-->\tsub-01_space-IXI549Space_label-CSF_probseg.nii\n",
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"asub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-stc_bold.nii\n",
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"usub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-realignUnwarp_bold.nii\n",
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"rp_sub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_desc-confounds_regressors.tsv\n",
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"rp_asub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_desc-confounds_regressors.tsv\n",
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"meansub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"meanusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"meanuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-mean_bold.nii\n",
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"wsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wrsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wrasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii\n",
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"wmeanusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-mean_bold.nii\n",
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"swsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swuasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swusub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swrsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"swrasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-IXI549Space_desc-smth_bold.nii\n",
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"ssub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"suasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"susub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"srsub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n",
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"srasub-01_task-auditory_bold.nii\t-->\tsub-01_task-auditory_space-individual_desc-smth_bold.nii\n"
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]
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}
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],
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"metadata": {}
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},
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{
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"cell_type": "markdown",
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"id": "cdb56e9a-3757-45a6-ba5a-c1228f478a3e",
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"metadata": {},
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"source": [
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"# Override the default name map"
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]
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],
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"metadata": {}
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"id": "547873ea-d673-4338-998e-a10ea80b1682",
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"metadata": {},
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"outputs": [],
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"source": [
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"map = Mapping();\n",
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"\n",
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" 'name_spec', name_spec);\n",
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"\n",
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"map = map.flatten_mapping();\n"
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]
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],
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"outputs": [],
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"metadata": {}
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},
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{
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"cell_type": "code",
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"execution_count": 21,
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"id": "6dde6430-e419-4771-8a61-1b5ba6d362d6",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"c1sub-01_T1w.surf.gii\t-->\tsub-01_desc-pialsurf_T1w.gii\n",
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"wmsub-01_desc-skullstripped_T1w.nii\t-->\tsub-01_space-IXI549Space_res-1pt0_desc-preproc_T1w.nii\n",
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"wmsub-01_desc-skullstripped_T2w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T2w.nii\n",
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"wmsub-01_desc-preproc_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n"
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]
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}
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],
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"source": [
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"input_output = {'c1sub-01_T1w.surf.gii'; ... % new mapping for surface data\n",
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" 'wmsub-01_desc-skullstripped_T1w.nii'; ... % new mapping for skulltripped data\n",
@@ -202,7 +237,20 @@
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" fprintf(1, '%s\\t-->\\t%s\\n', input_output{i, 1}, filename);\n",
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"\n",
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"end"
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]
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],
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"outputs": [
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{
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"output_type": "stream",
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"name": "stdout",
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"text": [
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"c1sub-01_T1w.surf.gii\t-->\tsub-01_desc-pialsurf_T1w.gii\n",
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"wmsub-01_desc-skullstripped_T1w.nii\t-->\tsub-01_space-IXI549Space_res-1pt0_desc-preproc_T1w.nii\n",
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"wmsub-01_desc-skullstripped_T2w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T2w.nii\n",
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"wmsub-01_desc-preproc_T1w.nii\t-->\tsub-01_space-IXI549Space_desc-preproc_T1w.nii\n"
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]
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}
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],
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"metadata": {}
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}
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],
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"metadata": {
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

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