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set up binder, notebooks and infra
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‎binder/apt.txt‎

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octave
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liboctave-dev
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gnuplot
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ghostscript
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tree

‎binder/environment.yml‎

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dependencies:
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- octave_kernel

‎binder/postBuild‎

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cd ${HOME}
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octave --no-gui --no-window-system --silent --eval "addpath (getenv (\"HOME\")); savepath ();"
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octave --no-gui --no-window-system --silent --eval "addpath (fullfile (getenv (\"HOME\"), \"+bids\")); savepath ();"
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git clone git://github.com/gllmflndn/JSONio.git --depth 1
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cd JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
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octave --no-gui --no-window-system --silent --eval "addpath (fullfile (getenv (\"HOME\"), \"JSONio\")); savepath ();"
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cd ${HOME}/examples
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‎examples/.gitignore‎

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.ipynb_checkpoints

‎examples/demo.ipynb‎

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{
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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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},
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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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"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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"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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},
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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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" 'y_sub-01_T1w.nii'; ...\n",
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" 'iy_sub-01_T1w.nii'; ...\n",
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" 'y_sub-01_T2w.nii'; ...\n",
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" 'susub-01_task-auditory_bold.nii'; ...\n",
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" 'swuasub-01_task-auditory_bold.nii'; ...\n",
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" 'c1sub-01_T1w.nii'; ... \n",
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" 'c2sub-01_T1w.nii'; ... \n",
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" 'c3sub-01_T1w.nii'; ... \n",
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" 'msub-01_T1w.nii'; ... \n",
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" 'wmsub-01_T1w.nii'; ... \n",
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" 'wsub-01_T1w.nii'; ...\n",
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" 'wc1sub-01_T1w.nii'; ... \n",
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" 'wc2sub-01_T1w.nii'; ... \n",
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" 'wc3sub-01_T1w.nii'; ... \n",
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" 'asub-01_task-auditory_bold.nii'; ...\n",
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" 'usub-01_task-auditory_bold.nii'; ...\n",
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" 'rp_sub-01_task-auditory_bold.nii'; ... \n",
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" 'rp_asub-01_task-auditory_bold.nii'; ...\n",
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" 'meansub-01_task-auditory_bold.nii'; ... \n",
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" 'meanusub-01_task-auditory_bold.nii'; ... \n",
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" 'meanuasub-01_task-auditory_bold.nii'; ...\n",
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" 'wsub-01_task-auditory_bold.nii'; ... \n",
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" 'wuasub-01_task-auditory_bold.nii'; ... \n",
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" 'wusub-01_task-auditory_bold.nii'; ... \n",
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" 'wrsub-01_task-auditory_bold.nii'; ... \n",
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" 'wrasub-01_task-auditory_bold.nii'; ...\n",
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" 'wmeanusub-01_task-auditory_bold.nii'; ...\n",
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" 'swsub-01_task-auditory_bold.nii'; ... \n",
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" 'swuasub-01_task-auditory_bold.nii'; ... \n",
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" 'swusub-01_task-auditory_bold.nii'; ... \n",
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" 'swrsub-01_task-auditory_bold.nii'; ... \n",
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" 'swrasub-01_task-auditory_bold.nii'; ...\n",
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" 'ssub-01_task-auditory_bold.nii'; ... \n",
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" 'suasub-01_task-auditory_bold.nii'; ... \n",
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" 'susub-01_task-auditory_bold.nii'; ... \n",
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" 'srsub-01_task-auditory_bold.nii'; ... \n",
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" 'srasub-01_task-auditory_bold.nii'; ...\n",
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"};\n",
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" \n",
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"\n",
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"for i = 1:size(input_files, 1)\n",
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"\n",
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" filename = spm_2_bids(input_files{i, 1});\n",
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" \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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{
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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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{
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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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"map = map.default();\n",
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"\n",
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"name_spec = map.cfg.preproc_norm;\n",
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"name_spec.entities.res = '1pt0';\n",
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"map = map.add_mapping('prefix', 'wm', ...\n",
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" 'suffix', 'T1w', ...\n",
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" 'ext', '.nii', ...\n",
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" 'entities', struct('desc', 'skullstripped'), ...\n",
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" 'name_spec', name_spec);\n",
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"\n",
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"name_spec = struct('suffix', 'T1w', ...\n",
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" 'ext', '.gii', ...\n",
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" 'entities', struct('desc', 'pialsurf'));\n",
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"map = map.add_mapping('prefix', 'c1', ...\n",
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" 'suffix', 'T1w', ...\n",
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" 'ext', '.surf.gii', ...\n",
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" 'entities', '*', ... % allows any entity, if empty only prefix is used\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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{
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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",
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" 'wmsub-01_desc-skullstripped_T2w.nii'; ... % wrong suffix: use only prefix\n",
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" 'wmsub-01_desc-preproc_T1w.nii'; ... % wrong entity: use only prefix\n",
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" };\n",
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"\n",
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"for i = 1:size(input_output, 1)\n",
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"\n",
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" filename = spm_2_bids(input_output{i, 1}, map);\n",
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" \n",
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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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],
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"metadata": {
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"kernelspec": {
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"display_name": "Octave",
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"language": "octave",
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"name": "octave"
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},
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"language_info": {
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"file_extension": ".m",
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"help_links": [
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{
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"text": "GNU Octave",
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"url": "https://www.gnu.org/software/octave/support.html"
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},
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{
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"text": "Octave Kernel",
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"url": "https://github.com/Calysto/octave_kernel"
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},
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{
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"text": "MetaKernel Magics",
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"url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
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}
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],
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"mimetype": "text/x-octave",
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"name": "octave",
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"version": "4.2.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎miss_hit.cfg‎

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line_length: 100
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regex_function_name: "[a-z]+(_[a-z0-9]+)*"
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regex_script_name: "[a-z]+(_[a-z0-9]+)*"
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# regex_parameter_name: "[a-z]+(_[a-z0-9]+)*"
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regex_class_name: "[A-Z]{1}[a-z]+"
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regex_script_name: "[a-z]+(_[a-z]+)*"
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regex_parameter_name: "[a-z]+(_[a-z0-9]+)*"
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exclude_dir: "lib"
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copyright_entity: "spm_2_bids developers"
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# metric for code quality
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metric "cnest": limit 6
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metric "cnest": limit 5
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metric "file_length": limit 500
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metric "cyc": limit 25
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metric "cyc": limit 15
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metric "parameters": limit 5

‎requirements.txt‎

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Sphinx
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sphinxcontrib-matlabdomain
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sphinxcontrib-napoleon
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sphinx_rtd_theme
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miss_hit==0.9.22
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pre-commit
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miss_hit==0.9.26
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pre-commit
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jupyterlab
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octave_kernel
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jinja2
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-r docs/requirements.txt

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