{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\")
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# BIDS conversion\n",
"\n",
"Author: Thuy Dao\n",
"\n",
"Citation:\n",
"- dcm2niix: https://doi.org/10.1016/j.jneumeth.2016.03.001\n",
"- bidscoin: https://doi.org/10.3389/fninf.2021.770608\n",
"- heudiconv: https://doi.org/10.5281/zenodo.1012598\n",
"- FSL: https://doi.org/10.1016/j.neuroimage.2011.09.015\n",
"- OSF: https://doi.org/10.5195/jmla.2017.88\n",
"- NiiVue: https://github.com/niivue/niivue"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup Neurodesk"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"vscode": {
"languageId": "plaintext"
}
},
"outputs": [],
"source": [
"%%capture\n",
"import os\n",
"import sys\n",
"IN_COLAB = 'google.colab' in sys.modules\n",
"\n",
"if IN_COLAB:\n",
" os.environ[\"LD_PRELOAD\"] = \"\";\n",
" os.environ[\"APPTAINER_BINDPATH\"] = \"/content,/tmp,/cvmfs\"\n",
" os.environ[\"MPLCONFIGDIR\"] = \"/content/matplotlib-mpldir\"\n",
" os.environ[\"LMOD_CMD\"] = \"/usr/share/lmod/lmod/libexec/lmod\"\n",
"\n",
" !curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh\n",
" !chmod +x googlecolab_setup.sh\n",
" !./googlecolab_setup.sh\n",
"\n",
" os.environ[\"MODULEPATH\"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"vendor_id\t: GenuineIntel\n",
"model name\t: Intel(R) Core(TM) i5-9400H CPU @ 2.50GHz\n"
]
}
],
"source": [
"# Output CPU information:\n",
"!cat /proc/cpuinfo | grep 'vendor' | uniq\n",
"!cat /proc/cpuinfo | grep 'model name' | uniq"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## BIDS conversion and Open data sharing\n",
"\n",
"1. In this interactive example notebook, we first download DICOM data using `datalad`.\n",
"\n",
"2. Next we will convert DICOMS into the BIDS data structure using:\n",
" - 2.1. `dcm2niix` which convert data to NIfTi and then manually organize the folder.\n",
" - 2.2. `heudiconv` to automate the conversion and organization with a provided heuristic file.\n",
" - 2.3. `bidscoin` to automate the conversion and organization with bideditor interface.\n",
"\n",
"3. We will then run skull stripping using FSL BET.\n",
"\n",
"4. Finally, we will upload output from FSL BET to share in OSF project."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 1. Data preparation\n",
"\n",
"This example uses a phantom dataset generated by the University of Arizona on their Siemens Skyra 3T with Syngo MR VE11c software on 2018_02_08.\n",
"\n",
"Download DICOM data from Datalad."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Cloning: 100%|██████████████████████| 2.00/2.00 [00:01<00:00, 1.22 candidates/s]\n",
"Enumerating: 0.00 Objects [00:00, ? Objects/s]\u001b[A\n",
" \u001b[A\n",
"Counting: 0%| | 0.00/12.4k [00:00\n",
" Options :\n",
" -1..-9 : gz compression level (1=fastest..9=smallest, default 6)\n",
" -a : adjacent DICOMs (images from same series always in same folder) for faster conversion (n/y, default n)\n",
" -b : BIDS sidecar (y/n/o [o=only: no NIfTI], default y)\n",
" -ba : anonymize BIDS (y/n, default y)\n",
" -c : comment stored in NIfTI aux_file (up to 24 characters e.g. '-c VIP', empty to anonymize e.g. 0020,4000 e.g. '-c \"\"')\n",
" -d : directory search depth. Convert DICOMs in sub-folders of in_folder? (0..9, default 5)\n",
" -e : export as NRRD (y) or MGH (o) or JSON/JNIfTI (j) or BJNIfTI (b) instead of NIfTI (y/n/o/j/b, default n)\n",
" -f : filename (%a=antenna (coil) name, %b=basename, %c=comments, %d=description, %e=echo number, %f=folder name, %g=accession number, %i=ID of patient, %j=seriesInstanceUID, %k=studyInstanceUID, %m=manufacturer, %n=name of patient, %o=mediaObjectInstanceUID, %p=protocol, %r=instance number, %s=series number, %t=time, %u=acquisition number, %v=vendor, %x=study ID; %z=sequence name; default '%f_%p_%t_%s')\n",
" -g : generate defaults file (y/n/o/i [o=only: reset and write defaults; i=ignore: reset defaults], default n)\n",
" -h : show help\n",
" -i : ignore derived, localizer and 2D images (y/n, default n)\n",
" -l : losslessly scale 16-bit integers to use dynamic range (y/n/o [yes=scale, no=no, but uint16->int16, o=original], default o)\n",
" -m : merge 2D slices from same series regardless of echo, exposure, etc. (n/y or 0/1/2, default 2) [no, yes, auto]\n",
" -n : only convert this series CRC number - can be used up to 16 times (default convert all)\n",
" -o : output directory (omit to save to input folder)\n",
" -p : Philips precise float (not display) scaling (y/n, default y)\n",
" -q : only search directory for DICOMs (y/l/n, default y) [y=show number of DICOMs found, l=additionally list DICOMs found, n=no]\n",
" -r : rename instead of convert DICOMs (y/n, default n)\n",
" -s : single file mode, do not convert other images in folder (y/n, default n)\n",
" -u : up-to-date check\n",
" -v : verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]\n",
" -w : write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)\n",
" -x : crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquistions)\n",
" -z : gz compress images (y/o/i/n/3, default n) [y=pigz, o=optimal pigz, i=internal:zlib, n=no, 3=no,3D]\n",
" --big-endian : byte order (y/n/o, default o) [y=big-end, n=little-end, o=optimal/native]\n",
" --progress : Slicer format progress information (y/n, default n)\n",
" --ignore_trigger_times : disregard values in 0018,1060 and 0020,9153\n",
" --terse : omit filename post-fixes (can cause overwrites)\n",
" --version : report version\n",
" --xml : Slicer format features\n",
" Defaults file : /home/jovyan/.dcm2nii.ini\n",
" Examples :\n",
" dcm2niix /Users/chris/dir\n",
" dcm2niix -c \"my comment\" /Users/chris/dir\n",
" dcm2niix -o /users/cr/outdir/ -z y ~/dicomdir\n",
" dcm2niix -f %p_%s -b y -ba n ~/dicomdir\n",
" dcm2niix -f mystudy%s ~/dicomdir\n",
" dcm2niix -o \"~/dir with spaces/dir\" ~/dicomdir\n",
"Example output filename: 'myFolder_MPRAGE_19770703150928_1.nii'\n"
]
}
],
"source": [
"!dcm2niix -h"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": true,
"vscode": {
"languageId": "plaintext"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)\n",
"Found 791 DICOM file(s)\n",
"Slices not stacked: orientation varies (vNav or localizer?) [0.0964069 0.780133 0.618141 0.0553476 0.615871 -0.7859] != [0.718684 0.55589 0.417708 0.0695744 0.540223 -0.838641]\n",
"Convert 2 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_3_i00001 (162x162x2x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_3_i00002 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_3_i00003 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_3_i00004 (162x162x1x1)\n",
"Convert 128 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_1 (160x160x128x1)\n",
"Convert 128 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_2 (160x160x128x1)\n",
"Convert 4 DICOM as ./dcm2niix_bids/dicom_func_task-rest_20190208142838_16 (64x64x44x4)\n",
"Convert 132 DICOM as ./dcm2niix_bids/dicom_fmap_dir-PA_20190208142838_15 (122x122x66x2)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_4_i00001 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_4_i00002 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_4_i00003 (162x162x1x1)\n",
"Convert 16 DICOM as ./dcm2niix_bids/dicom_dwi_dir-AP_20190208142838_9 (122x122x66x16)\n",
"Slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
"Convert 44 DICOM as ./dcm2niix_bids/dicom_fmap_acq-4mm_20190208142838_7_e1 (64x64x44x1)\n",
"Convert 44 DICOM as ./dcm2niix_bids/dicom_fmap_acq-4mm_20190208142838_7_e2 (64x64x44x1)\n",
"Convert 240 DICOM as ./dcm2niix_bids/dicom_anat-T1w_acq-MPRAGE_20190208142838_6 (224x224x240x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_5_i00001 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_5_i00002 (162x162x1x1)\n",
"Convert 1 DICOM as ./dcm2niix_bids/dicom_anat-scout_20190208142838_5_i00003 (162x162x1x1)\n",
"Convert 44 DICOM as ./dcm2niix_bids/dicom_fmap_acq-4mm_20190208142838_8_e2_ph (64x64x44x1)\n",
"Conversion required 25.579993 seconds (1.793082 for core code).\n"
]
}
],
"source": [
"!mkdir dcm2niix_bids\n",
"!dcm2niix n -o ./dcm2niix_bids ./heudiconv-reproin-example/REPROIN/dicom"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### 2.1.2. Organize data into BIDS structure"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"mkdir -p ./dcm2niix_bids/anat\n",
"mkdir -p ./dcm2niix_bids/fmap\n",
"mkdir -p ./dcm2niix_bids/dwi\n",
"mkdir -p ./dcm2niix_bids/func\n",
"\n",
"find ./dcm2niix_bids -maxdepth 1 -type f -name *anat* -exec mv {} ./dcm2niix_bids/anat \\;\n",
"find ./dcm2niix_bids -maxdepth 1 -type f -name *fmap* -exec mv {} ./dcm2niix_bids/fmap \\;\n",
"find ./dcm2niix_bids -maxdepth 1 -type f -name *dwi* -exec mv {} ./dcm2niix_bids/dwi \\;\n",
"find ./dcm2niix_bids -maxdepth 1 -type f -name *func* -exec mv {} ./dcm2niix_bids/func \\;"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[01;34m./dcm2niix_bids/\u001b[0m\n",
"├── \u001b[01;34manat\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-T1w_acq-MPRAGE_20190208142838_6.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-T1w_acq-MPRAGE_20190208142838_6.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_1.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_1.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_2.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_2.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00001.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00001.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00002.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00002.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00003.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00003.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00004.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_3_i00004.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00001.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00001.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00002.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00002.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00003.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_4_i00003.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_5_i00001.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_5_i00001.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_5_i00002.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_5_i00002.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_anat-scout_20190208142838_5_i00003.json\u001b[0m\n",
"│ └── \u001b[00mdicom_anat-scout_20190208142838_5_i00003.nii\u001b[0m\n",
"├── \u001b[01;34mdwi\u001b[0m\n",
"│ ├── \u001b[00mdicom_dwi_dir-AP_20190208142838_9.bval\u001b[0m\n",
"│ ├── \u001b[00mdicom_dwi_dir-AP_20190208142838_9.bvec\u001b[0m\n",
"│ ├── \u001b[00mdicom_dwi_dir-AP_20190208142838_9.json\u001b[0m\n",
"│ └── \u001b[00mdicom_dwi_dir-AP_20190208142838_9.nii\u001b[0m\n",
"├── \u001b[01;34mfmap\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_7_e1.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_7_e1.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_7_e2.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_7_e2.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_8_e2_ph.json\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_acq-4mm_20190208142838_8_e2_ph.nii\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_dir-PA_20190208142838_15.bval\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_dir-PA_20190208142838_15.bvec\u001b[0m\n",
"│ ├── \u001b[00mdicom_fmap_dir-PA_20190208142838_15.json\u001b[0m\n",
"│ └── \u001b[00mdicom_fmap_dir-PA_20190208142838_15.nii\u001b[0m\n",
"└── \u001b[01;34mfunc\u001b[0m\n",
" ├── \u001b[00mdicom_func_task-rest_20190208142838_16.json\u001b[0m\n",
" └── \u001b[00mdicom_func_task-rest_20190208142838_16.nii\u001b[0m\n",
"\n",
"4 directories, 42 files\n"
]
}
],
"source": [
"!tree ./dcm2niix_bids/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.2. Using HeuDiConv (automated workflow)\n",
"Typical use of heudiconv will require the creation and editing of your heuristics file.\n",
"\n",
"But heudiconv also comes with existing heuristics which can be used as is, like `convertall` or `ReproIn` could be immediately reused and represent two ends of the spectrum in heuristics:\n",
"- `convertall` is very simple and does not automate anything – it is for a user to modify filenames in the prepared conversion table, and then rerun with `-c dcm2niix`\n",
"- `reproin` can be used fully automated, if original sequences were named according to its ReproIn convention."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"await lmod.load('heudiconv/1.3.1')"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO: Running heudiconv version 1.3.1 latest 1.3.2\n",
"INFO: Analyzing 791 dicoms\n",
"INFO: Filtering out 0 dicoms based on their filename\n",
"INFO: Generated sequence info for 1 studies with 11 entries total\n",
"INFO: Processing sequence infos to deduce study/session\n",
"INFO: Study session for StudySessionInfo(locator='Patterson/Coben', session=None, subject='001')\n",
"INFO: Need to process 1 study sessions\n",
"INFO: PROCESSING STARTS: {'subject': '001', 'outdir': '/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben', 'session': None}\n",
"INFO: Processing 11 pre-sorted seqinfo entries\n",
"INFO: Processing 11 seqinfo entries\n",
"WARNING: Deduced datatype to be dwi from DICOM, but got fmap out of fmap_dir-PA\n",
"WARNING: Detected 4 duplicated run(s) for template {bids_subject_session_dir}/anat/{bids_subject_session_prefix}_scout: ['1-anat-scout', '2-anat-scout', '3-anat-scout', '4-anat-scout']\n",
"INFO: Doing conversion using dcm2niix\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_scout (3 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('dicom',)\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w (240 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:53:44,563 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niixfjrxeh_b/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niixfjrxeh_b/convert\".\n",
"241203-08:54:06,875 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:54:16,36 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:54:16.036679:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:54:16.036679:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:54:16,36 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:54:16.036679:Found 240 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:54:16.036679:Found 240 DICOM file(s)\n",
"241203-08:54:16,37 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:54:16.036679:Convert 240 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w_heudiconv962 (224x224x240x1)\n",
"INFO: stdout 2024-12-03T08:54:16.036679:Convert 240 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w_heudiconv962 (224x224x240x1)\n",
"241203-08:54:16,875 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:54:16.875335:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w_heudiconv962.nii\"\n",
"INFO: stdout 2024-12-03T08:54:16.875335:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w_heudiconv962.nii\"\n",
"241203-08:54:16,875 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:54:16.875335:Conversion required 9.313324 seconds (0.611796 for core code).\n",
"INFO: stdout 2024-12-03T08:54:16.875335:Conversion required 9.313324 seconds (0.611796 for core code).\n",
"241203-08:54:16,915 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 9.37085s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 9.37085s.\n",
"241203-08:54:49,216 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"embedder\" in \"/tmp/embedmetad8ent8cm/embedder\".\n",
"INFO: [Node] Setting-up \"embedder\" in \"/tmp/embedmetad8ent8cm/embedder\".\n",
"241203-08:54:56,165 nipype.workflow INFO:\n",
"\t [Node] Executing \"embedder\" \n",
"INFO: [Node] Executing \"embedder\" \n",
"241203-08:55:06,63 nipype.workflow INFO:\n",
"\t [Node] Finished \"embedder\", elapsed time 9.895711s.\n",
"INFO: [Node] Finished \"embedder\", elapsed time 9.895711s.\n",
"INFO: Post-treating /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w.json file\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude (88 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:55:06,938 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niixdg6k89no/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niixdg6k89no/convert\".\n",
"241203-08:55:14,498 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:55:16,759 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:16.759881:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:55:16.759881:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:55:16,760 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:16.759881:Found 88 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:55:16.759881:Found 88 DICOM file(s)\n",
"241203-08:55:16,760 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:16.759881:Slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
"INFO: stdout 2024-12-03T08:55:16.759881:Slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2). Use 'merge 2D slices' option to force stacking\n",
"241203-08:55:16,760 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:16.759881:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e1 (64x64x44x1)\n",
"INFO: stdout 2024-12-03T08:55:16.759881:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e1 (64x64x44x1)\n",
"241203-08:55:17,109 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:17.109081:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e1.nii\"\n",
"INFO: stdout 2024-12-03T08:55:17.109081:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e1.nii\"\n",
"241203-08:55:17,109 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:17.109081:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e2 (64x64x44x1)\n",
"INFO: stdout 2024-12-03T08:55:17.109081:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e2 (64x64x44x1)\n",
"241203-08:55:17,155 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:17.155855:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e2.nii\"\n",
"INFO: stdout 2024-12-03T08:55:17.155855:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_magnitude_heudiconv454_e2.nii\"\n",
"241203-08:55:17,156 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:17.155855:Conversion required 2.626588 seconds (0.166224 for core code).\n",
"INFO: stdout 2024-12-03T08:55:17.155855:Conversion required 2.626588 seconds (0.166224 for core code).\n",
"241203-08:55:17,217 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 2.718134s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 2.718134s.\n",
"WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff (44 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:55:22,66 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niixqzafuaep/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niixqzafuaep/convert\".\n",
"241203-08:55:25,300 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:55:26,514 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:26.514524:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:55:26.514524:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:55:26,514 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:26.514524:Found 44 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:55:26.514524:Found 44 DICOM file(s)\n",
"241203-08:55:26,514 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:26.514524:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff_heudiconv731_e2_ph (64x64x44x1)\n",
"INFO: stdout 2024-12-03T08:55:26.514524:Convert 44 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff_heudiconv731_e2_ph (64x64x44x1)\n",
"241203-08:55:26,574 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:26.574488:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff_heudiconv731_e2_ph.nii\"\n",
"INFO: stdout 2024-12-03T08:55:26.574488:Compress: \"/usr/bin/pigz\" -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff_heudiconv731_e2_ph.nii\"\n",
"241203-08:55:26,574 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:26.574488:Conversion required 1.246106 seconds (0.078724 for core code).\n",
"INFO: stdout 2024-12-03T08:55:26.574488:Conversion required 1.246106 seconds (0.078724 for core code).\n",
"241203-08:55:26,611 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 1.310015s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 1.310015s.\n",
"241203-08:55:28,884 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"embedder\" in \"/tmp/embedmetazcndhs1j/embedder\".\n",
"INFO: [Node] Setting-up \"embedder\" in \"/tmp/embedmetazcndhs1j/embedder\".\n",
"241203-08:55:30,140 nipype.workflow INFO:\n",
"\t [Node] Executing \"embedder\" \n",
"INFO: [Node] Executing \"embedder\" \n",
"241203-08:55:31,900 nipype.workflow INFO:\n",
"\t [Node] Finished \"embedder\", elapsed time 1.759341s.\n",
"INFO: [Node] Finished \"embedder\", elapsed time 1.759341s.\n",
"INFO: Post-treating /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_acq-4mm_phasediff.json file\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi (16 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:55:32,190 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niixyyc8i8n2/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niixyyc8i8n2/convert\".\n",
"241203-08:55:33,808 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:55:34,695 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:34.694991:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:55:34.694991:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:55:34,695 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:34.694991:Found 16 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:55:34.694991:Found 16 DICOM file(s)\n",
"241203-08:55:34,695 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:34.694991:Convert 16 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi_heudiconv910 (122x122x66x16)\n",
"INFO: stdout 2024-12-03T08:55:34.694991:Convert 16 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi_heudiconv910 (122x122x66x16)\n",
"241203-08:55:35,540 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:35.540615:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi_heudiconv910.nii\"\n",
"INFO: stdout 2024-12-03T08:55:35.540615:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi_heudiconv910.nii\"\n",
"241203-08:55:35,540 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:55:35.540615:Conversion required 1.706341 seconds (0.083458 for core code).\n",
"INFO: stdout 2024-12-03T08:55:35.540615:Conversion required 1.706341 seconds (0.083458 for core code).\n",
"241203-08:55:35,589 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 1.779693s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 1.779693s.\n",
"241203-08:55:53,318 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"embedder\" in \"/tmp/embedmeta9vydsgjc/embedder\".\n",
"INFO: [Node] Setting-up \"embedder\" in \"/tmp/embedmeta9vydsgjc/embedder\".\n",
"241203-08:55:53,809 nipype.workflow INFO:\n",
"\t [Node] Executing \"embedder\" \n",
"INFO: [Node] Executing \"embedder\" \n",
"241203-08:55:54,924 nipype.workflow INFO:\n",
"\t [Node] Finished \"embedder\", elapsed time 1.115019s.\n",
"INFO: [Node] Finished \"embedder\", elapsed time 1.115019s.\n",
"INFO: Post-treating /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/dwi/sub-001_dir-AP_dwi.json file\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi (132 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:55:56,244 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niix1k6knc1j/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niix1k6knc1j/convert\".\n",
"241203-08:56:06,298 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:56:10,272 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:10.271983:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:56:10.271983:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:56:10,272 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:10.271983:Found 132 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:56:10.271983:Found 132 DICOM file(s)\n",
"241203-08:56:10,272 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:10.271983:Convert 132 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi_heudiconv100 (122x122x66x2)\n",
"INFO: stdout 2024-12-03T08:56:10.271983:Convert 132 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi_heudiconv100 (122x122x66x2)\n",
"241203-08:56:10,436 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:10.436253:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi_heudiconv100.nii\"\n",
"INFO: stdout 2024-12-03T08:56:10.436253:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi_heudiconv100.nii\"\n",
"241203-08:56:10,436 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:10.436253:Conversion required 4.109884 seconds (0.260785 for core code).\n",
"INFO: stdout 2024-12-03T08:56:10.436253:Conversion required 4.109884 seconds (0.260785 for core code).\n",
"241203-08:56:10,476 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 4.177402s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 4.177402s.\n",
"241203-08:56:18,95 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"embedder\" in \"/tmp/embedmetah6tcp63t/embedder\".\n",
"INFO: [Node] Setting-up \"embedder\" in \"/tmp/embedmetah6tcp63t/embedder\".\n",
"241203-08:56:21,804 nipype.workflow INFO:\n",
"\t [Node] Executing \"embedder\" \n",
"INFO: [Node] Executing \"embedder\" \n",
"241203-08:56:27,185 nipype.workflow INFO:\n",
"\t [Node] Finished \"embedder\", elapsed time 5.380302s.\n",
"INFO: [Node] Finished \"embedder\", elapsed time 5.380302s.\n",
"INFO: Post-treating /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/fmap/sub-001_dir-PA_epi.json file\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold (4 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')\n",
"241203-08:56:27,291 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"convert\" in \"/tmp/dcm2niix8lh288h9/convert\".\n",
"INFO: [Node] Setting-up \"convert\" in \"/tmp/dcm2niix8lh288h9/convert\".\n",
"241203-08:56:27,645 nipype.workflow INFO:\n",
"\t [Node] Executing \"convert\" \n",
"INFO: [Node] Executing \"convert\" \n",
"241203-08:56:27,819 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:27.819712:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"INFO: stdout 2024-12-03T08:56:27.819712:Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) GCC10.2.1 x86-64 (64-bit Linux)\n",
"241203-08:56:27,819 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:27.819712:Found 4 DICOM file(s)\n",
"INFO: stdout 2024-12-03T08:56:27.819712:Found 4 DICOM file(s)\n",
"241203-08:56:27,820 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:27.819712:Convert 4 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold_heudiconv065 (64x64x44x4)\n",
"INFO: stdout 2024-12-03T08:56:27.819712:Convert 4 DICOM as /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold_heudiconv065 (64x64x44x4)\n",
"241203-08:56:27,933 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:27.933072:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold_heudiconv065.nii\"\n",
"INFO: stdout 2024-12-03T08:56:27.933072:Compress: \"/usr/bin/pigz\" -b 960 -n -f -6 \"/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold_heudiconv065.nii\"\n",
"241203-08:56:27,933 nipype.interface INFO:\n",
"\t stdout 2024-12-03T08:56:27.933072:Conversion required 0.255163 seconds (0.012036 for core code).\n",
"INFO: stdout 2024-12-03T08:56:27.933072:Conversion required 0.255163 seconds (0.012036 for core code).\n",
"241203-08:56:27,970 nipype.workflow INFO:\n",
"\t [Node] Finished \"convert\", elapsed time 0.324505s.\n",
"INFO: [Node] Finished \"convert\", elapsed time 0.324505s.\n",
"241203-08:56:28,526 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"embedder\" in \"/tmp/embedmeta7z2umecx/embedder\".\n",
"INFO: [Node] Setting-up \"embedder\" in \"/tmp/embedmeta7z2umecx/embedder\".\n",
"241203-08:56:28,682 nipype.workflow INFO:\n",
"\t [Node] Executing \"embedder\" \n",
"INFO: [Node] Executing \"embedder\" \n",
"241203-08:56:28,919 nipype.workflow INFO:\n",
"\t [Node] Finished \"embedder\", elapsed time 0.236424s.\n",
"INFO: [Node] Finished \"embedder\", elapsed time 0.236424s.\n",
"INFO: Post-treating /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/func/sub-001_task-rest_bold.json file\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_scout__dup-01 (128 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('dicom',)\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_scout__dup-02 (128 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('dicom',)\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_scout__dup-03 (5 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('dicom',)\n",
"INFO: Converting /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_scout__dup-04 (3 DICOMs) -> /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001/anat . Converter: dcm2niix . Output types: ('dicom',)\n",
"INFO: Adding \"IntendedFor\" to the fieldmaps in /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben/sub-001.\n",
"INFO: Populating template files under /data/books/workflows/heudiconv_reproin_bids/Patterson/Coben\n",
"INFO: PROCESSING DONE: {'subject': '001', 'outdir': '/data/books/workflows/heudiconv_reproin_bids/Patterson/Coben', 'session': None}\n"
]
}
],
"source": [
"!heudiconv -f reproin -b -o ./heudiconv_reproin_bids --files ./heudiconv-reproin-example/REPROIN/dicom/001"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.3. Using bidscoin (automated workflow)\n",
"\n",
"BIDScoin requires the source data repository to be organized according to a `subject/[session]/data` structure where `data` folder can be structured in DICOM series layout, DICOMDIR layout, flat DICOM layout. Refer to [this doc](https://bidscoin.readthedocs.io/en/stable/preparation.html) for more details.\n",
"\n",
"To perform BIDS conversion, running:\n",
"\n",
"- (1a) `bidsmapper` command\n",
"- once `bidsmapper` finishes, it automatically launches (1b) the `bidseditor`\n",
"- (2) `bidscoiner` command\n",
"\n",
""
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"vscode": {
"languageId": "plaintext"
}
},
"outputs": [],
"source": [
"await lmod.load('bidscoin/4.3.3')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"# %%bash\n",
"# mkdir bidscoin_bidsmap\n",
"# bidsmapper ./heudiconv-reproin-example/REPROIN/dicom ./bidscoin_bids --subprefix '00' --sesprefix 'Patterson_Coben' # Scans your data and creates a study bidsmap\n",
"# bidscoiner ./heudiconv-reproin-example/REPROIN/dicom ./bidscoin_bids # Converts your data to BIDS using the study bidsmap"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 3. Process data\n",
"\n",
"### Brain extraction using FSL BET"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['dcm2niix/v1.0.20240202', 'heudiconv/1.3.1', 'bidscoin/4.3.3', 'fsl/6.0.7.4']"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"await lmod.load('fsl/6.0.7.4')\n",
"await lmod.list()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Processing file: ./heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/sub-001_acq-MPRAGE_T1w.nii.gz\n",
"Saving output to: ./segmentation/sub-001_acq-MPRAGE_T1w_brain\n"
]
}
],
"source": [
"%%bash\n",
"mkdir -p segmentation\n",
"declare -a niifile=($(find ./heudiconv_reproin_bids/Patterson/Coben/sub-001/anat/ -type f -iname \"*.nii.gz\"));\n",
"\n",
"for filepath in \"${niifile[@]}\"; do\n",
" # Extract the base filename without the path\n",
" filename=$(basename \"$filepath\")\n",
"\n",
" # Extract the name without the extension\n",
" name=\"${filename%.*}\"\n",
"\n",
" # Output the current file\n",
" echo \"Processing file: $filepath\"\n",
"\n",
" # Run BET and save the result\n",
" output=\"./segmentation/${name%.*}_brain\"\n",
" echo \"Saving output to: $output\"\n",
" bet \"$filepath\" \"$output\"\n",
"done"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Visualize the brain segmentation"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "40a9e08f861947c09297a0cf2e197113",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"AnyNiivue()"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from ipyniivue import AnyNiivue\n",
"nv = AnyNiivue()\n",
"nv.load_volumes([{\"path\": \"/data/books/workflows/bidscoin_bids/sub-1/ses-1/anat/sub-1_ses-1_acq-anatT1wacqMPRAGE_T1w.nii.gz\"}])\n",
"nv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 4. Share your data to OSF\n",
"\n",
"To set the username, project ID and token by using a configuration file, create `.osfcli.config` in the current directory:\n",
"```markdown\n",
"[osf]\n",
"username = yourOSFaccount@example.com\n",
"project = 9zpcy\n",
"token = kej2R9IU6Gr2uThsswSNdP1cd0cu9eaCerVXjVf7zNwfXHyT0QzMZtX0PGTYmp9Fzaixwq\n",
"```\n",
"\n",
"To upload file to the project set in configuration file, run `osf upload source destination`."
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"!osf upload -r ./segmentation segmentation"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}