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[FIX] Fix command-line for fMRIPrep, MRIQC and HeuDiConv descriptors (n…
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…ipoppy#275)

fix command-line for fMRIPrep, MRIQC and HeuDiConv descriptors
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@michellewang
michellewang authored Jul 11, 2024
1 parent 2284c1b commit 2c1aa2f
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2 changes: 1 addition & 1 deletion nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
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"description": "fmriprep",
"tool-version": "20.2.7",
"schema-version": "0.5",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] fmriprep [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [ANAT_ONLY] [BOILERPLATE_ONLY] [MD_ONLY_BOILERPLATE] [AROMA_ERR_ON_WARN] [VERBOSE_COUNT] [IGNORE] [LONGITUDINAL] [OUTPUT_SPACES] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [MEDIAL_SURFACE_NAN] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [USE_AROMA] [AROMA_MELODIC_DIM] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [CIFTI_OUTPUT] [RUN_RECONALL] [OUTPUT_LAYOUT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [REPORTS_ONLY] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG] [SLOPPY]",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [ANAT_ONLY] [BOILERPLATE_ONLY] [MD_ONLY_BOILERPLATE] [AROMA_ERR_ON_WARN] [VERBOSE_COUNT] [IGNORE] [LONGITUDINAL] [OUTPUT_SPACES] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [MEDIAL_SURFACE_NAN] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [USE_AROMA] [AROMA_MELODIC_DIM] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [CIFTI_OUTPUT] [RUN_RECONALL] [OUTPUT_LAYOUT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [REPORTS_ONLY] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG] [SLOPPY]",
"inputs": [
{
"id": "bids_dir",
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2 changes: 1 addition & 1 deletion nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
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"description": "fmriprep",
"tool-version": "23.1.3",
"schema-version": "0.5",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] fmriprep [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [SLOPPY] [ANAT_ONLY] [BOILERPLATE_ONLY] [REPORTS_ONLY] [IGNORE] [OUTPUT_SPACES] [LONGITUDINAL] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [ME_T2S_FIT_METHOD] [OUTPUT_LAYOUT] [ME_OUTPUT_ECHOS] [MEDIAL_SURFACE_NAN] [PROJECT_GOODVOXELS] [MD_ONLY_BOILERPLATE] [CIFTI_OUTPUT] [USE_AROMA] [AROMA_MELODIC_DIM] [AROMA_ERR_ON_WARN] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [RUN_RECONALL] [TRACK_CARBON] [COUNTRY_CODE] [VERSION] [VERBOSE_COUNT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG]",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [SKIP_BIDS_VALIDATION] [PARTICIPANT_LABEL] [TASK_ID] [ECHO_IDX] [BIDS_FILTERS] [ANAT_DERIVATIVES] [BIDS_DATABASE_DIR] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [LOW_MEM] [USE_PLUGIN] [SLOPPY] [ANAT_ONLY] [BOILERPLATE_ONLY] [REPORTS_ONLY] [IGNORE] [OUTPUT_SPACES] [LONGITUDINAL] [BOLD2T1W_INIT] [BOLD2T1W_DOF] [USE_BBR] [SLICE_TIME_REF] [DUMMY_SCANS] [_RANDOM_SEED] [ME_T2S_FIT_METHOD] [OUTPUT_LAYOUT] [ME_OUTPUT_ECHOS] [MEDIAL_SURFACE_NAN] [PROJECT_GOODVOXELS] [MD_ONLY_BOILERPLATE] [CIFTI_OUTPUT] [USE_AROMA] [AROMA_MELODIC_DIM] [AROMA_ERR_ON_WARN] [REGRESSORS_ALL_COMPS] [REGRESSORS_FD_TH] [REGRESSORS_DVARS_TH] [SKULL_STRIP_TEMPLATE] [SKULL_STRIP_FIXED_SEED] [SKULL_STRIP_T1W] [FMAP_BSPLINE] [FMAP_NO_DEMEAN] [USE_SYN_SDC] [FORCE_SYN] [FS_LICENSE_FILE] [FS_SUBJECTS_DIR] [HIRES] [RUN_RECONALL] [TRACK_CARBON] [COUNTRY_CODE] [VERSION] [VERBOSE_COUNT] [WORK_DIR] [CLEAN_WORKDIR] [RESOURCE_MONITOR] [CONFIG_FILE] [WRITE_GRAPH] [STOP_ON_FIRST_CRASH] [NOTRACK] [DEBUG]",
"inputs": [
{
"id": "bids_dir",
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2 changes: 1 addition & 1 deletion nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2.json
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"description": "heudiconv",
"tool-version": "0.12.2",
"schema-version": "0.5",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] heudiconv [VERSION] [DICOM_DIR_TEMPLATE] [FILES] [SUBJS] [CONVERTER] [OUTDIR] [LOCATOR] [CONV_OUTDIR] [ANON_CMD] [HEURISTIC] [WITH_PROV] [SESSION] [BIDS_OPTIONS] [OVERWRITE] [DATALAD] [DEBUG] [COMMAND] [GROUPING] [MINMETA] [RANDOM_SEED] [DCMCONFIG] [QUEUE] [QUEUE_ARGS]",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [VERSION] [DICOM_DIR_TEMPLATE] [FILES] [SUBJS] [CONVERTER] [OUTDIR] [LOCATOR] [CONV_OUTDIR] [ANON_CMD] [HEURISTIC] [WITH_PROV] [SESSION] [BIDS_OPTIONS] [OVERWRITE] [DATALAD] [DEBUG] [COMMAND] [GROUPING] [MINMETA] [RANDOM_SEED] [DCMCONFIG] [QUEUE] [QUEUE_ARGS]",
"inputs": [
{
"name": "version",
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2 changes: 1 addition & 1 deletion nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json
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"description": "mriqc",
"tool-version": "23.1.0",
"schema-version": "0.5",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] mriqc [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [VERBOSE_COUNT] [SPECIES] [PARTICIPANT_LABEL] [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES] [DSNAME] [BIDS_DATABASE_DIR] [BIDS_DATABASE_WIPE] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [DEBUG] [FLOAT32] [PDB] [WORK_DIR] [VERBOSE_REPORTS] [REPORTS_ONLY] [WRITE_GRAPH] [DRY_RUN] [RESOURCE_MONITOR] [USE_PLUGIN] [NO_SUB] [EMAIL] [WEBAPI_URL] [WEBAPI_PORT] [UPLOAD_STRICT] [NOTRACK] [ANTS_FLOAT] [ANTS_SETTINGS] [FFT_SPIKES_DETECTOR] [FD_THRES] [DEOBLIQUE] [DESPIKE] [START_IDX] [STOP_IDX]",
"command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [VERBOSE_COUNT] [SPECIES] [PARTICIPANT_LABEL] [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES] [DSNAME] [BIDS_DATABASE_DIR] [BIDS_DATABASE_WIPE] [NPROCS] [OMP_NTHREADS] [MEMORY_GB] [DEBUG] [FLOAT32] [PDB] [WORK_DIR] [VERBOSE_REPORTS] [REPORTS_ONLY] [WRITE_GRAPH] [DRY_RUN] [RESOURCE_MONITOR] [USE_PLUGIN] [NO_SUB] [EMAIL] [WEBAPI_URL] [WEBAPI_PORT] [UPLOAD_STRICT] [NOTRACK] [ANTS_FLOAT] [ANTS_SETTINGS] [FFT_SPIKES_DETECTOR] [FD_THRES] [DEOBLIQUE] [DESPIKE] [START_IDX] [STOP_IDX]",
"inputs": [
{
"id": "bids_dir",
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