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[ENH] Add default tracker config files for fMRIPrep and FreeSurfer, a…
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…nd update default invocation files (nipoppy#265)

* move Nipoppy-specific default values from descriptors to invocation files

* use a single descriptor file for Heudiconv

* fix descriptors not having CLI entrypoints...

* add default tracker config files for fMRIPrep

* add default tracker config files for Freesurfer

* fix failing tests after merge

* add output_spaces to fMRIPrep invocations

* rename dcm2bids descriptors

* add `converter` field to heudiconv convert invocation (dcm2niix, default)
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@michellewang
michellewang authored Jun 14, 2024
1 parent 5f107e0 commit fc3971f
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Showing 21 changed files with 249 additions and 355 deletions.
14 changes: 4 additions & 10 deletions ...a/descriptors/dcm2bids-3.1.0-convert.json → ...oppy/data/descriptors/dcm2bids-3.1.0.json
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Expand Up @@ -13,10 +13,7 @@
"list": true,
"optional": false,
"command-line-flag": "-d",
"value-key": "[DICOM_DIR]",
"default-value": [
"[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]"
]
"value-key": "[DICOM_DIR]"
},
{
"name": "participant",
Expand All @@ -25,8 +22,7 @@
"type": "String",
"optional": false,
"command-line-flag": "-p",
"value-key": "[PARTICIPANT]",
"default-value": "[[NIPOPPY_PARTICIPANT_ID]]"
"value-key": "[PARTICIPANT]"
},
{
"name": "session",
Expand All @@ -35,8 +31,7 @@
"type": "String",
"optional": true,
"command-line-flag": "-s",
"value-key": "[SESSION]",
"default-value": "[[NIPOPPY_SESSION_ID]]"
"value-key": "[SESSION]"
},
{
"name": "config",
Expand All @@ -54,8 +49,7 @@
"type": "String",
"optional": true,
"command-line-flag": "-o",
"value-key": "[OUTPUT_DIR]",
"default-value": "[[NIPOPPY_DPATH_BIDS]]"
"value-key": "[OUTPUT_DIR]"
},
{
"name": "auto_extract_entities",
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8 changes: 2 additions & 6 deletions ...a/descriptors/dcm2bids-3.1.0-prepare.json → ...ta/descriptors/dcm2bids_helper-3.1.0.json
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Expand Up @@ -13,10 +13,7 @@
"list": true,
"optional": false,
"command-line-flag": "-d",
"value-key": "[DICOM_DIR]",
"default-value": [
"[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]"
]
"value-key": "[DICOM_DIR]"
},
{
"name": "output_dir",
Expand All @@ -25,8 +22,7 @@
"type": "String",
"optional": true,
"command-line-flag": "-o",
"value-key": "[OUTPUT_DIR]",
"default-value": "[[NIPOPPY_DPATH_SCRATCH]]/dcm2bids_helper"
"value-key": "[OUTPUT_DIR]"
},
{
"name": "nest",
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25 changes: 8 additions & 17 deletions nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
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Expand Up @@ -3,25 +3,23 @@
"description": "fmriprep",
"tool-version": "20.2.7",
"schema-version": "0.5",
"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]",
"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]",
"inputs": [
{
"id": "bids_dir",
"name": "bids_dir",
"description": "the root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).",
"optional": false,
"type": "String",
"value-key": "[BIDS_DIR]",
"default-value": "[[NIPOPPY_DPATH_BIDS]]"
"value-key": "[BIDS_DIR]"
},
{
"id": "output_dir",
"name": "output_dir",
"description": "the output path for the outcomes of preprocessing and visual reports",
"optional": false,
"type": "String",
"value-key": "[OUTPUT_DIR]",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]"
"value-key": "[OUTPUT_DIR]"
},
{
"id": "analysis_level",
Expand All @@ -32,8 +30,7 @@
"value-key": "[ANALYSIS_LEVEL]",
"value-choices": [
"participant"
],
"default-value": "participant"
]
},
{
"id": "version",
Expand Down Expand Up @@ -61,10 +58,7 @@
"type": "String",
"value-key": "[PARTICIPANT_LABEL]",
"list": true,
"command-line-flag": "--participant-label",
"default-value": [
"[[NIPOPPY_PARTICIPANT_ID]]"
]
"command-line-flag": "--participant-label"
},
{
"id": "task_id",
Expand Down Expand Up @@ -109,8 +103,7 @@
"optional": true,
"type": "String",
"value-key": "[BIDS_DATABASE_DIR]",
"command-line-flag": "--bids-database-dir",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_BIDS_DB]]"
"command-line-flag": "--bids-database-dir"
},
{
"id": "nprocs",
Expand Down Expand Up @@ -450,8 +443,7 @@
"optional": true,
"type": "String",
"value-key": "[FS_SUBJECTS_DIR]",
"command-line-flag": "--fs-subjects-dir",
"default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_BIDS_SESSION]]"
"command-line-flag": "--fs-subjects-dir"
},
{
"id": "hires",
Expand Down Expand Up @@ -505,8 +497,7 @@
"optional": true,
"type": "String",
"value-key": "[WORK_DIR]",
"command-line-flag": "-w",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_WORK]]"
"command-line-flag": "-w"
},
{
"id": "clean_workdir",
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25 changes: 8 additions & 17 deletions nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,25 +3,23 @@
"description": "fmriprep",
"tool-version": "23.1.3",
"schema-version": "0.5",
"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]",
"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]",
"inputs": [
{
"id": "bids_dir",
"name": "bids_dir",
"description": "The root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).",
"optional": false,
"type": "String",
"value-key": "[BIDS_DIR]",
"default-value": "[[NIPOPPY_DPATH_BIDS]]"
"value-key": "[BIDS_DIR]"
},
{
"id": "output_dir",
"name": "output_dir",
"description": "The output path for the outcomes of preprocessing and visual reports",
"optional": false,
"type": "String",
"value-key": "[OUTPUT_DIR]",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]"
"value-key": "[OUTPUT_DIR]"
},
{
"id": "analysis_level",
Expand All @@ -32,8 +30,7 @@
"value-key": "[ANALYSIS_LEVEL]",
"value-choices": [
"participant"
],
"default-value": "participant"
]
},
{
"id": "skip_bids_validation",
Expand All @@ -52,10 +49,7 @@
"type": "String",
"value-key": "[PARTICIPANT_LABEL]",
"list": true,
"command-line-flag": "--participant-label",
"default-value": [
"[[NIPOPPY_PARTICIPANT_ID]]"
]
"command-line-flag": "--participant-label"
},
{
"id": "task_id",
Expand Down Expand Up @@ -100,8 +94,7 @@
"optional": true,
"type": "String",
"value-key": "[BIDS_DATABASE_DIR]",
"command-line-flag": "--bids-database-dir",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_BIDS_DB]]"
"command-line-flag": "--bids-database-dir"
},
{
"id": "nprocs",
Expand Down Expand Up @@ -508,8 +501,7 @@
"optional": true,
"type": "String",
"value-key": "[FS_SUBJECTS_DIR]",
"command-line-flag": "--fs-subjects-dir",
"default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_BIDS_SESSION]]"
"command-line-flag": "--fs-subjects-dir"
},
{
"id": "hires",
Expand Down Expand Up @@ -578,8 +570,7 @@
"optional": true,
"type": "String",
"value-key": "[WORK_DIR]",
"command-line-flag": "-w",
"default-value": "[[NIPOPPY_DPATH_PIPELINE_WORK]]"
"command-line-flag": "-w"
},
{
"id": "clean_workdir",
Expand Down
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