From 789ae648cf18fa35ac038a46dffa3be3330faf6f Mon Sep 17 00:00:00 2001 From: Brianne Sutton <21200969+neurosutton@users.noreply.github.com> Date: Wed, 6 Mar 2024 06:56:09 -0700 Subject: [PATCH] Update qsiprep --- gears/flywheel/bids-qsiprep.json | 663 +++++++++---------------------- 1 file changed, 177 insertions(+), 486 deletions(-) diff --git a/gears/flywheel/bids-qsiprep.json b/gears/flywheel/bids-qsiprep.json index c53f3453..bd2e8d81 100644 --- a/gears/flywheel/bids-qsiprep.json +++ b/gears/flywheel/bids-qsiprep.json @@ -1,495 +1,186 @@ { - "author": "Flywheel", - "cite": "https://qsiprep.readthedocs.io/en/latest/citing.html", - "command": "python /flywheel/v0/run.py", - "config": { - "acquisition_type": { - "description": "select a specific acquisition type to be processed.", - "optional": true, - "type": "string" - }, - "anat-only": { - "description": "run anatomical workflows only.", - "optional": true, - "type": "boolean" - }, - "b0-motion-corr-to": { - "description": "align to the 'first' b0 volume or do an 'iterative' registration of all b0 images\nto their midpoint image (default: iterative)", - "enum": [ - "", - "iterative", - "first" - ], - "optional": true, - "type": "string" - }, - "b0-threshold": { - "description": "any value in the .bval file less than this will be considered a b=0 image.\nCurrent default threshold = 100; this threshold can be lowered or increased.\nNote, setting this too high can result in inaccurate results.", - "optional": true, - "type": "number" - }, - "b0-to-t1w-transform": { - "description": "Degrees of freedom when registering b0 to T1w images. 6 degrees (rotation and translation) are used by default.", - "enum": [ - "", - "Rigid", - "Affine" - ], - "optional": true, - "type": "string" - }, - "bids_app_args": { - "default": "", - "description": "[arg1 [arg2 ...]]", - "type": "string" - }, - "boilerplate": { - "description": "generate boilerplate only.", - "optional": true, - "type": "boolean" - }, - "debug": { - "default": false, - "description": "Log debug messages", - "type": "boolean" - }, - "denoise-after-combining": { - "description": "run dwidenoise after combining dwis. Cannot be used with --separate-all-dwis.", - "optional": true, - "type": "boolean" - }, - "denoise-method": { - "description": "Image-based denoising method.\nEither 'dwidenoise' (MRtrix), 'patch2self' (DIPY) or none.", - "enum": [ - "", - "dwidenoise", - "patch2self" - ], - "optional": true, - "type": "string" - }, - "denoised_image_sdc": { - "description": "use denoised b=0 images if available instead of raw (from BIDS) images in SDC.", - "optional": true, - "type": "boolean" - }, - "distortion-group-merge": { - "description": "Possible choices: concat, average, none\n concatenate: append images in the 4th dimension\n average: if a whole sequence was duplicated in both PE directions, average the corrected images of the same q-space coordinate\n none: Default. Keep distorted groups separate", - "enum": [ - "", - "concatenate", - "average" - ], - "optional": true, - "type": "string" - }, - "do-reconall": { - "description": "Run the FreeSurfer recon-all pipeline", - "optional": true, - "type": "boolean" - }, - "dwi-no-biascorr": { - "description": "skip b0-based dwi spatial bias correction.", - "optional": true, - "type": "boolean" - }, - "dwi-only": { - "description": "ignore anatomical (T1w/T2w) data and process DWIs only.", - "optional": true, - "type": "boolean" - }, - "dwi_denoise_window": { - "description": "window size in voxels for dwidenoise. Must be odd (default: 5). If 0, dwidwenoise will not be run.", - "optional": true, - "type": "integer" - }, - "fmap-bspline": { - "description": "fit a B-Spline field using least-squares (experimental)", - "optional": true, - "type": "boolean" - }, - "fmap-no-demean": { - "description": "do not remove median (within mask) from fieldmap (default: True)", - "optional": true, - "type": "boolean" - }, - "force-syn": { - "description": "EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to fieldmap correction, if available", - "optional": true, - "type": "boolean" - }, - "freesurfer_license_key": { - "description": "Text from license file generated during FreeSurfer registration. *Entries should be space separated*", - "optional": true, - "type": "string" - }, - "gear-dry-run": { - "default": false, - "description": "Do everything except actually executing qsiprep", - "type": "boolean" - }, - "gear-ignore-bids-errors": { - "default": false, - "description": "By default, the gear will not run if there are any BIDS errors detected. Set this to run even if BIDS errors are detected", - "type": "boolean" - }, - "gear-intermediate-files": { - "default": "", - "description": "Space separated list of FILES to retain from the intermediate work directory.", - "type": "string" - }, - "gear-intermediate-folders": { - "default": "", - "description": "Space separated list of FOLDERS to retain from the intermediate work directory.", - "type": "string" - }, - "gear-keep-output": { - "default": false, - "description": "Don't delete output. Output is always zipped into a single file for easy download. Choose this option to prevent output deletion after zipping.", - "type": "boolean" - }, - "gear-run-bids-validation": { - "default": true, - "description": "Gear will run BIDS validation after downloading data. If validation fails qsiprep will NOT be run.", - "type": "boolean" - }, - "gear-save-intermediate-output": { - "default": false, - "description": "Gear will save ALL intermediate output into qsiprep_work.zip", - "type": "boolean" - }, - "hmc-transform": { - "description": "transformation to be optimized during head motion correction (default: affine)", - "enum": [ - "", - "Affine", - "Rigid" - ], - "optional": true, - "type": "string" - }, - "hmc_model": { - "description": "model used to generate target images for hmc. If 'none' the non-b0 images will be warped using the same transform as their nearest b0 image. If '3dSHORE', SHORELine will be used. If 'eddy_ingress', the dwis are assumed to have been run through fsls eddy.", - "enum": [ - "", - "3dSHORE", - "eddy" - ], - "optional": true, - "type": "string" - }, - "ignore": { - "default": "", - "description": "Ignore selected aspects of the input dataset to disable corresponding parts of the workflow (a space delimited list) Possible choices: fieldmaps, slicetiming, sbref", - "type": "string" - }, - "impute-slice-threshold": { - "description": "impute data in slices that are this many SDs from expected. If 0 (default), no slices will be imputed", - "optional": true, - "type": "number" - }, - "infant": { - "description": "configure pipelines to process infant brains.", - "optional": true, - "type": "boolean" - }, - "interactive-reports-only": { - "description": "create interactive report json files on already preprocessed data.", - "optional": true, - "type": "boolean" - }, - "intramodal-template-iters": { - "description": "Number of iterations for finding the midpoint image from the b0 templates from all groups.\nHas no effect if there is only one group.\nIf 0, all b0 templates are directly registered to the t1w image.", - "optional": true, - "type": "integer" - }, - "intramodal-template-transform": { - "description": "Transformation used for building the intramodal template.", - "enum": [ - "", - "Rigid", - "Affine", - "BSplineSyN", - "SyN" - ], - "optional": true, - "type": "string" - }, - "longitudinal": { - "description": "treat dataset as longitudinal - may increase runtime.", - "optional": true, - "type": "boolean" - }, - "mem_mb": { - "description": "Maximum memory to use (MB). Leave blank or set to 0 to use the maximum available in the system.", - "optional": true, - "type": "integer" - }, - "n_cpus": { - "description": "Number of CPUs/cores to use. Leave blank or set to 0 to use the maximum available in the system.", - "optional": true, - "type": "integer" - }, - "no-b0-harmonization": { - "description": "skip re-scaling dwi scans to have matching b=0 intensities.", - "optional": true, - "type": "boolean" - }, - "output-resolution": { - "default": 1, - "description": "the isotropic voxel size in mm the data will be resampled to after preprocessing.\nIf set to a lower value than the original voxel size, your data will be upsampled using BSpline interpolation.", - "type": "number" - }, - "output-space": { - "description": "Volume and surface spaces to resample dwis into\n T1w: subject anatomical volume\n template: deprecated. Will be ignored", - "enum": [ - "", - "T1w", - "template" - ], - "optional": true, - "type": "string" - }, - "pepolar_method": { - "description": "select which SDC method to use for PEPOLAR fieldmaps", - "enum": [ - "", - "TOPUP", - "DRBUDDI" - ], - "optional": true, - "type": "string" - }, - "prefer_dedicated_fmaps": { - "description": "forces unwarping to use files from the fmap directory instead of using an RPEdir scan from the same session.", - "optional": true, - "type": "boolean" - }, - "reports-only": { - "description": "only generate reports, don't run workflows. This will only rerun report aggregation, not reportlet generation for specific nodes.", - "optional": true, - "type": "boolean" - }, - "separate-all-dwis": { - "description": "don't attempt to combine dwis from multiple runs. Each will be processed separately.", - "optional": true, - "type": "boolean" - }, - "shoreline_iters": { - "description": "number of SHORELine iterations. (default: 2)", - "optional": true, - "type": "integer" - }, - "skip-t1-based-spatial-normalization": { - "description": "skip running the t1w-based normalization to template space. Default is to run the normalization.", - "optional": true, - "type": "boolean" - }, - "skull-strip-fixed-seed": { - "description": "do not use a random seed for skull-stripping - will ensure run-to-run replicability when used with -omp-nthreads 1", - "optional": true, - "type": "boolean" - }, - "skull-strip-template": { - "description": "select ANTs skull-stripping template (default: OASIS)", - "enum": [ - "", - "OASIS", - "NKI" - ], - "optional": true, - "type": "string" - }, - "template": { - "description": "volume template space (default: MNI152NLin2009cAsym)", - "enum": [ - "", - "MNI152NLin2009cAsym" - ], - "optional": true, - "type": "string" - }, - "unringing-method": { - "description": "mrdegibbs: use mrdegibbs from mrtrix3", - "enum": [ - "", - "mrdegibbs" - ], - "optional": true, - "type": "string" - }, - "use-syn-sdc": { - "description": "EXPERIMENTAL: Use fieldmap-free distortion correction. To use this option, 'template' must be passed to -output-space", - "optional": true, - "type": "boolean" - }, - "verbose": { - "default": "v", - "description": "increases log verbosity for each occurrence, debug level is -vvv", - "enum": [ - "", - "v", - "vv", - "vvv" - ], - "type": "string" - }, - "write-graph": { - "default": false, - "description": "Write workflow graph", - "type": "boolean" - }, - "write-local-bvecs": { - "description": "write a series of voxelwise bvecs, relevant if writing preprocessed dwis to template space.", - "optional": true, - "type": "boolean" - } - }, - "custom": { - "analysis-level": "participant", - "bids-app-binary": "qsiprep", - "bids-app-modalities": [ - "anat", - "dwi", - "fmap" - ], - "flywheel": { - "suite": "BIDS Apps" - }, - "gear-builder": { - "category": "analysis", - "image": "flywheel/bids-qsiprep:1.0.4_0.16.1" - }, - "license": { - "dependencies": [ - { - "name": "Other", - "url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence" + "author": "Matthew Cieslak, Philip A. Cook, Theodore D. Satterthwaite, et al.", + "cite": "https://qsiprep.readthedocs.io/en/latest/citing.html", + "command": "/opt/flypy/bin/python run.py", + "config": { + "bids_app_command": { + "default": "", + "description": "OPTIONAL. The gear will run the algorithm defaults, if no command is supplied. See https://qsiprep.readthedocs.io/en/latest/usage.html for options. e.g., `qsiprep bids_dir output_dir participant [arg1 [arg2 ...]] -w work_dir`", + "type": "string" + }, + "debug": { + "default": false, + "description": "Log debug messages", + "type": "boolean" + }, + "gear-dry-run": { + "default": false, + "description": "Do everything Flywheel-related except actually execute BIDS App command. Different from passing '--dry-run' in the BIDS App command.", + "type": "boolean" }, - { - "name": "Other", - "url": "https://github.com/ANTsX/ANTs/blob/v2.2.0/COPYING.txt" + "gear-post-processing-only": { + "default": false, + "description": "REQUIRES archive file (aka recon_input). Gear will skip the BIDS algorithm and go straight to generating the HTML reports and processing metadata.", + "type": "boolean" }, - { - "name": "Other", - "url": "https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.copyright.html" + "gear-keep-output": { + "default": false, + "description": "Keep ALL the extra output files that are created during the run in addition to the normal, zipped output. Note: This option may cause a gear failure because there are too many files for the engine.", + "type": "boolean" }, - { - "name": "Other", - "url": "https://dsi-studio.labsolver.org/download.html" + "gear-save-intermediate-output": { + "default": false, + "description": "Gear will save ALL intermediate output into bids_qsiprep_work.zip", + "type": "boolean" }, - { - "name": "MPL-2.0", - "url": "https://github.com/MRtrix3/mrtrix3/blob/master/LICENCE.txt" + "output-resolution": { + "description": "Spatial resolution of the prepocessed DWI series. For more help, see https://qsiprep.readthedocs.io/en/latest/quickstart.html#specifying-outputs", + "optional": false, + "type": "number" + }, + "notrack": { + "default": true, + "description": "Opt out of statistical usage tracking.", + "type": "boolean" } - ], - "main": { - "name": "BSD-3-Clause", - "url": "https://github.com/PennLINC/qsiprep/blob/0.16.1/LICENSE" - }, - "non-commercial-use-only": false - } - }, - "description": "BIDS qsiprep 1.0.*_0.16.1 \n qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data. The main features of this software are:\n\nA BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.\n\nAutomatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, co-register and resample your scans, producing visual reports and QC metrics.\n\nA system for running state-of-the-art reconstruction pipelines that include algorithms from Dipy, MRTrix, DSI Studio and others.\n\nA novel motion correction algorithm that works on DSI and random q-space sampling schemes", - "environment": { - "AFNI_IMSAVE_WARNINGS": "NO", - "AFNI_INSTALLDIR": "/opt/afni-latest", - "ANTSPATH": "/opt/ants/bin", - "ANTS_DEPS": "zlib1g-dev", - "ARTHOME": "/opt/art", - "C3DPATH": "/opt/convert3d-nightly", - "CRN_SHARED_DATA": "/niworkflows_data", - "CUDA_VERSION": "10.2.89", - "DIPY_HOME": "/home/qsiprep/.dipy", - "DSI_STUDIO_DEPS": "qt512base qt512charts-no-lgpl", - "FLYWHEEL": "/flywheel/v0", - "FREESURFER_DEPS": "bc ca-certificates curl libgomp1 libxmu6 libxt6 tcsh perl", - "FREESURFER_HOME": "/opt/freesurfer", - "FSF_OUTPUT_FORMAT": "nii.gz", - "FSLDIR": "/opt/fsl-6.0.5.1", - "FSLGECUDAQ": "cuda.q", - "FSLMULTIFILEQUIT": "TRUE", - "FSLOUTPUTTYPE": "NIFTI_GZ", - "FSL_DEPS": "libquadmath0", - "FSL_DIR": "/opt/fsl-6.0.5.1", - "FS_OVERRIDE": "0", - "FUNCTIONALS_DIR": "/opt/freesurfer/sessions", - "IS_DOCKER_8395080871": "1", - "KMP_WARNINGS": "0", - "LD_LIBRARY_PATH": "/opt/qt512/lib/x86_64-linux-gnu:/opt/qt512/lib:/opt/qt512/lib/x86_64-linux-gnu:/opt/qt512/lib:/opt/ants/lib:/opt/fsl-6.0.5.1/lib:/usr/local/nvidia/lib:/usr/local/nvidia/lib64", - "LOCAL_DIR": "/opt/freesurfer/local", - "MINC_BIN_DIR": "/opt/freesurfer/mni/bin", - "MINC_LIB_DIR": "/opt/freesurfer/mni/lib", - "MKL_NUM_THREADS": "1", - "MNI_DATAPATH": "/opt/freesurfer/mni/data", - "MNI_DIR": "/opt/freesurfer/mni", - "MNI_PERL5LIB": "/opt/freesurfer/mni/lib/perl5/5.8.5", - "MRTRIX3_DEPS": "bzip2 ca-certificates curl libpng16-16 libblas3 liblapack3", - "MRTRIX_NTHREADS": "1", - "NCCL_VERSION": "2.11.4", - "NVARCH": "x86_64", - "NVIDIA_DRIVER_CAPABILITIES": "compute,utility", - "NVIDIA_REQUIRE_CUDA": "cuda>=10.2 brand=tesla,driver>=396,driver<397 brand=tesla,driver>=410,driver<411 brand=tesla,driver>=418,driver<419 brand=tesla,driver>=440,driver<441", - "NVIDIA_VISIBLE_DEVICES": "all", - "NV_CUDA_CUDART_VERSION": "10.2.89-1", - "NV_CUDA_LIB_VERSION": "10.2.89-1", - "NV_LIBCUBLAS_PACKAGE": "libcublas10=10.2.2.89-1", - "NV_LIBCUBLAS_PACKAGE_NAME": "libcublas10", - "NV_LIBCUBLAS_VERSION": "10.2.2.89-1", - "NV_LIBCUSPARSE_VERSION": "10.2.89-1", - "NV_LIBNCCL_PACKAGE": "libnccl2=2.11.4-1+cuda10.2", - "NV_LIBNCCL_PACKAGE_NAME": "libnccl2", - "NV_LIBNCCL_PACKAGE_VERSION": "2.11.4-1", - "NV_LIBNPP_VERSION": "10.2.89-1", - "NV_ML_REPO_ENABLED": "1", - "NV_ML_REPO_URL": "https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64", - "NV_NVTX_VERSION": "10.2.89-1", - "OMP_NUM_THREADS": "1", - "OS": "Linux", - "PATH": "/opt/poetry/bin:/opt/qt512/bin:/opt/art/bin:/opt/convert3d-nightly/bin:/usr/local/miniconda/bin:/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/qt512/bin:/opt/fsl-6.0.5.1/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/ants/bin:/opt/dsi-studio/dsi_studio_64:/opt/mrtrix3-latest/bin:/opt/3Tissue/bin:/opt/afni-latest", - "PERL5LIB": "/opt/freesurfer/mni/lib/perl5/5.8.5", - "PKG_CONFIG_PATH": "/opt/qt512/lib/pkgconfig:/opt/qt512/lib/pkgconfig:", - "POETRY_HOME": "/opt/poetry", - "POETRY_VERSION": "1.1.13", - "POETRY_VIRTUALENVS_CREATE": "false", - "PYTHONUNBUFFERED": "1", - "QSIRECON_ATLAS": "/atlas/qsirecon_atlases", - "QTDIR": "/opt/qt512", - "QT_BASE_DIR": "/opt/qt512", - "SHLVL": "1", - "SUBJECTS_DIR": "/opt/freesurfer/subjects" - }, - "inputs": { - "api-key": { - "base": "api-key", - "read-only": true - }, - "bidsignore": { - "base": "file", - "description": "A .bidsignore file to provide to the bids-validator that this gear runs before running the main command.", - "optional": true }, - "eddy-config": { - "base": "file", - "description": "path to a json file with settings for the call to eddy. If no json is specified, a default one will be used. The current default json can be found here: https://github.com/PennBBL/qsiprep/blob/master/qsiprep/data/eddy_params.json", - "optional": true + "custom": { + "analysis-level": "participant", + "bids-app-binary": "qsiprep", + "bids-app-data-types": [ + "anat", + "dwi", + "fmap" + ], + "flywheel": { + "suite": "BIDS Apps" + }, + "gear-builder": { + "category": "analysis", + "image": "flywheel/bids_qsiprep:1.1.0_0.20.0" + }, + "license": { + "dependencies": [ + { + "name": "Other", + "url": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence" + }, + { + "name": "Other", + "url": "https://github.com/ANTsX/ANTs/blob/v2.2.0/COPYING.txt" + }, + { + "name": "Other", + "url": "https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.copyright.html" + }, + { + "name": "Other", + "url": "https://dsi-studio.labsolver.org/download.html" + }, + { + "name": "MPL-2.0", + "url": "https://github.com/MRtrix3/mrtrix3/blob/master/LICENCE.txt" + } + ], + "main": { + "name": "BSD-3-Clause", + "url": "https://github.com/PennLINC/qsiprep/blob/0.16.1/LICENSE" + }, + "non-commercial-use-only": false + } }, - "freesurfer_license_file": { - "base": "file", - "description": "FreeSurfer license file, provided during registration with FreeSurfer. This file will be copied to the $FSHOME directory and used during execution of the Gear.", - "optional": true + "description": "BIDS qsiprep 1.1.*_0.20.0 \n qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data. The main features of this software are:\n\nA BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.\n\nAutomatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, co-register and resample your scans, producing visual reports and QC metrics.\n\nA system for running state-of-the-art reconstruction pipelines that include algorithms from Dipy, MRTrix, DSI Studio and others.\n\nA novel motion correction algorithm that works on DSI and random q-space sampling schemes", + "environment": { + "FLYWHEEL": "/flywheel/v0", + "PATH": "/opt/qt512/bin:/opt/art/bin:/opt/convert3d-nightly/bin:/usr/local/miniconda/bin:/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/qt512/bin:/opt/fsl-6.0.5.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/ants/bin:/opt/dsi-studio/dsi_studio_64:/opt/mrtrix3-latest/bin:/opt/3Tissue/bin:/opt/afni-latest:/src/TORTOISEV4/bin", + "FSLDIR": "/opt/fsl-6.0.5.1", + "FSLOUTPUTTYPE": "NIFTI_GZ", + "FSLMULTIFILEQUIT": "TRUE", + "FSLGECUDAQ": "cuda.q", + "LD_LIBRARY_PATH": "/opt/qt512/lib/x86_64-linux-gnu:/opt/qt512/lib:/opt/qt512/lib/x86_64-linux-gnu:/opt/qt512/lib:/opt/ants/lib:/opt/fsl-6.0.5.1/lib:", + "FSL_DEPS": "libquadmath0", + "ANTSPATH": "/opt/ants/bin", + "ANTS_DEPS": "zlib1g-dev", + "QT_BASE_DIR": "/opt/qt512", + "QTDIR": "/opt/qt512", + "PKG_CONFIG_PATH": "/opt/qt512/lib/pkgconfig:/opt/qt512/lib/pkgconfig:", + "DSI_STUDIO_DEPS": "qt512base qt512charts-no-lgpl", + "MRTRIX3_DEPS": "bzip2 ca-certificates curl libpng16-16 libblas3 liblapack3", + "FSL_DIR": "/opt/fsl-6.0.5.1", + "OS": "Linux", + "FS_OVERRIDE": "0", + "FSF_OUTPUT_FORMAT": "nii.gz", + "FREESURFER_HOME": "/opt/freesurfer", + "SUBJECTS_DIR": "/opt/freesurfer/subjects", + "FUNCTIONALS_DIR": "/opt/freesurfer/sessions", + "MNI_DIR": "/opt/freesurfer/mni", + "LOCAL_DIR": "/opt/freesurfer/local", + "MINC_BIN_DIR": "/opt/freesurfer/mni/bin", + "MINC_LIB_DIR": "/opt/freesurfer/mni/lib", + "MNI_DATAPATH": "/opt/freesurfer/mni/data", + "PERL5LIB": "/opt/freesurfer/mni/lib/perl5/5.8.5", + "MNI_PERL5LIB": "/opt/freesurfer/mni/lib/perl5/5.8.5", + "FREESURFER_DEPS": "bc ca-certificates curl libgomp1 libxmu6 libxt6 tcsh perl", + "AFNI_INSTALLDIR": "/opt/afni-latest", + "AFNI_IMSAVE_WARNINGS": "NO", + "TORTOISE_DEPS": "libeigen3-dev fftw3 libfftw3-dev", + "C3DPATH": "/opt/convert3d-nightly", + "MKL_NUM_THREADS": "1", + "OMP_NUM_THREADS": "1", + "MRTRIX_NTHREADS": "1", + "KMP_WARNINGS": "0", + "CRN_SHARED_DATA": "/niworkflows_data", + "IS_DOCKER_8395080871": "1", + "ARTHOME": "/opt/art", + "DIPY_HOME": "/home/qsiprep/.dipy", + "QSIRECON_ATLAS": "/atlas/qsirecon_atlases" + }, + "inputs": { + "api-key": { + "base": "api-key", + "read-only": true + }, + "bidsignore": { + "base": "file", + "description": "A .bidsignore file to provide to the bids-validator that this gear runs before running the main command.", + "optional": true + }, + "eddy-config": { + "base": "file", + "description": "path to a json file with settings for the call to eddy. If no json is specified, a default one will be used. The current default json can be found here: https://github.com/PennBBL/qsiprep/blob/master/qsiprep/data/eddy_params.json", + "optional": true + }, + "freesurfer_license_file": { + "base": "file", + "description": "FreeSurfer license file, provided during registration with FreeSurfer. This file will be copied to the $FSHOME directory and used during execution of the Gear.", + "optional": true + }, + "recon-input": { + "base": "file", + "description": "Previous output (zip archive) of qsiprep run (e.g., bids-qsiprep_*.zip)", + "optional": true, + "type": { + "enum": [ + "archive" + ] + } + }, + "recon-spec": { + "base": "file", + "description": "json file specifying a reconstruction pipeline to be run after preprocessing.", + "optional": true + }, + "archived_runs": { + "base": "file", + "description": "Previous output (zip archive) of qsiprep run (e.g., bids-qsiprep_*.zip)", + "optional": true + } }, - "recon-spec": { - "base": "file", - "description": "json file specifying a reconstruction pipeline to be run after preprocessing.", - "optional": true - } - }, - "label": "BIDS QSIPrep", - "license": "MIT", - "maintainer": "Flywheel ", - "name": "bids-qsiprep", - "source": "https://qsiprep.readthedocs.io/en/latest/", - "url": "https://gitlab.com/flywheel-io/flywheel-apps/bids-qsiprep", - "version": "1.0.4_0.16.1" -} + "label": "BIDS QSIPrep", + "license": "BSD-3-Clause", + "maintainer": "Flywheel ", + "name": "bids-qsiprep", + "source": "https://qsiprep.readthedocs.io/en/latest/", + "url": "https://gitlab.com/flywheel-io/scientific-solutions/gears/bids-apps/bids-qsiprep", + "version": "1.1.0_0.20.0" +} \ No newline at end of file