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Remove sdcflows and model ASLPrep on fMRIPrep/next (#338)
* Try this. * keep working. * Update plotting.py * Update base.py * Update base.py * Update. * Update plotting.py * Update plotting.py * fix. * Update plotting.py * Update plotting.py * Update plotting.py * Update. * Update cbf.py * Update cbf.py * Update cbf.py * Update cbf.py * Set Infs to 0. The Philips M0 scan has values of zero for some in-mask voxels, which, when used to calculate CBF, results in Infs. * Try just using standard ASL preproc pipeline. * Try that. * Update tests.py * Update outputs.py * Update base.py * Update base.py * More work. * More work. * More work. * Update utility.py * More work. * Run black and isort. * Update. * Update. * More work. * Update. * Fix. * Update gecbf.py * Update. * Update misc.py * Update fit.py * Update. * Update. * Fix? * Update fit.py * Update fit.py * Update fit.py * Update reference.py * Update reference.py * Update fit.py * Update fit.py * Whoops! * Update fit.py * Update fit.py * Update fit.py * Update fit.py * Update fit.py * Lots of changes. * Update config.py * Update base.py * Update base.py * Update base.py * Update base.py * Update. * Update base.py * Update. * Update. * Update base.py * Update confounds.py * Update. * Update base.py * Update. * Update confounds.py * Update. * Update. * Update. * Update workflows.rst * Update fit.py * Use new fMRIPrep! * Update. * Update. * update. * Update reference.py * Update. * Fix some things. * Fix many things. * Try 3.10. * Update. * Bump build Docker image version. * Update. * Update lint.yml * Update. * Update run.py * Update test_cli.py * Update test_cli.py * Update parser.py * Update parser.py * Update parser.py * Update parser.py * Update. * Update base.py * Update base.py * Update fit.py * Update fit.py * Update base.py * Update qc.py * Update apply.py * Update base.py * Update reference.py * Update base.py * Update base.py * Fix connections. * Make ApplyTransforms calls verbose. * Fix ApplyTransforms calls. * Try that. * Update. * Try fixing m0scan_native. * Try that then. * Try that then. * Update cbf.py * Update test_cli.py * Update aslprep_bids_config.json * Update test_cli.py * Write out native-space derivatives. * Update outputs.py * Update expected outputs. * Update base.py * Update expected outputs. * Update. * Parcellate data no matter what. * More cleanup. * Try adding numpy to build requirements. * Run isort. * Update __init__.py * Deal with style issues. * Add precomputed (will be empty). * Ignore unused parameter. * Try fixing install. * precomputed is a dictionary. * Outsource more workflows to fmriprep. * Try to implement functional cache. * Update BASIL output names. * Update base.py * Update hmc.py * Update bids.py * Remove GE workflows. * Try to fix GE HMC. * Whoops! * Run isort. * Update hmc.py * Update hmc.py * Update expected outputs. * Write out QC file. * Update utility.py * Add outputnode back in. * Try to debug motion params more. * Support single-volume motion parameters. * Add source to docstring. * Keep cleaning up GE processing. * Set confounds min volumes to 2. * Update confounds.py * Make QC calculations flexible. * Remove unused import. * Remove unused data files. * Write out QC file correctly. * Rename QC json filename. * Add confounds to GE outputs. * Drop unused functions and classes. * Try fixing tests. * Use GenericLabel instead of MultiLabel. * Use fMRIPrep's resampling interfaces. * Remove unnecessary comment. * Outsource more workflows to fMRIPrep. * Update expected_outputs_test_002.txt * Update expected outputs. * Update expected_outputs_test_001.txt * Don't use FixHeadersApplyTransforms. * Fix some connections in fit. * Add checks. * Fix logger name. * Retain niftis for now. * Override DDS for some workflow calls. * Disable aslref-space outputs unless requested Copies nipreps/fmriprep#3159. * Pass FLAIR images to anatomical workflow builder Copied from nipreps/fmriprep#3146. * Tag memory estimates in resamplers Copied from nipreps/fmriprep#3150. * Use M0 scan for reference for GE data. * Try to fix transform name. * Add reference image smoothing step. * Give smoothing output a BIDS-ish name. * Update fit.py * Remove unused modules. * Pin sMRIPrep version. * Reduce mask. * Squeeze masks before merging. * Fix module name. * Drop niftis from test outputs. * Update workflows.rst * Improve documentation. * Update api.rst * Update workflows.rst * Update citations. * More documentation improvements. * Remove dropped coverage files from expected outputs. * Update license and output docs. * Fix issues with CIFTI connections. * Update base Docker image. The new version has MSM. * Add level testing jobs. * Update expected outputs. * Try fixing more issues. * Draft workflow to produce CIFTI CBF maps. * Keep working on CIFTI CBF workflow. * Keep working on CIFTI CBF workflow. * Add reference images. * Update outputs.py * Address multiple bugs with GIFTI outputs. * Try outputting fsaverage. * Add docstrings. * Ignore unused argument. * Update tests. * Fix! * Update test_002 cache (it was already v3). * Update. * Update test_cli.py * Update config.yml * Update config.yml * Fix things. * Update test_cli.py * Update config.yml * Combine QC and confounds modules. * Remove unused functions/interfaces. * Remove another unused function. * Remove unused interface function. * Bump anatomical test data version. * Fix import. * Update expected outputs. * Create expected_outputs_qtab.txt * Grab MNI152NLin2009cAsym xfm for resampling. * Update expected outputs. * Add topup to boilerplate BibTeX file. * Revert some changes. * Update expected outputs. * Move asl_anat_wf from resampling to full. * Try outputting CIFTI for one test. * Add updated fsLR workflow from fMRIPrep. * Update resampling.py * Speed up test_003. * Use internal version of init_bold_surf_wf. * Fix style issues. * Remove unused script. * Fix typos. * Drop CIFTI test and sort expected outputs.
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