From 6cc0fc77d52461a619eeded22b46a9a863aef3be Mon Sep 17 00:00:00 2001 From: Jenny Chen Date: Fri, 13 Dec 2024 12:48:45 -0500 Subject: [PATCH] rpe_all bug fix: consistent naming for eddy scratch --- lib/designer_func_wrappers.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/lib/designer_func_wrappers.py b/lib/designer_func_wrappers.py index bcfd989..89affa6 100644 --- a/lib/designer_func_wrappers.py +++ b/lib/designer_func_wrappers.py @@ -906,15 +906,18 @@ def run_eddy(shell_table, dwi_metadata): 'topup_corrected_brain')) run.command('mrcat -axis 3 working.mif dwirpe.mif dwipe_rpe.mif') + if app.ARGS.eddy_fakeb is None: - run.command('dwifslpreproc -nocleanup -eddy_options %s -rpe_all -pe_dir "%s" -eddy_mask "%s" dwipe_rpe.mif dwiec.mif' % - (eddyopts, + run.command('dwifslpreproc -nocleanup -scratch "%s" -eddy_options %s -rpe_all -pe_dir "%s" -eddy_mask "%s" dwipe_rpe.mif dwiec.mif' % + ('eddy_processing', + eddyopts, pe_dir, 'topup_corrected_brain_mask' + fsl_suffix )) else: - run.command('dwifslpreproc -nocleanup -grad "%s" -eddy_options %s -rpe_all -pe_dir "%s" -eddy_mask "%s" dwipe_rpe.mif dwiec.mif' % - ('fakeb_grad.txt', + run.command('dwifslpreproc -nocleanup -scratch "%s" -grad "%s" -eddy_options %s -rpe_all -pe_dir "%s" -eddy_mask "%s" dwipe_rpe.mif dwiec.mif' % + ('eddy_processing', + 'fakeb_grad.txt', eddyopts, pe_dir, 'topup_corrected_brain_mask' + fsl_suffix @@ -923,11 +926,11 @@ def run_eddy(shell_table, dwi_metadata): elif app.ARGS.rpe_header: if app.ARGS.eddy_fakeb is None: - cmd = ('dwifslpreproc -nocleanup -eddy_options %s -rpe_header working.mif dwiec.mif' % - (eddyopts)) + cmd = ('dwifslpreproc -nocleanup -scratch "%s" -eddy_options "%s" -rpe_header working.mif dwiec.mif' % + ('eddy_processing',eddyopts)) else: - cmd = ('dwifslpreproc -nocleanup -grad "%s" -eddy_options %s -rpe_header working.mif dwiec.mif' % - ('fakeb_grad.txt', eddyopts)) + cmd = ('dwifslpreproc -nocleanup -scratch "%s" -grad "%s" -eddy_options %s -rpe_header working.mif dwiec.mif' % + ('eddy_processing','fakeb_grad.txt', eddyopts)) run.command(cmd) elif not app.ARGS.rpe_header and not app.ARGS.rpe_all and not app.ARGS.rpe_pair: