From 904386550359494b8d32a8cb5dda7171e4b00c9b Mon Sep 17 00:00:00 2001 From: Jenny Chen Date: Thu, 12 Dec 2024 13:00:18 -0500 Subject: [PATCH] fix bug in -rpe_all: b0rpe2pe registration --- lib/designer_func_wrappers.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/designer_func_wrappers.py b/lib/designer_func_wrappers.py index e5ff63d..bcfd989 100644 --- a/lib/designer_func_wrappers.py +++ b/lib/designer_func_wrappers.py @@ -871,7 +871,8 @@ def run_eddy(shell_table, dwi_metadata): run.command('mrconvert -strides -1,+2,+3,+4 -grad grad.txt "%s" dwirpe.mif' % (app.ARGS.rpe_all)) run.command('dwiextract -bzero dwirpe.mif - | mrconvert -coord 3 0 - b0rpe.nii') - run.command('flirt -in b0rpe.nii -ref b0pe.mif -dof 6 -out b0rpe2pe.nii.gz') + run.command('mrconvert b0pe.mif b0pe.nii') + run.command('flirt -in b0rpe.nii -ref b0pe.nii -dof 6 -out b0rpe2pe.nii.gz') run.command('mrcat -axis 3 b0pe.mif b0rpe2pe.nii.gz b0_pair_topup.nii') # if any of the image dims are odd dont subsample during topup. might be better off changing this to padding so topup doesnt take forever