Dear FSL experts,
I am trying to use applywarp to transform a mask from standard to diffusion space using successive affine, non-linear, affine transformations (standard to structural to diffusion). However, when I try to use --premat to enter my standard2str.mat matrix file, I am getting the message: --premat: Missing non-optional argument. I am using fsl-5.0.9.
This is my code if it helps at all:
applywarp -i /data/levans/GambDTI/dist/data/tbss/ROIs/OFCsphere.nii.gz
-r /opt/fsl-5.0.9/data/standard/MNI152_T1_2mm_brain.nii.gz
-o /data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/probtrackx/ROIs/OFCsphere_diff.nii.gz
--premat /data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/xfms/standard2str.mat
--postmat /data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/xfms/str2diff.mat
-w /data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/xfms/standard2str_warp.nii.gz
I would greatly appreciate any help with this.
Thank you,
Lisa
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