Dear Lisa,
double -- options (like for example --premat) require an = sign before their argument. I.e.,
--postmat=/data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/xfms/str2diff.mat
instead of
--postmat /data/levans/GambDTI/dist/data/003/1/imaging/DTI.bedpostX/xfms/str2diff.mat
I personally always only use the -- versions, just to keep things consistent.
Jesper
On 27 Apr 2016, at 21:07, Lisa Evans <[log in to unmask]> wrote:
> 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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