Hi,
You cannot use the .par file in this way.
If you want to combine a warp and the motion correction matrices, then you need to make one file that is the concatenation of all the *matrices* from the mcflirt output. This can be done like this:
cat blahblah.feat/mc/prefiltered_func_data_mcf.mat/MAT* > blahblah.feat/all_mc.mat
and then use this output file (all_mc.mat) in your applywarp command.
All the best,
Mark
> On 5 Apr 2018, at 05:11, Catherine <[log in to unmask]> wrote:
>
> Dear All,
>
> I encountered a strange error while using applywarp command line.
> Below is my command:
>
> applywarp -i /run/media/fsluser/PRE/1217/Practice_st.nii.gz -r /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -o /run/media/fsluser/PRE/1217/Practice_st_PRE.feat/normalized.nii.gz --premat=/run/media/fsluser/PRE/1217/Practice_st_PRE.feat/mc/prefiltered_func_data_mcf.par -w /run/media/fsluser/PRE/1217/Practice_st_PRE.feat/combinedwarp.nii.gz
>
> The error message I got is this:
> Image Exception : #24 :: Number of premats (209) does not match number of volumes (837)
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>
> I did check my prefiltered_func_data_mcf.par file, which has 837 rows, so I'm not sure what's causing the issue here, as both files match, but fsl indicated otherwise........
>
> Attached is my prefiltered_func_data_mcf.par file.
>
> Thanks!
> Catherine
> <prefiltered_func_data_mcf.par>
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