Hi FreeSurfer community, I am trying to run 'trac-all -corr -c <config file>' on the tutorial data, specifically for the single subject: Diff001. To start from 'scratch', I've deleted all but the './scripts' and the './orig' directories in the Diff001 parent folder. When I run the following command:
trac-all -corr -c <config file>
I receive the following error:
ERROR BEGINS----> flip4fsl /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz x -y z /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz Cannot open volume /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip for reading! ----> ERROR ENDS
Looking in my 'Diff001/dmri' directory, I cannot locate a 'dwi_orig_flip.nii.gz' file. I assume this is where the script breaks. I tried to run the 'flip4fsl' command singly, but received the same error.
I'm working on a: 3.2.0-35-generic #55-Ubuntu SMP Wed Dec 5 17:42:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
I've unsuccessfully searched through the mailing list archive to find if others had encountered the same issue previously. Does anybody have any suggestions?
Thanks! Susie