I have two sets of images, one collected at timepoint 1 and one at timepoint 2, for each patient and control in an MS study. I am now trying to run autorecon1 on this data, at the same time attempting to form a combined model fit. I am using the following script:
for subject in ***; do
if [ ! -f $SUBJECTS_DIR/$subject-1/mri/brainmask.mgz ]; then fsl_sub -q short.q -a lx24-amd64 -l ../group_study/logs recon-all -i $subject/00/struct_noneck.nii.gz -i $subject/02/struct_noneck.nii.gz -subjid $subject-1 -autorecon1 -force
The following error message is generated for the around half of the subjects, yet there seems to be nothing especially different between the ones that work and the ones that fail.
error reading from file /Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img
mri_average: MRIread(/Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img) failed
Any ideas?
Thanks, Damian
Dr Damian Jenkins Department of Clinical Neurology Oxford University