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