Do you have fsl installed? This is needed for creating the brain masks.
Balaji Goparaju wrote:
Hi Doug and all,
I used the new version of mkbrainmask-sess. It looks like the file is getting created but it cannot find fslmaths for avmaths. Is this error something to do with the freesurfer software itself, or is there anything I can do about it?
Thu Jul 24 09:15:51 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update
/Users/balajigoparaju/Desktop/subjectdata/LD-functional Thu Jul 24 09:15:52 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold mkbrainmask -i 006/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0
ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed
Thank you for any help!