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

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/Users/balajigoparaju/Desktop/subjectdata/LD-functional 

Thu Jul 24 09:15:52 EDT 2008

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/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold

mkbrainmask -i 006/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0

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ERROR: cannot find either fslmaths for avwmaths

ERROR: mkbrainmask failed

ERROR: mkbrainmask-sess failed

Thank you for any help!

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting