If you don't have FSL installed, then yes it will need to be.

doug

dahlia@nmr.mgh.harvard.edu wrote:

Perhaps I should have asked: Do I need to separately install FSL? Thanks

...

Hi,

I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out?

Thanks! Dahlia.

I ran: preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5

The error message was: ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed

mkbrainmask-sess.log says: mkbrainmask-sess $Id: mkbrainmask-sess,v 1.12.2.1 2008/10/02 21:56:15 greve Exp $ Linux mbc.stanford.edu 2.6.22.9-61.fc6 #1 SMP Thu Sep 27 18:07:59 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Tue Jun 30 11:01:46 PDT 2009 /home/dahlia.sharon/functionals/fba_study_mtloc -maskstem brain -fsd bold -s mtloc_19may07 -d /home/dahlia.sharon/functionals/subj31 -update

This is the command preproc-sess invoked: mkbrainmask -i 025/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0

The data is not on the network so I can't give paths.

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