Re: [Freesurfer] -notalairach problem

Laouchedi,

you will need to edit your recon-all script to correct a bug. find this line:

if ($DoNuMakeUchar) set cmd = ($cmd --uchar transforms/talairach.xfm)

and replace it with this:

if ($DoNuMakeUchar) then if ( ! -e transforms/talairach.xfm) then echo "WARNING: transforms/talairach.xfm does not exist!" |& tee -a $LF echo "It will not be used by mri_nu_correct.mni." |& tee -a $LF else set cmd = ($cmd --uchar transforms/talairach.xfm) endif endif

N.

On Thu, 2012-01-19 at 15:42 +0000, LAOUCHEDI MAKHLOUF wrote:

hi

i have run freesurfer using -notalairach flag and i had the following message :

  mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar

transforms/talairach.xfm --n 2

   ERROR: cannot find transforms/talairach.xfm

can anyone know why is it searching the transforms/talairach.xfm when we run without talairach,

thanks

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