Hi Corinna

you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)

cheers
Bruce

On Wed, 2 Jul 2014, Corinna Bauer wrote:

Hi Bruce,

I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask
--o ${subj_dir}/mri/wmdivided --annot aparc.split

After the slice labeling, I get the following:

Used brute-force search on 872 voxels
Fixing Parahip LH WM
  Found 0 clusters
Fixing Parahip RH WM
  Found 0 clusters
Writing output aseg to
/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
unknown file type for file
(/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
subject = FSH_09062013
annotation = wmdivided
hemi = lh
outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
surface   = white

Any suggestions?

Thanks,
Corinna



On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Corinna

      not really, as that is a surface-based utility. You could divide
      the
      cortical labels and then recrate the wmparc from it, which might
      do what
      you want.

      cheers
      Bruce


      On Tue, 1 Jul 2014, Corinna
      Bauer wrote:

      > hello,
      > I was wondering if it was possible to use
      mris_divide_parcellation on white
      > matter labels.
      >
      > Thanks,
      >
      > Corinna
      >
      >
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.