Doug, that worked very well, thanks.

mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot aparc.split
mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh --annotation aparc.split --outdir ${subj_dir}/smaller_labels
mri_extract_label ${subj_dir}/mri/wmdivided.nii 3001 ${subj_dir}/smaller_labels/wm-lh-bankssts.nii 

On Mon, Jul 7, 2014 at 1:05 PM, Corinna Bauer <corinnab83@gmail.com> wrote:
great, thanks! I'll give that a try and let you know how it goes.


On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Right, this is going to be a problem. One of the things you can do is to
use the --ctab option of mri_annotation2label to create a colortable,
something like

  mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
--annotation newannot --outdir junk

  You can do this for both hemis, then concatenate them together along
with the ROIs from the subcortical. Then take the two new.?h.ctabs and
add 3000
to the indices and change the name to be wm- instead of ctx- and include
those in the new ctab

clunky, but it should work

doug


On 07/07/2014 12:29 PM, Corinna Bauer wrote:
> the new white matter divided labels. I was not able to extract the
> labels using the matching grey matter names, but was able to do so
> using the label number seen in the tools from tkmedit. Seeing as there
> are over 100 labels, is there a more efficient way?
>
>
> On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     The name of which label?
>
>     On 07/02/2014 02:00 PM, Corinna Bauer wrote:
>     > Whereby the label name is derived from which, the GM labels? i.e.
>     > lh.rostralmiddlefrontal_div3
>     >
>     >
>     > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
>     > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>
>     <mailto:fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >     yes, or mri_binarize --match
>     >
>     >
>     >     cheers
>     >     Bruce
>     >
>     >
>     >     On Wed, 2 Jul 2014, Corinna Bauer wrote:
>     >
>     >         And then for breaking the individual labels up, would
>     >         mri_extract_label be
>     >         the best option?
>     >
>     >
>     >         On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
>     >         <fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>
>     <mailto:fischl@nmr.mgh.harvard.edu
>     <mailto:fischl@nmr.mgh.harvard.edu>>>
>     >         wrote:
>     >               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
>     <mailto:fischl@nmr.mgh.harvard.edu>
>     >         <mailto:fischl@nmr.mgh.harvard.edu
>     <mailto: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
>     >                           >
>     >                           >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
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