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 <corinna...@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 <
> gr...@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
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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
>> > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>
>> > <mailto:fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@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
>> > > <fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@nmr.mgh.harvard.edu>
>> > <mailto:fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@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
>> > > <fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@nmr.mgh.harvard.edu>
>> > > <mailto:fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@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
>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
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