I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer <corinna...@gmail.com> 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>
> 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>
>>> 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>
>>> 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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