Hello Doug, Anastasia,
Thank you so much for your helpful solutions!
Best, -Prad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 1:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM lobes and Corpus Callosum
You can use mri_binarize to replace the CC values with WM values, eg
mri_binarize --i aseg.mgz --replace 251 2 --replace 252 2 ... --o aseg.nocc.mgz
If your version of mri_binarize does suppor the --replace option, you can get this versoin
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
On 01/17/2017 05:37 PM, Bharadwaj, Pradyumna - (prad) wrote:
Hi,
I've been trying to create WM lobes using the following steps:
mri_annotation2label --lobesStrict
Outputting the labels from step 1, & creating a simpler annotation
without limbic and insular lobes
- Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub
--annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown
However, as the corpus callosum is not labelled as wm, it is not included in any WM lobe.
Is there any workaround to assigning the corpus callosum to the different WM lobes or do I have to manually edit aseg.mgz to change the corpus callosum's value to match that of WM ?
Thanks,
-Prad
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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