Hi Prad - That part of the corpus callosum belongs neither to the left nor to the right hemi, it connects the two. So any split would be arbitrary. You could write a script that finds if a voxel is closer to the left or the right hemi for example.

Best, a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna - (prad) [prad@email.arizona.edu] Sent: Wednesday, January 18, 2017 12:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] WM lobes and Corpus Callosum

Hello Anastasia,

Thank you for your reply!

I had created the 4 WM lobes for each hemisphere to extract regional volumes for white matter lesions in each lobe.

As some of our participants have WML in the corpus callosum very close to the midline, they are not included in the WM lobes created earlier.

Do I need to manually edit the labels for the parts of the corpus callosum between the hemispheres to have them be included in one of the lobes ?

Or is there some alternate way to split the CC in aseg.mgz along the hemispheric midline and assign its parts to the WM in each hemisphere ?

Best,

-Prad

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Tuesday, January 17, 2017 5:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] WM lobes and Corpus Callosum

Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region from the cortical parcellation. Which cortical region would you want to assign the corpus callosum to? What's labeled as corpus callosum in the aseg is the part of the corpus callosum between the 2 hemis.

Best, a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna - (prad) [prad@email.arizona.edu] Sent: Tuesday, January 17, 2017 5:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] WM lobes and Corpus Callosum

Hi,

I've been trying to create WM lobes using the following steps:

1) mri_annotation2label --lobesStrict

2) Outputting the labels from step 1, & creating a simpler annotation without limbic and insular lobes

3) 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

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:

1. mri_annotation2label --lobesStrict

2. Outputting the labels from step 1, & creating a simpler annotation

without limbic and insular lobes

3. 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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ 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.