Re: [Freesurfer] WM lobes and Corpus Callosum

2017-01-19 Thread Bharadwaj, Pradyumna - (prad)
: [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

Re: [Freesurfer] WM lobes and Corpus Callosum

2017-01-18 Thread Douglas N Greve
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/mr

Re: [Freesurfer] WM lobes and Corpus Callosum

2017-01-18 Thread Yendiki, Anastasia
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna - (prad) [p...@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

Re: [Freesurfer] WM lobes and Corpus Callosum

2017-01-18 Thread Bharadwaj, Pradyumna - (prad)
hemisphere ? Best, -Prad From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia 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

Re: [Freesurfer] WM lobes and Corpus Callosum

2017-01-17 Thread Yendiki, Anastasia
, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna - (prad) [p...@email.arizona.edu] Sent: Tuesday, January 17, 2017 5:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] WM lobe

[Freesurfer] WM lobes and Corpus Callosum

2017-01-17 Thread Bharadwaj, Pradyumna - (prad)
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 Step2Anno