No. I'd write a script to do it
On 02/12/2018 12:17 PM, Michiko H. wrote:
> Hi Doug,
>
> Thanks - this is extremely helpful!
>
> With regard to the first command: mri_binarize --replace 1001 3001 --i
> aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz
> Since I'd like to
Hi Doug,
Thanks - this is extremely helpful!
With regard to the first command: mri_binarize --replace 1001 3001 --i
aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz
Since I'd like to replace every cortical label with its corresponding WM
label on both hemispheres, is there a
On 2/6/18 5:26 PM, Michiko H. wrote:
Hi Doug,
That's very helpful, thank you! I have 2 follow-up questions though:
1. Is it possible to merge the cortical label (e.g. label 1001
ctx-lh-bankssts) with its corresponding label that extends into the WM
(e.g. label 3001 wm-lh-bankssts)? I'm not
Hi Doug,
That's very helpful, thank you! I have 2 follow-up questions though:
1. Is it possible to merge the cortical label (e.g. label 1001
ctx-lh-bankssts) with its corresponding label that extends into the WM
(e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may
not give
You mean you want to remove everything but the WM labels? You can do it
in two steps:
1. Create a mask of the wm labels:
mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o
wm.mask.nii.gz
2. Mask the wmparc:
mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz
Hi Freesurfer experts,
I am wondering if it is possible to remove the original labels after
extending the parcellation by 2mm into the WM for tractography? I don't
wish to have tractography run on both sets of labels considering the
algorithm would take into account the streamlines terminating at
