the new white matter divided labels. I was not able to extract the labels using the matching grey matter names, but was able to do so using the label number seen in the tools from tkmedit. Seeing as there are over 100 labels, is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer 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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna you need to give some output extension so it knows whatfile
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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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