Right, this is going to be a problem. One of the things you can do is to use the --ctab option of mri_annotation2label to create a colortable, something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh --annotation newannot --outdir junk You can do this for both hemis, then concatenate them together along with the ROIs from the subcortical. Then take the two new.?h.ctabs and add 3000 to the indices and change the name to be wm- instead of ctx- and include those in the new ctab clunky, but it should work doug On 07/07/2014 12:29 PM, Corinna Bauer wrote: > 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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@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 > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > wrote: > > Hi Corinna > > > > you need to give some output extension so it knows > what file > > 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 > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@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> > > <mailto: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> > > <mailto: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> > <mailto: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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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 gr...@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
