Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log file for an example command line that generates wmparc.mgz
doug On 04/10/2014 09:52 AM, Corinna Bauer wrote: > For creating corresponding wm segmentations to the rois derived from > mris_divide_parcellation, should mri_aparc2wmseg be used or should I > follow the steps outlined in this posting > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html > > ? > > Thanks > > Corinna > > > On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinna...@gmail.com > <mailto:corinna...@gmail.com>> wrote: > > Perfect. Thanks! > > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > you'll need to figure it out from the volume itself by loading > the seg > with both -seg and -aux. When you find the label you want, > click on it > and the aux value in the control window will tell you what the > id is > > doug > > On 04/09/2014 09:41 AM, Corinna Bauer wrote: > > In the mri_extract_label, there is a label number. Where > would I find > > this for the new labels? > > > > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035 > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii > > > > > > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > yep, exactly > > > > > > On 4/8/14 6:00 PM, Corinna Bauer wrote: > >> Hi Doug, > >> After I have the labels then in each subject's T1 > space, I will > >> need to then put them into diffusion and resting state > space. > >> > >> I already have scripts that put the parcellations into > >> subject-specific diffusion/resting state space (using > bbregister, > >> tkregister2, mri_vol2vol (using the inverse > registration from > >> bbregister to put the T1 into diffusion space), > mri_extract_label > >> (extract labels from aparc+aseg.mgz), and then > mri_label2vol > >> (register each of the extracted labels into diffusion > space). > >> Would a similar approach work for the new labels? > >> > >> Corinna > >> > >> > >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > >> > >> > >> Exactly what you have described won't work very > well because > >> it would be > >> in the volume. I would divide up the parcellations in > >> fsaverage space > >> like you've done, then map the parcellation to each > subject using > >> mri_surf2surf (--sval-annot, see example 6) > >> > >> doug > >> > >> On 04/08/2014 04:54 PM, Corinna Bauer wrote: > >> > Hello all, > >> > > >> > I am planning to use mris_divide_parcellation to > split the > >> Desikan > >> > atlas into smaller ROIs, but will need the new > ROIs to be > >> consistent > >> > between subjects. > >> > > >> > Can I achieve this if I register each subject to > fsaverage > >> space and > >> > then apply the inverse transform to the divided > >> parcellations (which > >> > are currently done on the fsaverage brain)? > >> > > >> > If so, for extracting each label, what would be > used for > >> the label > >> > number? > >> > (i.e. mri_extract_label > ${subj_dir}/mri/aparc+aseg.mgz *2035* > >> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii) > >> > > >> > > >> > 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 > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > >> Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > >> > >> Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > >> > <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> > >> <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 > > > > > > _______________________________________________ > > 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
