Hi Anastasia, I intend to use mri_label2vol to map the label file into the diffusion space. Can you say me what for a diffusion file I can use for that and where I can find it?
Thanks again for your help Andre ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 26. Februar 2015 19:05 An: Freesurfer support list Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography Hi Andre - I'd go through the multimodal integration tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview a.y On Thu, 26 Feb 2015, André Schmidt wrote: > Hi Anastasia, > > Thank you very much for your help. I have created such a label nii file, for > example for ID 9, the left thalamus. > > Can you please help me how I can map that file into diffusion space using > bbregister? I would like to use it then for probtrackx. > > Many thanks again. > Andre > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Anastasia > Yendiki [ayend...@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 26. Februar 2015 16:09 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography > > Hi Andre - You find the ID number of each of the regions you're interested > in, from $FREESURFER_HOME/FreeSurferColorLUT.txt. Then you run: > mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o yourlabel.nii.gz > > Then you'll have to map that label into DWI space. We recommend bbregister > for the cross-modal registration. > > a.y > > On Thu, 26 Feb 2015, André Schmidt wrote: > >> Dear freesurfer experts, >> I intend to use the aparc.a2009s.annot file as seed regions for a >> tractography analysis. I like to compute streamlines between every region >> in the annot file. Can you please guide me how I can create masks for every >> region in the annot file (or a text file with all seeds >> including their paths)? >> >> Many thanks for your help. >> Andre >> >> > _______________________________________________ > Freesurfer mailing list > 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 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.
