It works! Thanks, Doug. At 2014-11-25 01:19:13, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the >aparc annot. You can look in the recon-all.log file for the command line >(just make sure to change the output file name too so that you don't >overwrite aparc+aseg.mgz) > >doug > >On 11/24/2014 07:54 AM, wangzhiwei3233 wrote: >> Hi Freesurfer experts, >> I want creat some ROI masks or parcellation from Caret >> PALS_B12_Visuotopic.annot file in fsaverage's label folder. >> >> I used the command mri_label2vol, >> mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp >> $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject >> fsaverage --hemi lh --identity >> The parcellation in output volume were like some lines located at the >> boundry of white matter , and did not cover the gray matter (see picture). >> >> Then, I used another methods as follows. >> Firstly, I converted the annotation file into some label files using >> mri_annotation2label command; >> Secondly, I created ROIs using these labels by mri_vol2roi. >> However, the masks also couldn't cover the gray matter. >> >> Could anyone help me creat good masks? >> Thanks a lot! >> >> Zhiwei >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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 > > >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. >
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