what happens if you load it into freeview instead of tksurfer? How did you create lh.surf_combined-magn_CL_fwhm1.mgh ? Does it look ok on the surface? Are the values integers?
On 2/20/19 12:56 PM, Barletta, Valeria wrote: > Thank you Doug, > As you suggested, I tried to use that command > (mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s > MS072_R01_04 --hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot) > but I got this error on tksurfer: > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % reading colortable from annotation file... > colortable with 7 entries read (originally MS072_R01_04.txt) > Found embedded color table in annotation. > 131940 vertices did not have an annotation! > surfer: WARNING: no labels imported; annotation was empty > I attach my color table file... > Thanks for your help, > Vale > _______________________________________________________________________________________________________ > *>Greve, Douglas N.,Ph.D.*DGREVE at mgh.harvard.edu > <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20clusters%20annotation%20file%20in%20surface&In-Reply-To=%3C2b8a798d-7cff-1db2-4508-51e52751f3eb%40mgh.harvard.edu%3E> > />Tue Feb 19 16:33:32 EST 2019/ > >You can create an annotation with mris_seg2annot (you basically have a > >surface-based segmentation). Run it with --help to get more info > >including examples. You will need to create your own color table > > On 2/19/19 3:21 PM, Barletta, Valeria wrote: > >//>/Dear Freesurfers, />//>/I have a 3D volume mask of cortical lesions with > >8 different clusters />/(8 cortical lesions). />//>/I projected this mask to > >the cortex and obtained a .mgh file with the />/command vol2surf: > >/>//>/mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out > >/>/$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" > >/>/--projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj />//>//>/Now I > >need to extract label files from this surface file, one />/label for each > >cluster, and then an annotation file summarizing all />/the label files. > >/>//>/How can I do this? />//>/Thanks, />//>/Vale/ > > > > ------------------------------------------------------------------------ > *From:* Barletta, Valeria > *Sent:* Tuesday, February 19, 2019 3:21 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* clusters annotation file in surface > > Dear Freesurfers, > > I have a 3D volume mask of cortical lesions with 8 different clusters > (8 cortical lesions). > > I projected this mask to the cortex and obtained a .mgh file with the > command vol2surf: > > mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out > $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" > --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj > > > Now I need to extract label files from this surface file, one > label for each cluster, and then an annotation file summarizing all > the label files. > > How can I do this? > > Thanks, > > Vale > > > > > > _______________________________________________ > 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
