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/

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*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

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