There are several layers of difficulty here:
1. If you just wanted to use a different cortical segmentation, say, aparc.a2009s or aparc.DKTatlas, then you can run gtmseg with --ctx-annot aparc.a2009s 11100 12100 or --ctx-annot aparc.DKTatlas 1000 2000. The numbers are the base numbers in $FREESURFER_HOME/FreeSurferColorLUT.txt that correspond to these atlases (the DKT atlas is the same as the aparc). Probably you'll want to change the output name with, eg, --o gtmseg.a2009s.
2. If you do not have a whole cortex segmentation, then you will need to create one along with a color table like that in FreeSurferColorLUT.txt
On 07/04/2017 06:41 PM, Lu Zhao wrote:
Dear freesurfer support,
I am using the PetSurfer to process our PET data. But by default, it would only generate stats for the segmentation with the aparc atlas. However, I want to obtain the stats for different freesurfer atlases, like in the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, ?h.aparc.DKTatlas.stats, etc.) How should I set the ‘gtmseg' to make it produce segmentations for the GTM with different freesurfer atlases? I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation can be set using --ctx-annot --wm-annot. However, I still don’t know how exactly these should be set. I will be very grateful if you could give me some suggestions and detailed guidance to help me obtain the PetSurfer stats for different freesurfer segmentations.
Best regards,
Lu
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