Dear Douglas,

Thank you for your kind reply and instruction. But I still have a few questions:

1. how can I get the segmentation for BA areas, which have no hemisphere bases?
2. when the cortical atlas is changed, should the '--wm-annot’ be changed accordingly? For instance, use '—wm-annot aparc.a2009s 13100 14100' when use '--ctx-annot  aparc.a2009s 11100 12100’?
3. is there any function, like aparcstats2table/asegstats2table, can be used to generate the table from the gm.stats.dat file?
4. the DKT atlas is the same as the aparc? Please correct me if I was wrong. I think the aparc segmentation is from the Desikan-Killiany Atlas, while the DKT atlas is a different one which is used to produce the aparc.DKTatlas40.annot.

Best,

Lu


On Jul 12, 2017, at 9:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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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