On 07/12/2017 05:11 PM, Lu Zhao wrote:
Dear Douglas,
Thank you for your kind reply and instruction. But I still have a few questions:
- how can I get the segmentation for BA areas, which have no
hemisphere bases?
Not so easy because you need to have complete cortical coverage. If you are not doing partial volume correction (or correcting for the volume fraction effect), then you can use mri_label2vol to create and ROI of the BA in the PET space, then use mri_segstats to extract the mean from the ROI (ie, bypass gtmseg and mri_gtmpvc).
- 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’?
No, the --wm-annot is for segmenting white matter.
- is there any function, like aparcstats2table/asegstats2table, can
be used to generate the table from the gm.stats.dat file?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table
- 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.
They are not identical but they do segment the same structures. They use different atlases derived from different manual labellings.
Best,
Lu */ /* */ /*
On Jul 12, 2017, at 9:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There are several layers of difficulty here:
- 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.
- 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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