Why do you need to create a new atlas? Why not just compute the stats from wmparc.lobes.mgz ?

On 10/6/2022 5:23 PM, James Brown wrote:

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Dear colleagues Freesurfer experts,

I would like to create an atlas (my atlas) for the white matter like "wmparc.mgz" so I can generate statistics.

I would like this atlas to belimited to the following structures (frontal lobe, parietal lobe, occipital lobe and temporal lobe). I reviewed Freesurfer tutorials  and Q&A in Freesurfer forum then ran the following commands:

mri_annotation2label --subject subject --hemi lh --lobesStrict lobes

mri_annotation2label --subject subject --hemi rh --lobesStrict lobes

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz --annot lobes --base-offset 200

Then,

mris_ca-train -t ./color.tab lh ../surf/lh.sphere.reg ../label/lh.lobes.annot SUBJECT_TEST lh.my_atlas.gcs

mris_ca-train -t ./color.tab rh ../surf/rh.sphere.reg ../label/rh.lobes.annot SUBJECT_TEST rh.my_atlas.gcs

I would like to use mri_segstats with “my atlas” to generate statistics in lobes not in parcellates.  How can I convert lh.my_atlas.gcs and rh.my_atlas.gcs to myatlas.mgz ?

Thanks for your help

James

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