This is a little tricky to do, but I can probably step you thru the process. The first thing you have to do is to transfer your ROI from fsaverage space to the individual using mri_label2label with the --regmethod surface option (view it on the surface to make sure it is ok).

The next thing to do is to create a new annotation with your label in it. To do this, first break the ?h.aparc.annot file into individual labels using mri_annoation2label with the --outdir option. This will create a label file for each parcellation in the aparc. Copy your label into the output folder (make sure the name is unique). Next, create a new annotation that includes your label using mris_label2annot. You will need a color table for this. Start with the ctab in subject/label/aparc.annot.ctab. You will see the names for all the labels. Add your label as the last one, giving it a new num (eg, 36) name and RGB (RGB = red, green, blue 0-255; actual values don't matter, just don't replicate; it will show up as this color in the annotation). Then run something like

mris_label2annot --hemi lh --subject yoursubject --ctab your.ctab --ldir labeldirectory --no-unknown --a myaparc

This will create yoursubject/label/lh.myaparc.annot. View this to make sure it looks ok.

Let me know when you get to this point, and I'll step you through the rest

On 02/08/2017 03:34 AM, Donatas Sederevicius wrote:

​Hello FreeSurfer Developers,

I have done partial volume correction of PET data as described in PETSurfer stream. Now, I want to extract a mean intensity value of my ROI for each subject. This ROI is defined in the fsaverage space and saved as a label. What would be the best way to do it? Should I start from mri_label2label command to map the label to the individual anatomical space or there is another, maybe easier way to do it?

Thanks in advance.

-Donatas

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