Dear. Freesurfer experts.

Hi. How are you?

I have a question about making ROI.

This might be a naive question, but any input would be greatly appreciated.

I preprocessed scans per run, thus I have register.dof6.dat file inside all run epi directories.

Then, I made ROIs per single subject based on the single subject's functional contrast map using the command:

tksurfer replay06 lh inflated -curv -gray

I overlayed the single subject's contrast result sig.nii.gz (obtained from 3 runs) and the registration file in 1 run(register.dof6.dat in 1 among 3 runs), then I cut the plane and then flattenr the cortex, made ROI.

While trying to check the ROIs, I realized that this ROI seems to be slightly different depending on which register.dof6.dat I use (I tried all 3 runs' register.dof6.dat when overlaying). tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01

I thought ideally, this functional ROI should be the same across all runs if thes register files are perfectly registering each functional sans to anatomical scan.

Is this a usual way when people make ROI based on functional contrast map per each subject?

The way I did in the past did not have this kind of problem because I did motion correction as targetting the first EPI (aligning all images to the first EPI) and then used only 1 (same) register.dat file..

Please share your idea with me.

Thank you very much.

Best, Ji Won