You should load
$chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz into
freeview with the surfaces, eg
cd subject/mri
freeview nu.mgz
$chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz -f
../surfs/?h.white ../surfs/?h.pial
and see if the lesion maps between the white and pial surfaces
For vol2surf, use --projfrac-max
Also, make sure that the freeview threshold is not so high that it will
exclude your segmentation
On 12/7/2023 5:22 AM, 李浩 wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I am currently engaged in a project where I need to measure the
cortical thickness of a segmented cortical lesion (ROI) in the volume
space.
After running recon-all for my subjects, i employed 'mri_vol2surf'
function to project my ROI from the native T1 space to indiviaul
surface space. My command was as follows:
mri_vol2surf —mov
$chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz --hemi rh
--surf white --projfrac-avg -0.1 1 0.05 --interp nearest --o
"$sub"_chronic-CMI_4-1_rh.mgh --regheader "$sub" --trgsubject “$sub”
However, I encountered an issue where I could not locate the ROI in
the individual surface space, as the values in
"$sub"_chronic-CMI_4-1_rh.mgh were all zero.
I suspect this might be due to a registration error or possibly the
small size of my ROI (only 4 voxels). Do you have any suggestions on
how to address this issue?
Additionally, I am wondering whether it's possible to register the
cortical thickness map from the surface space back to the individual
volume space, then calculate the mean cortical thickness of my ROI
there. Alternatively, is it feasible to convert the coordinates of my
ROI's center point to the MNI152 coordinate and then surface-based
coordinates and directly create an ROI in the surface space?
Any feedback on these questions would be greatly appreciated. Thanks
in advance.
Bests,
Hao Li
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