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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
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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李浩