I'm not sure what is happening here. First, what is input_volume? Based on your commands, it should be the same as input_mri Second, what thresholds are you using on the overlay? It could be that you just need to reduce the threshold and those gray bits will turn red. Note that this does not necessarily mean it is right (see first concern)
On 12/26/2024 7:25 PM, Pandey, Shraddha wrote:
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Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the |mri_vol2surf| tool. The process I am following is as follows:
I first create the registration file using |bbregister| with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
Here, the goal is to generate the |.dat| registration file.
Next, I use this |.dat| file in |mri_vol2surf| to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the |bbregister| command is flash data, and the input volume for |mri_vol2surf| is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by |mri_vol2surf| contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards,
Shraddha
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