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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:

1. 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
   

2. Here, the goal is to generate the .dat registration file.

3. 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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