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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

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