Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output

What kind of image is that? FS will only work on T1-weighted. I'm surprised it did that good.

On 1/3/2025 2:12 PM, Pandey, Shraddha wrote:

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Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons:

1. When I overlay |lh.white| on the original volume, I notice some misregistration (see the figure below).
2. To address this, I applied the |transformationvolume.dat| file generated from |bbregister|, which I used to create the surface with |mri_vol2surface|.

However, the transformed |lh.white| surface generated using the |transformationvolume.dat| file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your  help. Shraddha

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu *Sent:* Friday, December 27, 2024 9:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output

Hi Shraddha

Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window

cheers

Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Pandey, Shraddha *Sent:* Thursday, December 26, 2024 7:25 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output

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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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