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

External Email - Use Caution

Hi, Thank you for your response. The images in the first figure represent the paramagnetic files (output from the Chi Separation algorithm). The lh.white surface, registered using the transformationvolume.dat file, has been overlaid on the paramagnetic volume (2nd Figure). Thanks, Shraddha

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, January 6, 2025 9:12 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output

You don't often get email from dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1DHHZZqbPVJc8QIPuaS2as282S5cxR3I9uCXilc8nYZZTeKg_UMtwFuZZBr3b9QZNw34NUkoTkQF-Eck-RK6gLvxGjS6UqNVqkXN6kZX0SwMaxUxvIzZuCEfnWyBx2AVwT0qSI3oPvw5REIybFHI_pYRQPWuC1HSDG0kWURuInx7UqczsPAQfck0uR3nkut1hag86RoO6UhTgQVxgORNPs-I0ouUlxdhGJKYW-2eUV6vrpPbwTN8N7PCMysYuhGMTcsMSqCgybEfQTYhFLbl_I0bXKoHk4l_xKguBf4x_hmU3hkvZtocnWldtqUpcAzP6PDlBNh8-JJMpkXt4_Yi3Gw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification 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: External Email - Use Caution 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

[cid:part1.gZtQI51H.497KNzaK@mgh.harvard.edu] [cid:part2.RUOjCmJR.drhbvDBq@mgh.harvard.edu] ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu Sent: Friday, December 27, 2024 9:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output

External Email - Use Caution

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

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

[cid:part3.w07RwhVX.fdRjQF08@mgh.harvard.edu]

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1g2zyXq_tSlOwLy4acAPd3j0rcdMg-fsLeRaQRxk7LYqxTv...