Glad to hear it 😊 Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yujia Huang Sent: Monday, October 21, 2024 10:09 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] lost volume geometry information using read_surf.m and write_surf.m

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Works like a charm. Thank you, Bruce!

Best,

Yujia

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> Date: Friday, October 18, 2024 at 14:19 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] lost volume geometry information using read_surf.m and write_surf.m

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Hi Yujia

Have you tried using mris_expand instead? That is what I wrote it for.

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 Yujia Huang Sent: Friday, October 18, 2024 12:11 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] lost volume geometry information using read_surf.m and write_surf.m

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Hi Freesurfers,

I'm attempting to create equal-distant surface layers between the ?h.pial and ?h.white surface segmentation using the MATLAB functions read_surf and write_surf. I used read_surf to get the vertex coordinates and face information out of the ?h.pial and ?h.white and saved the modified vertex coordinates for the new surface into "?h.new_surface.pial" using write_surf. After loading the new surface files into freeview the command line shows the following warning message:

Did not find any volume info

The surface however was showing correctly on freeview. Furthermore, when I'm attempting to calculate the surface orientation angles of the newly generated surface using mris_convert --angle, I got the following error indicating the same thing about missing volume info:

************************************* CAUTION **************************************

If you are running "mris_convert --angle" on an original surface (i.e. has not

been transformed by mris_surf2surf), then you can ignore this message.

However, if you need to calculate orientation angles of a TRANSFOMRED surface you

will need to convert the .lta/.dat registration file first and force the original

volume as the source. Otherwise important header information will be lost and the

angles will be incorrect (do not be fooled, they might appear close, but they won't

be exact). A detailed description and example can be found on the freesurfer wiki.

************************************************************************************

error: volume size must be greater than 0 in every dimension

I see similar problems have been reported previously but I was not able to locate the solution of such matter. Does anyone know what is the cause of this and how to trouble shoot? Thanks in advance!

1. Freesurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0 2. Platform: Ubuntu 20.04.6 LTS 3. uname -a: Linux hawaii 5.15.0-91-generic #101~20.04.1-Ubuntu SMP Thu Nov 16 14:22:28 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4. MATLAB: 2019b

Best,

Yujia Huang

Research Assistant I

Advanced Imaging Research Center

UT Southwestern Medical Center

2201 Inwood Rd.

Dallas, TX, USA, 75390

Office: 214.645.5241

Pronouns: He, Him, His

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