Re: Freesurfer Digest, Vol 257, Issue 32 - Freesurfer

9 Jul 2025

      External Email - Use Caution
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James Hartzell, PhD(2x), EMBA
Donostia-San Sebastián, Spain
...
On 9 Jul 2025, at 15:44, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:

Re: mri_convert error: Floating point exception (core dumped)
(Huang, Yujing)

Message: 1
Date: Wed, 9 Jul 2025 13:44:11 +0000
From: "Huang, Yujing" YHUANG43@mgh.harvard.edu
Subject: [Freesurfer] Re: mri_convert error: Floating point exception
   (core dumped)
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
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We will investigate the issue further.
From: Óscar Peña-Nogales opennog@gmail.com
Sent: Wednesday, July 9, 2025 3:00 AM
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Re: mri_convert error: Floating point exception (core dumped)
   External Email - Use Caution

Yes, that seems to execute the command correctly as in FS7.4.1. Is it however possible to modify something and execute it as it should be in FS8.0.0?
Thanks
On Mon, 7 Jul 2025 at 15:33, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote:
Can you try ‘-dsold’ in FS8.0.0 instead? It should behave the same as ‘-ds’ in FS7.4.1
Yujing
From: Óscar Peña-Nogales <opennog@gmail.commailto:opennog@gmail.com>
Sent: Monday, July 7, 2025 7:27 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_convert error: Floating point exception (core dumped)
   External Email - Use Caution

Dear,
I'm attempting to increase the resolution of an image but I get the following error when I run the mri_convert command:
Command:
mri_convert -rt nearest -it nii -i XX.nii.gz -ds 0.2 0.2 0.2 -ot nii -o XX_sr_temp.nii.gz
Log:
reading from XX.nii.gz...
TR=10.01, TE=4.75, TI=0.00, flip angle=50.00
i_ras = (-0.99768, -0.0561452, 0.0384932)
j_ras = (0.0571764, -0.998019, 0.026235)
k_ras = (0.036944, 0.0283751, 0.998914)
DownsampleFactor = 0.200000, 0.200000, 0.200000
Error:
Floating point exception (core dumped)
I was not able to find any similar error on the mailing list. Does anyone have any thoughts on how to trouble-shoot this one?
More info:

FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a
Platform:

Distributor ID: Ubuntu
Description: Ubuntu 22.04.5 LTS
Release: 22.04
Codename: jammy

uname -a: Linux eec78b7407cc 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linu

Note1: I also tried with FreeSurfer 7.4.1, and the command, with the same input data, works in that version. Nevertheless, I wanted to update to 8.0.0.
Note2: The same command does work on 8.0.0 when -ds >1
Thanks in advance.
Óscar

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