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: 1) FreeSurfer version:* freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a* 2) Platform: Distributor ID: Ubuntu Description: *Ubuntu 22.04.5 LTS* Release: 22.04 Codename: jammy
3) 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
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.com Sent: Monday, July 7, 2025 7:27 AM To: 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: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a 2) Platform: Distributor ID: Ubuntu Description: Ubuntu 22.04.5 LTS Release: 22.04 Codename: jammy
3) 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
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.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.com *Sent:* Monday, July 7, 2025 7:27 AM *To:* 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* 2) 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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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: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a 2) Platform: Distributor ID: Ubuntu Description: Ubuntu 22.04.5 LTS Release: 22.04 Codename: jammy
3) 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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freesurfer@nmr.mgh.harvard.edu
-
Huang, Yujing -
Óscar Peña-Nogales