OK, can you run mri_glmfit-sim with --debug as the first option and send me the output?
On 11/11/2021 4:08 PM, Brown, Alexander wrote:
External Email - Use Caution
Hi,
Yes, see attached.
-Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, November 11, 2021 3:05 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror What are the contents of /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can you send me the ls of it?
On 11/11/2021 3:38 PM, Brown, Alexander wrote:
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Hi,
Now attached is the mri_glmfit-sim terminal output. the only output is the error message.
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, November 11, 2021 2:27 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror That is for mri_glmfit, not mri_glmfit-sim.
On 11/11/2021 3:24 PM, Brown, Alexander wrote:
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Yes, please see the attached text file.
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, November 11, 2021 2:04 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror Can you capture and send the full terminal output from mri_glmfit-sim?
On 11/10/2021 10:41 PM, Brown, Alexander wrote:
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Hi Dr. Greve,
I am using FS 6.0 on Ubuntu 18.04.
Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run mri_glmfit-sim.
Best, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Wednesday, November 10, 2021 4:40 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. Which version of FS are you using? Can you send the log file created by mri_glmfit-sim (different than the one you sent)?
On 11/10/2021 3:49 PM, Brown, Alexander wrote:
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Hello,
I am attempting to run a permutation simulation to correct for multiple comparisons and am getting the following error:
< mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg --perm-resid ERROR: cannot find residual /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save >
Attached is the mri glmfit log. I ran the command with the --eres-save flag, and the eres.mgh file is generated in the glm directory.
I have downloaded the patch and have run this style of analysis multiple times without issue until today.
I appreciate any help!
Please let me know if you need any additional information.
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
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