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 <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu <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 <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu <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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