what happens if you run
/usr/local/freesurfer/bin/stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres

On 11/12/2021 6:19 PM, Brown, Alexander wrote:

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Hi,

< cns_2@CNS-Super-Server:/usr/local/freesurfer/bin$ which stem2fname
/usr/local/freesurfer/bin/stem2fname >

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: Friday, November 12, 2021 1:09 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
wait a minute, that worked!
what do you get when you run
which stem2fname
(make sure it is not your copy, but when you try to run FS)

On 11/12/2021 1:08 PM, Brown, Alexander wrote:
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Yep!

Attached is the output from the edited stem2fname command.

-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: Friday, November 12, 2021 11:47 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
This is bizarre. Can you try this?
Make a copy of stem2fname, then edit the first line
From: #! /bin/csh -f
To: #! /bin/csh -fex
Then run your copy like
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres

On 11/12/2021 10:49 AM, Brown, Alexander wrote:
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Yes, the eres file is a .mgh file. Attached is the output from the mri_info command.

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: Friday, November 12, 2021 9:40 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
Can you try this command? It is a .mgh file, right?
mri_info /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres.mgh

On 11/12/2021 9:57 AM, Brown, Alexander wrote:
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Hi,

I am using FS 6.0.0 on Ubuntu 18.04.5

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 8:45 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
ok, that is the problem. What computer platform are you using and which version of FS do you have?

On 11/11/2021 6:42 PM, Brown, Alexander wrote:
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< stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
ERROR: could not determine file for /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres >

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 5:39 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
What do you get if you run
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
?

On 11/11/2021 6:35 PM, Brown, Alexander wrote:
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See attached.

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 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] permutation simulation errror
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:
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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 <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, November 11, 2021 2:27 PM
To: freesurfer@nmr.mgh.harvard.edu <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 <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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