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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@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:
External Email - Use Caution
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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