[RESOLVED] General_extract_glm_volumes

Issues
1

Hi, I have been trying to use general_extract_glm_volumes to extract betas. I have a very large number of regressors that I used to calculate the glm. I sense that the command is unable extract the regressors that are later in this list of regressors. I am able to extract the regressors that are early on in this list, but not those that are past around 30 or so on the list, and get an error. I am not sure if this is the problem or if there is another issue. Any help would be appreciated. Thank you!

The command is:

qunex general_extract_glm_volumes \
  --flist=/gpfs/gibbs/pi/n3/Studies/WM.Reward/GLM.Analyses/Results_PALM_BOLD_Behav/AR_PALM_BOLD_Calibrate_Prefrustration_Frustration_2x2/RERUN_PrefrustFrust/WMR_N31_AR_Calibrate_correct_Behavior_smooth2.list \
  --outf=RERUN_2x2_PreFrustFrust_N31 \
  --effects="pre-frust-E, pre-frust-D, frustration-E, frustration-D" \
  --saveoption="by_session" \
  --verbose=true

The error is:
… Running QuNex v0.99.2 …

— Full QuNex call for command: general_extract_glm_volumes

gmri general_extract_glm_volumes --flist=“/gpfs/gibbs/pi/n3/Studies/WM.Reward/GLM.Analyses/Results_PALM_BOLD_Behav/AR_PALM_BOLD_Calibrate_Prefrustration_Frustration_2x2/RERUN_PrefrustFrust/WMR_N31_AR_Calibrate_correct_Behavior_smooth2.list” --outf=“RERUN_2x2_PreFrustFrust_N31” --effects=“pre-frust-E, pre-frust-D, frustration-E, frustration-D” --saveoption=“by_session” --verbose=“true”

Running:

general_extract_glm_volumes(‘/gpfs/gibbs/pi/n3/Studies/WM.Reward/GLM.Analyses/Results_PALM_BOLD_Behav/AR_PALM_BOLD_Calibrate_Prefrustration_Frustration_2x2/RERUN_PrefrustFrust/WMR_N31_AR_Calibrate_correct_Behavior_smooth2.list’, ‘RERUN_2x2_PreFrustFrust_N31’, ‘pre-frust-E, pre-frust-D, frustration-E, frustration-D’, , ‘by_session’, ‘’, true, ‘’)

                                                                < M A T L A B (R) >
                                                      Copyright 1984-2023 The MathWorks, Inc.
                                                 R2023a Update 2 (9.14.0.2254940) 64-bit (glnxa64)
                                                                   April 17, 2023

Warning: X does not support locale en_US.UTF-8

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For product information, visit www.mathworks.com.

—> checking file list
—> processing session: pb0929
Matlab Error! Processing Failed!
The logical indices contain a true value outside of the array bounds.

ERROR: general_extract_glm_volumes failed! Please check output / log!

2

Youngsun, hi!

It would be easiest if you can share either here or privately:

– example fidl file used
– exact command used to compute the GLM
– example resulting GLM file

I can then inspect these and identify exact reason for the error. Additionally, there are in the <session id>/images/functional/glm folder .png and .txt files with the matrix used in the GLM computation – these might be helpful as well.

All the best,

Grega

3

Hi Grega–thanks so much for looking into this! I sent you the files you requested via email. Please let me know if you need anything else.
-youngsun

4

Hi,

I see you are running outside of the container. Running outside of container on our HPC (Grace) is no longer supported as there are issues with the environment. Can you try this:

qunex_container general_extract_glm_volumes \
  --flist=/gpfs/gibbs/pi/n3/Studies/WM.Reward/GLM.Analyses/Results_PALM_BOLD_Behav/AR_PALM_BOLD_Calibrate_Prefrustration_Frustration_2x2/RERUN_PrefrustFrust/WMR_N31_AR_Calibrate_correct_Behavior_smooth2.list \
  --outf=RERUN_2x2_PreFrustFrust_N31 \
  --effects="pre-frust-E, pre-frust-D, frustration-E, frustration-D" \
  --saveoption="by_session" \
  --verbose=true \
  --container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.99.2d.sif" \
  --scheduler="SLURM,time=8:00:00,cpus-per-task=2,mem-per-cpu=16G,partition=day"

Best, Jure

5

Hi,

Any updates here? Was this issue resolved?

Best, Jure