[RESOLVED] General_extract_glm_volumes failure

Issues
1

Description:

< I’m trying to extract the GLM effects of interest using “general_extract_glm_volumes”, but it doesn’t work.>

Call:

< Here is the command I run (through sshcpu on grace):

qxCntnr=/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.90.1.sif
qunex_container general_extract_glm_volumes \
     --flist=DP5-2ndLevel-Placebo_noBF.list \
	 --outf=DP5_GLM_EM_PL_noBF \
     --effects="encode" \
     --saveoption="by_session" \
	 --container=$qxCntnr 

here is a part of the .list file I use:

session id: ta6143
file:/gpfs/project/fas/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6143/images/functional/bold_Atlas_conc_AR_noBF_pl_DP5_EM_pl_s_res-menoBF_pl_Bcoeff.dtseries.nii
session id: ta5880
file:/gpfs/project/fas/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta5880/images/functional/bold_Atlas_conc_AR_noBF_pl_DP5_EM_pl_s_res-menoBF_pl_Bcoeff.dtseries.nii
session id: ta5927
file:/gpfs/project/fas/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta5927/images/functional/bold_Atlas_conc_AR_noBF_pl_DP5_EM_pl_s_res-menoBF_pl_Bcoeff.dtseries.nii![Screen Shot 2021-12-23 at 3.18.12 PM|690x89](upload://8sCtt9sjGs22hl0PZzGcbh5fr6H.png)
>

Logs:

< while it says check the log file in the output:
 ---> Setting up Octave  

 ---> QuNex environment set successfully! 


 ........................ Running QuNex v0.90.1 ........................ 


    ---> Resetting to defaults: 


 ==> Note: general_extract_glm_volumes is part of the QuNex MATLAB.


--- Full QuNex call for command: general_extract_glm_volumes 

gmri general_extract_glm_volumes --flist="DP5-2ndLevel-Placebo_noBF.list" --outf="DP5_GLM_EM_PL_noBF" --effects="encode" --saveoption="by_session" 

--------------------------------------------------------- 



Running:
>>> general_extract_glm_volumes('DP5-2ndLevel-Placebo_noBF.list', 'DP5_GLM_EM_PL_noBF', 'encode', [], 'by_session', '', [], '')


Matlab Error! Processing Failed!
structure has no member 'glm'


ERROR: general_extract_glm_volumes failed! Please check output / log!

>

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2

Hi! We will take a look at this and get back to you once we figure out what is going on.

3

Hi!

Thank you for your report! The general_extract_glm_volumes function looks for glm files in the file list. These have to be specified as:

session id: ta6143
    glm:/gpfs/project/fas/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6143/images/functional/bold_Atlas_conc_AR_noBF_pl_DP5_EM_pl_s_res-menoBF_pl_Bcoeff.dtseries.nii

As no glm entries were found for the listed sessions, the function referenced a non-existing field and exited with an error. The solution is to adjust the list file and replace file: specifications with glm: specification. I have prepared and tested a corrected file list file, which you can find here:

/gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/analysis/SecondLevel/

along with the results. The fact that glm files have to be specified using the glm: rather than a general file: definition was not present in the inline documentation. I have now changed the relevant part of the inline help so that the specification is clearer:

   --flist       List of files / sessions to process. For each session id 
                 in the list, there has to be a `glm:` file listed that 
                 is a result of GLM analyses (a 'Bcoeff' file).

Also, the function will now explicitly check that all sessions listed in the list file have a glm: entry. It will print out a warning and exit with a clear error if that is not the case. Example:

...
     WARNING: Session id: pb3425 has  no glm file specified!
     WARNING: Session id: pb2572 has  no glm file specified!
     WARNING: Session id: pb4039 has  no glm file specified!
ERROR: Some sessions do not have a glm file specified in the file list.
       Please, check your list file!

The listed changes will be a part of a future QuNex release.

4

The next release (0.92.0) should be out within a week or so and it will include Grega’s patch.

5

For future use of list files, the descriptors in use are listed in the specification of the file format on the QuNex wiki page.