[RESOLVED] Fc_compute_seedmaps: Matlab Error! Processing Failed! mark_as_constructed: invalid object

Issues
1

Description:

I tried to execute fc_compute_seedmaps with only one seed (ROI), but I got “Matlab Error! Processing Failed!”.
Because I cannot find the log associated with this error, would you please advise me how I can fix this error? Thanks!!

Call:

python3 qunex_container fc_compute_seedmaps \
    --flist="/media/aikenchung/Disk4/qunex/qunex_ext4/processing/lists/sessions24_trimed.list" \
    --sessionsfolder="/media/aikenchung/Disk4/qunex/qunex_ext4/sessions" \
    --logfolder="/media/aikenchung/Disk4/qunex/qunex_ext4/processing/logs/fc_compute_seedmaps" \
    --roiinfo="/media/aikenchung/Disk4/qunex/qunex_ext4/ROI_parcels/roi5_info1.names" \
    --frames=0 \
    --targetf="/media/aikenchung/Disk4/qunex/qunex_ext4/analysis/seed_maps" \
    --options="roimethod:mean|saveind:all_by_roi|savesessionid:true|verbose:true|debug:true" \
    --dockeropt="-v /media/aikenchung/Disk4/qunex:/media/aikenchung/Disk4/qunex" \
    --container="${QUNEX_CONTAINER}"

Logs:
The only output/log is qunex_container log:

========================================================================
Generated by QuNex
------------------------------------------------------------------------
Version: 0.100.0 [QX IO]
User: root
System: 957a0e231205
OS: Debian Linux #202405300957~1738770968~22.04~d5f7c84 SMP PREEMPT_DYNAMIC Wed F
------------------------------------------------------------------------

        ██████\                  ║      ██\   ██\                       
       ██  __██\                 ║      ███\  ██ |                      
       ██ /  ██ |██\   ██\       ║      ████\ ██ | ██████\ ██\   ██\    
       ██ |  ██ |██ |  ██ |      ║      ██ ██\██ |██  __██\\██\ ██  |
       ██ |  ██ |██ |  ██ |      ║      ██ \████ |████████ |\████  /    
       ██ ██\██ |██ |  ██ |      ║      ██ |\███ |██   ____|██  ██\     
       \██████ / \██████  |      ║      ██ | \██ |\███████\██  /\██\    
        \___███\  \______/       ║      \__|  \__| \_______\__/  \__|   
            \___|                ║                                      


                       DEVELOPED & MAINTAINED BY:

                    Anticevic Lab, Yale University
               Mind & Brain Lab, University of Ljubljana
                     Murray Lab, Dartmouth College

                      COPYRIGHT & LICENSE NOTICE:

Use of this software is subject to the terms and conditions defined in
QuNex LICENSES which can be found in the LICENSES folder of the QuNex
repository or at https://qunex.yale.edu/qunex-registration
========================================================================

---> Setting up Octave 


 ........................ Running QuNex v0.100.0 [QX IO] ........................


--- Full QuNex call for command: fc_compute_seedmaps

qunex fc_compute_seedmaps --flist="/media/aikenchung/Disk4/qunex/qunex_ext4/processing/lists/sessions24_trimed.list" --sessionsfolder="/media/aikenchung/Disk4/qunex/qunex_ext4/sessions" --logfolder="/media/aikenchung/Disk4/qunex/qunex_ext4/processing/logs/fc_compute_seedmaps" --roiinfo="/media/aikenchung/Disk4/qunex/qunex_ext4/ROI_parcels/roi5_info1.names" --frames="0" --targetf="/media/aikenchung/Disk4/qunex/qunex_ext4/analysis/seed_maps" --options="roimethod:mean|saveind:all_by_roi|savesessionid:true|verbose:true|debug:true"

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

Running:
>>> fc_compute_seedmaps('/media/aikenchung/Disk4/qunex/qunex_ext4/processing/lists/sessions24_trimed.list', '/media/aikenchung/Disk4/qunex/qunex_ext4/ROI_parcels/roi5_info1.names', '0', '/media/aikenchung/Disk4/qunex/qunex_ext4/analysis/seed_maps', 'roimethod:mean|saveind:all_by_roi|savesessionid:true|verbose:true|debug:true')


fc_compute_seedmaps options used:
--------------------------------
      sessions: all
     roimethod: mean
     eventdata: all
        ignore: use,fidl
     badevents: use
     fcmeasure: r
     savegroup: all
       saveind: all_by_roi
 savesessionid: true
      itargetf: sfolder
       verbose: true
         debug: true


Checking ...
... found results folder (/media/aikenchung/Disk4/qunex/qunex_ext4/analysis/seed_maps)
 ... listing files to process
 ... reading file list: 
     - session id: 1001_01_MR
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/1001_01_MR/images/functional/bold2_clean.nii.gz)
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/1001_01_MR/images/functional/bold4_clean.nii.gz)

     - session id: 1002_01_MR
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/1002_01_MR/images/functional/bold2_clean.nii.gz)
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/1002_01_MR/images/functional/bold4_clean.nii.gz)
       ...
       ...
       ...
     - session id: 4091_01_MR
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/4091_01_MR/images/functional/bold2_clean.nii.gz)
       ... found image file (/media/aikenchung/Disk4/qunex/qunex_ext4/sessions/4091_01_MR/images/functional/bold4_clean.nii.gz)

 ... done ... done.

---------------------------------
Processing session 1001_01_MR     ... creating ROI mask ... read 1 ROI
     ... reading image file(s)
Matlab Error! Processing Failed!
mark_as_constructed: invalid object


ERROR: fc_compute_seedmaps failed! Please check output / log!
2

Hi!

First, can you please check your sessions24_trimed.list file? The output of checking seems off with lines containing only ....

Second, there is no log saved in this case. You can get a more detailed error report, if you run the command directly in octave/matlab. The exact command to run is printed out in the printout:

Running:
>>> fc_compute_seedmaps('/media/aikenchung/Disk4/qunex/qunex_ext4/processing/lists/sessions24_trimed.list', '/media/aikenchung/Disk4/qunex/qunex_ext4/ROI_parcels/roi5_info1.names', '0', '/media/aikenchung/Disk4/qunex/qunex_ext4/analysis/seed_maps', 'roimethod:mean|saveind:all_by_roi|savesessionid:true|verbose:true|debug:true')

Third, can you please try running with the latest version of the QuNex container? It might be a bug that we have already squashed.

Let me know, what you find out.

All the best,

Grega

3

Hi Grega,

Thanks so much for your prompt response and suggestions!

I tried the latest version of qunex container (version 1.1.1), and it works very well. There is no error what so ever.

As for the list file, I chopped the files names listed in the middle of all printed prompts and replaced them with “…”. Sorry for the misinformation. It’s all good with the list file.

Currently the “fc_compute_seedmaps” is in the middle of computing for all the files and functioning well with expected outputs.

If there is any issue encountered later on, I will update you here.

Thanks again for your supports, and I wish you all the best!!

Appreciate it,
Aiken

4

Hi Aiken,

I’m glad it worked out! Let us know if you run into any other issues or need further help.

All the best,

Grega