GUI Quantified tab - error when navigating results

MRS Software Osprey
1

After running data through the Osprey pipeline, when I go to the Quantified tab in the GUI and navigate to the individual subjects, the results table does not update in the GUI window (stays on sub-001), and I get the following error. I’m using the latest version from the develop branch. Data are unedited Siemens IMA (not fMRS) fit with LCModel.

Screen Shot 2022-09-15 at 9.23.37 AM
Screen Shot 2022-09-15 at 9.23.37 AM4084×326 26.3 KB

Text of error message:

Unrecognized field name "resBasisSet".

Error in osp_updateQuantifyWindow (line 28)
        basisSet = MRSCont.fit.resBasisSet.metab.(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){gui.controls.act_z,1,gui.controls.act_y};

Error in osp_onListSelection (line 44)
                osp_updateQuantifyWindow(gui);
 
Error while evaluating UIControl Callback.
2

Hi @Meredith,

this should now be fixed in the latest version on the develop branch.

Best,
Helge

1 Like
3

Confirmed that it’s working for me. Thanks!

4

Hi @Helge,

I think I found a related bug in OspreyHTMLReport:

Unrecognized field name "resBasisSet".

Error in OspreyHTMLReport (line 718)
        basisSet    = MRSCont.fit.resBasisSet.(which_spec).(['np_sw_' num2str(round(dataToPlot.sz(1))) '_' num2str(round(dataToPlot.spectralwidth))]){1,1,VoxelIndex(2)};

Error in RunOspreyJob (line 58)
        [MRSCont] = OspreyHTMLReport(MRSCont,kk);
5

Hi @Meredith,

actually, LCModel was not considered as model option for the OspreyHTML report. I have added a fix to the develop branch to resolve the issue.

Helge

1 Like
6

Hi

I am fairly new to Osprey and I am running some MEGA-press pilot data. The data are analyzed perfectly, however when I am navigating through the results in the GUI window I am experiencing the same problem as described above. I cannot switch between subjects, the result table does not update (this is for all tabs, not only for the Quantified tab) and I get the error below.

However, when I load the output mat file, and run the GUI separately, I have no problem with the GUI and can easily switch between subjects.

Unrecognized function or variable 'osp_updateLoadWindow'.

Error in osp_onListSelection (line 33)
                osp_updateLoadWindow(gui);
 
Error while evaluating UIControl Callback.

Unrecognized function or variable 'osp_updateLoadWindow'.

Error in osp_onListSelection (line 33)
                osp_updateLoadWindow(gui);
 
Error while evaluating UIControl Callback.

Does someone have an idea? Any suggestions would be highly appreciated!
(Please let me know if I should be more specific/clear)

Best,
Katrien

7

Hi @KatrienNoelmans,

Thank you for reaching out and picking up Osprey for the analysis of your data.

I have tried to reproduce the behavior you are describing on my machine, but I have been unable to do so. Could you try the following to see if this resolves the issues:

  1. Delete the SPMpath.mat file from the osprey/GUI folder (if it exists)
  2. Remove Osprey from your path (with subfolders)
  3. Remove spm12 from your path
  4. Run rehash toolboxcache in the command window
  5. Add Osprey with subfolders to your path
  6. Add spm12 without subfolders to your path
  7. Try to run the MEGA-PRESS example data from the exampledata/sdat/MEGA/jobSDAT_MEGA.m the same way you ran your data.

Let me know how this works out.

Best,
Helge

8

Hi @Helge,

Thanks for the answer, I have tried your suggestions and ran the example data you mentioned. Unfortunately, I am still encountering the exact same error when navigating in the GUI. Do you maybe have other suggestions?

Many thanks in advance!

9

Hi @KatrienNoelmans,

I assume you are using the most recent version from the develop branch?

So, does it actually work when you load a fully processed .mat file with the GUI? At which step of the analysis are you unable to navigate between different subjects.

Which tab is active when you see the error message? One problem with the GUI is that as soon as there is an error, it is most likely broken and needs a restart. Therefore, I have to know precisely when the described error message appears.

Could you share a screenshot of what the GUI actually looks like when you cannot change subjects?

Best,
Helge