Error in Osprey Quantification?

MRS Software Osprey
1

Hello!

While running HERMES data, I ran into this error on the quantification step. The GUI seems to get stuck here. Any idea how to fix it?

Thanks!

Quantifying dataset   2 out of   2 total datasets...
... done.
 Elapsed time 0.094643 seconds
Timestamp November 19, 2021 16:15:52 Osprey 1.1.0  OspreyOverview

Gathering spectra from subspectrum 8 out of 8 total subspectra...
... done.
Gathering fit models from fit 4 out of 4 total fits...
... done.
Interpolating fit models from fit 4 out of 4 total fits...
... done.

Scaling data from dataset 2 out of 2 total datasets...... done.
 Elapsed time 0.835501 seconds
Runtime Breakdown................
OspreyLoad runtime: 58.861565 seconds
OspreyProcess runtime: 104.845057 seconds
OspreyFit runtime: 3000.307131 seconds
OspreyFit metab runtime: 2996.718079 seconds
OspreyFit reference runtime: 3.589053 seconds
OspreyCoreg runtime: 11.135346 seconds
OspreySeg runtime: 1851.878690 seconds
OspreyOverview runtime: 0.835501 seconds
Full Osprey runtime: 5027.957934 seconds
Reference to non-existent field 'sum'.

Error in OspreyMinReport (line 131)
    strings = fieldnames(MRSCont.quantify.tables.sum);

Error in OspreyOverview (line 1239)
    [MRSCont] = OspreyMinReport(MRSCont);

Error in osp_onQuant (line 46)
    MRSCont = OspreyOverview(MRSCont);
 
Error while evaluating UIControl Callback.

Opening external nii viever...
... done.
Opening external nii viever...
... done.
Opening external nii viever...
... done.
Timestamp November 19, 2021 16:36:13 Osprey 1.1.0  OspreyQuantify

Quantifying dataset   2 out of   2 total datasets...
... done.
 Elapsed time 0.051593 seconds
Timestamp November 19, 2021 16:36:19 Osprey 1.1.0  OspreyOverview

Gathering spectra from subspectrum 8 out of 8 total subspectra...
... done.
Gathering fit models from fit 4 out of 4 total fits...
... done.
Interpolating fit models from fit 4 out of 4 total fits...
... done.

Scaling data from dataset 2 out of 2 total datasets...... done.
 Elapsed time 0.659060 seconds
Runtime Breakdown................
OspreyLoad runtime: 58.861565 seconds
OspreyProcess runtime: 104.845057 seconds
OspreyFit runtime: 3000.307131 seconds
OspreyFit metab runtime: 2996.718079 seconds
OspreyFit reference runtime: 3.589053 seconds
OspreyCoreg runtime: 11.135346 seconds
OspreySeg runtime: 1851.878690 seconds
OspreyOverview runtime: 0.659060 seconds
Full Osprey runtime: 5027.738443 seconds
Reference to non-existent field 'sum'.

Error in OspreyMinReport (line 131)
    strings = fieldnames(MRSCont.quantify.tables.sum);

Error in OspreyOverview (line 1239)
    [MRSCont] = OspreyMinReport(MRSCont);

Error in osp_onQuant (line 46)
    MRSCont = OspreyOverview(MRSCont);
2

The problem seems similar to that described in this post

but not fully analogous.

3

Hi Cristian,

Which options are you setting in the job file, and which Osprey version are you running? It appears that the functions themselves run through, and it’s just the GUI that breaks when trying to access them (copying @Helge in). Can you see the OspreyQuantify output tables in your output folder?

Thanks,
Georg

4

Hello Georg,

I am running Osprey 1.1.0, according to Matlab (though the GUI says its 1.0.0). This is the Version that was linked in the Wiki. Yes, it does seem that the functions have run through and the OspreyQuantify output tables are in the designated output folder. It would just be nice to have the visualization to verify the accuracy of the output.
Thank you so much for your time. It is well appreciated.

Best,
C

5

Hi Cristian,

just a quick follow up about your job file. Are you using 'Separate' or 'Concatenated' for the fit.style option:

opts.fit.style = 'Separate';

The concatenated model is currently not well optimized and is also causing the error that you are reporting. I would recommend using the 'Separate' model for now. Let me know if this works for you.

I’ve also just committed a Bug Fix to the develop-branch to resolve this issue.

Best,
Helge