jobNIfTImrs Osprey errors

[JillNaaijen]

Hi Osprey folks!

For a large multi-center project I’d like to start processing mrs data in NIfTI format because all the non-MRS people involved are less familiar with twix, sdat, .7 files etc and it would be great to standardise the processing pipeline across centers.

Using the example data and jobNIfTImrs.m from osprey-develop, however, stops at the modelling step with the following error:

Reference to non-existent field 'basisSetFile'.

Error in osp_fitInitialise (line 126)
        basisSet = load(MRSCont.opts.fit.basisSetFile);

Error in OspreyFit (line 51)
[MRSCont] = osp_fitInitialise(MRSCont);

Using my own siemens 3T PRESS data, transformed to .nii.gz using spec2nii goes wrong at the load stage:

Error using plot
Data cannot have more than 2 dimensions.

Error in osp_plotLoad (line 217)
        plot(axesHandles.A, dataToPlot.ppm, dataToPlot.specs(:,rr) + rr*stag, 'k', 'LineWidth',
        0.5, 'Color',MRSCont.colormap.Foreground);

Error in osp_plotModule (line 216)
                temp = osp_plotLoad(MRSCont, kk,'ref' );

Error in osp_plotAllPDF (line 39)
                    osp_plotModule(MRSCont, 'OspreyLoad', kk, 'ref');

Error in OspreyLoad (line 202)
    osp_plotAllPDF(MRSCont, 'OspreyLoad')

Any suggestions?

Thanks in advance!

Jill

[meggon]

Hi @JillNaaijen!

I know this is an old post, but I am running into a similar issue- I’m wondering if you ended up finding any solutions to these errors?

I circumvented the basis set issue by using the one provided by Osprey in the “fit” folder. However, when I try to CoRegister using my nii files, I get this error:

We just upgrade our Siemens scanner and I’m thinking this is definitely contributing to the problem.

Any help would be greatly appreciated!
Thanks in advance!!
Meg