I am interested in using Osprey to process 2D-PRESS MRSI Philips data but I have had a few difficulties loading in the data correctly and subsequent processing steps. Is there an example data set and job file available that I could compare to my files? I see example datasets for SVS across many vendors (which has been very helpful so thank you for those!) but I am unable to find a corresponding MRSI dataset and jobfile.
thank you kindly for your help!
MRSI support in Osprey is currently limited to the ‘MRSI’ branch of the repository, not in a release version, so we don’t share example data. @Helge has been doing some work behind the scenes for some of our local projects that involve Philips CSI. If you can clarify your difficulties, we might be able to help.
Just to make sure, by ‘2D-PRESS’ you mean 2D phase-encoded CSI, not some sort of two-dimensional spectroscopy experiment?
Thank you for quick response! I understand. Also, yes that is correct. I am looking at a single slice comprised of 10 by 11 voxels. Any guidance you are able to provide is much appreciated!
When I load the data specifying “seqType”: “unedited” and “dataScenario”: “MRSI” in the jobfile, the data loads as seen in screenshot 1 and processed as in screenshot 2.
This does not look correct so I added a line to the jobfile
“MultiVoxel”: “MRSI”,
This results in the isMRSI flag being set. But still, the OspreyLoad function selects case ‘SDAT’ on line 209 (OspreyLoad.m; 2019-02-19: First version):
case ‘Philips’
switch MRSCont.datatype
case ‘SDAT’
[MRSCont] = osp_LoadSDAT(MRSCont);
case ‘DATA’
if ~MRSCont.flags.isMRSI
[MRSCont] = osp_LoadDATA(MRSCont);
else
[MRSCont] = load_mrsi_data(MRSCont);
end
When I run OspreyGUI(MRSCont), I get the following errors:
Unrecognized field name “Xvoxels”.
Error in op_takeVoxel (line 37)
if in.dims.Xvoxels==0
Error in osp_plotLoad (line 222)
dataToPlot=op_takeVoxel(MRSCont.raw_ref{ExpIndex,kk},VoxelIndex);
Error in osp_iniLoadWindow (line 418)
temp = osp_plotLoad(MRSCont, gui.controls.Selected,‘ref’); %re_mm
Error in OspreyGUI (line 485)
osp_iniLoadWindow(gui);
Error in script (line 5)
OspreyGUI (MRSCont)
If I force the OspreyLoad function to open load_mrsi_data by the following modification :
case 'Philips'
switch MRSCont.datatype
% case ‘SDAT’
% [MRSCont] = osp_LoadSDAT(MRSCont);
case ‘SDAT’ % note this has been changed from case ‘DATA’
if ~MRSCont.flags.isMRSI
[MRSCont] = osp_LoadDATA(MRSCont);
else
[MRSCont] = load_mrsi_data(MRSCont);
End
I get the following errors when I run OspreyGUI(MRSCont):
Unrecognized field name “Xvoxels”.
Error in op_takeVoxel (line 37)
if in.dims.Xvoxels==0
Error in osp_plotLoad (line 222)
dataToPlot=op_takeVoxel(MRSCont.raw_ref{ExpIndex,kk},VoxelIndex);
Error in osp_iniLoadWindow (line 418)
temp = osp_plotLoad(MRSCont, gui.controls.Selected,‘ref’); %re_mm
Error in OspreyGUI (line 485)
osp_iniLoadWindow(gui);
This now seems to be trying to call PRIAM data in the op_takeVoxel function and I’m not sure why.
If it is easier that I contact you directly with the dataset, please let me know!