I am currently working with fMRS data using a PRESS sequence, where the unsuppressed water reference is embedded within the main data (Siemens, .dat). The sequence is structured such that one unsuppressed water reference is followed by seven suppressed water references, and this pattern repeats multiple times.
When attempting to load the data, I encounter the following error: Error using plot Data cannot have more than 2 dimensions.
* * Error in osp_plotLoad (line 290)
* plot(axesHandles.A, dataToPlot.ppm, real(dataToPlot.specs(:,rr)) + rrstag, ‘k’, ‘LineWidth’, 0.5, ‘Color’, MRSCont.colormap.Foreground);
* * Error in osp_plotModule (line 191)
* temp = osp_plotLoad(MRSCont, kk,‘mets’,Exp);*
* * Error in osp_plotAllPDF (line 37)
* osp_plotModule(MRSCont, ‘OspreyLoad’, kk,[1 1], ‘metabolites’);*
* * Error in OspreyLoad (line 426)
* osp_plotAllPDF(MRSCont, ‘OspreyLoad’)*
To bypass this error, I can load the data in Osprey version 2.4.0 by changing the job file details to an edited sequence (MEGA). However, this approach results in incorrect measurements/averages and I suspect will lead to further issues down the line.
While this is an fMRS dataset, at first, I would like to model the aggregation of all the water-suppressed data and use the unsuppressed water ref for the pre-processing. Could you recommend a method to achieve splitting these two experiments in such a way that they can feed into Osprey?
Any guidance or recommendations would be greatly appreciated!
I am happy to provide more information if needed.
I’m unsure from KianaK’s description if this is how the data is set up, but on Siemens 7T Terra.X (XA60) product STEAM sequence, if the Ref. Scan Mode option is set to Save All, I think the water and metabolite TWIX data are in one file, or at least there is only one TWIX file output (I haven’t tried using the TWIX myself yet). The corresponding DICOM output is svs_st_ave with individual averages, svs_st_ECC with a corrected single averaged spectrum, svs_st_noECC with an uncorrected single averaged spectrum, and svs_st_ref with a single averaged water spectrum. Hope this info helps.
Hi Georg and Meredith,
Thank you for your help and patience. I consulted with my supervisor and reviewed the documentation.
It is a commercial/common SVS Siemens 3T Magnetom Skyra PRESS sequence (voxel size 27 ×20 ×12 mm in the left DLPFC).
The TE is 33 ms and TR 2000ms, 8 Averages, 25 measurements, rel. SNR = 1.00
Further details: 4 preparation scans, delta frequency = -2.3ppm, 1 ref. Scan, Phase cycling set to Auto, bandwidth of 1200 Hz, Acquisition duration 853 ms and remove oversampling set to On.
Regarding Meredtih’s reply:
The Ref. Scan mode option is set to Inline correction and I have one file as output aved as …E_sync_svs_se_30_DLPC…dat.
I hope this information is helpful. Please let me know if you need any further details or clarification.
Thank you once again for your support!
Kiana
I have been asked to assist @KianaK with processing this dataset, but I was not involved with setting this one up. If it may be helpful, please find attached the scan protocol or let me know if sharing an example file may be more useful.
If we could get OspreyLoad to read this data properly, I should be able to isolate the two conditions. That said, the hacked attempt running this file as a two condition edited sequence did not read properly (i.e., incorrect number of measurements per condition - 16v16, rather than 25 v 175). Thinking head, once the water refs are isolated, I am not quite certain how best to read them back into the job file, which I believe expects dicoms or .dats, not the OspreyLoad .mat.
@Meredith, thank you for this insight. When I look into our dicom file output for this scan, I see 50 .IMA files, with each containing “SPEC NUM” = 4. This would correspond to the 200 expected measurements. Given this configuration, a less than ideal solution could be to use only the IMA files that contain 4 suppressed dataset (4x25) and then the other 25 IMA files that contain 1 unsuppressed and 3 suppressed) as the water ref… On reflection, I suspect there is a better way to isolate these two conditions, but thought I would keep this in here incase it helps in troubleshooting.
I suppose this is just a newer product sequence flavor that we have not yet encountered (or at least not with the ref scans included) - is this an XA-type scanner?.
If you can share the TWIX (.dat) dataset (fully de-identified; otherwise a phantom scan with the same protocol will do), we can take a look and see if we can make it work (I suppose we can).
Thank you for your help with this. This data was collected on VE11C.
I have a de-identified Twix file, but it seems that .dat is an unauthorised file extension and cannot be uploaded here. I tried compressing the file within a directory and uploading a .zip, but this file size exceeded the max upload allowance. Is there a preferred email address I could send this file to?