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I totally understand that for every study, single version of a particular software should be used for analysis. We have used (and published) analysis using Gannet 3.0. I like some of the improvements in peak alignment in newer version(s), but I find the reported difference in values of GABA/Cr somewhat shocking. Was there a change in fitting procedure as well?

MEGAPRESS_GABA_MPFC_noMM_GABAGlx_fit.pdf
MEGAPRESS_GABA_MPFC_noMM_vox1_fit.pdf

Hi,

We got the following problem when using Gannet v3.3.0 with MATLAB on a Linux system.

GannetLoad was not able to load our spectra. We also use a Mac Computer and on this computer, with the same Gannet version (3.3.0) and same MATLAB version (R2022a), GannetLoad was able to load the data.
Long story short, it turns out the the dir() function in MATLAB Linux is case sensitive while the dir() function in MATLAB Mac is not.
Indeed, our dicom files are named: '*.IMA' and are not detected with the filter in SiemensDICOMRead.m on the Linux system with the following line:

ima_file_list = dir(fullfile(folder, '*.ima'));

The workaround we used in our Linux system was to change the line above with the following:

ima_file_list = dir(fullfile(folder, '*.IMA'));

Hi, I've just collected a GE Pfile.7 with PRESS Seq with TE=30 following the console update to rdbm_rev_num=30.("SoftwareVersions": "30_LX_SIGNA_LX1.MR30.0_R01_2242.a").Gannet-3.3.1 throws an error that "GERead.m is not fully functional with header revision number 30." How can I help get Gannet updated to read the new format?
Cheers,
Carl

Contact details

[email protected]

Describe bug

Hi,
I am running Ganner to analyse .dat Siemens MRS data file using Matlab R2019b in Windows 10. I load the data located in the following path: F:\Leipzig_20181101\mrs_raw\28998.75_181101_112048(.,..) but the program complains about the sprintf function. Even though this seems to be predominantly a Matlab problem, I have never had an issue with sprintf for any of my folders's name. Actually, I have changed the name of the main folder several times, but it always complains about this "escaped character".

I want to know if it is a Windows problem, Matlab problem or somehow the "path" I add into the GannetLoad should be a string instead of a char array (and maybe that complains about the folder's name).

Steps to reproduce bug

No response

Screenshots

Warning: ********** An error occured while loading dataset:
'F:\Leipzig_20181101\mrs_raw\28998.75_181101_112048\meas_MID131_svs_st_FID40704.dat'. Check data.
Skipping to next dataset in batch **********

In GannetLoad (line 723)
Warning: Escaped character '\L' is not valid. See 'doc sprintf' for supported special characters.
In GannetLoad (line 724)

Version

3.3.1

Operating system

Windows

MATLAB version

R2019b

Additional context

No response

Having issues with HERMES Philips data in both raw and sdat/spar formats. Additionally, the same things happen when trying to process MEGAPRESS data from SIEMENS in .dat format.

Hi,
Thank you for providing and maintaining such a useful tool!

We recently came across the following issue:
GannetLoad was complaining about a missing parameter in the DICOM header: DicomHeader.editRF.centerFreq

We did not get this error with Gannet version 3.1.5.

This is due to this change in 'SiemensDICOMHeader.m' .

In version 3.1.5:

if isfield(MRS_struct.p, 'Siemens')
    MRS_struct.p.Siemens.deltaFreq = DicomHeader.deltaFreq;
    MRS_struct.p.Siemens.editRF.freq = DicomHeader.editRF.freq;
    MRS_struct.p.Siemens.editRF.bw = DicomHeader.editRF.bw;
    MRS_struct.p.Siemens.editRF.centerFreq = DicomHeader.editRF.centerFreq;
end

In version 3.3.0:

if isfield(DicomHeader, 'editRF')
    MRS_struct.p.deltaFreq         = DicomHeader.deltaFreq;
    MRS_struct.p.editRF.freq       = DicomHeader.editRF.freq;
    MRS_struct.p.editRF.bw         = DicomHeader.editRF.bw;
    MRS_struct.p.editRF.centerFreq = DicomHeader.editRF.centerFreq;
end

Our Siemens dicom (coming from a 3T Prisma with Syngo VE11C) headers have indeed a field editRF with fields freq and bw but not centerFreq. In version 3.1.5, since the Field Siemens was not present, this loop was not used.

The workaround I did for now is to comment the line:

%MRS_struct.p.editRF.centerFreq = DicomHeader.editRF.centerFreq;

Hello

In the documentation
https://markmikkelsen.github.io/Gannet-docs/getting-started.html

Under the description of how to load dicom files, the example code is:

MRS_struct = GannetLoad(metab({'metab/file1.ima'}, {'water/file1.ima'});

the metab(
bit is not needed (and doesn't work). Instead, I think it should be

MRS_struct = GannetLoad({'metab/file1.ima'}, {'water/file1.ima'});

Thanks

Michael

The default install instructions point to the zip of the master branch, this could be an unknown version, I suggest instead linking to the Releases URL, https://github.com/markmikkelsen/Gannet/releases and note that development code can be downloaded via git.

Contact details

[email protected]

Describe the bug

We have used Gannet 3.0 to co-register .rda spectra (PRESS in muscle, not MEGA-PRESS) on anatomical images and it works fine. However it doesn't work properly in 3.3.x. Not sure f relevant, but noticed that newer version reports voxel dimensions flipped compared to old version.

Steps to reproduce the bug

disp('Loading spectra');
MRS_Struct=GannetLoad({rda_file});
MRS_Struct.ii=1; % trick Gannet to use any spectra, not just MEGAPRESS
MRS_Struct.p.numScans=1; % trick Gannet 3.3 to use any spectra
disp('Co-registering');
MRS_Struct=GannetCoRegister(MRS_Struct,{anat_file});

Screenshots

Version

33.1

Operating system

Windows

MATLAB version

R2022b

Additional context

No response

Can Gannet process GE DICOM (.dcm)？