Gannet on Siemens .dcm files

Analysis / Modeling
21

@alex, that’s a different issue, but thanks for the heads up! A simple fix, I think, would be to change line 51 in DICOMRead.m to:

[~,~,ext] = fileparts(metabfile);
dcm_file_list = dir(fullfile(folder, ['*' ext]));

(You would do the same for the water files on line 130.)

22

I am unable to load the .dcm and .ima files. Would it be better if I convert them to .dat format?

23

@Gao,

You cannot convert .dcm/.ima files to .dat files. You will need to export the original raw data on the scanner in the .dat format.

Mark

24

Hi @mmikkel,

I am having a similar issue to @Lejia I think. I am missing a .dat file for my MEGAPRESS water reference because it didn’t get saved at the time of the scan. I have 3 DICOM files instead, all are 141KB and look similar to other scans which have been analysed (using .dat files) without any issue. I have a metabolite .dat file.

I get this error when I tried to run the analysis with .dcm files as you suggested:

image
image1138×720 102 KB

Do you know what I might be doing wrong?

Many thanks, James

25

Hi @jbarnacle,

Please see this post: Gannet on Siemens .dcm files - #20 by admin

Are you sure you’ve exported your data correctly?

Mark

26

Hi @mmikkel, I read through this and the Gannet manual, but I’m still confused how to load .dcm GE (rather than Siemens) files. I have only 1 dicom file, rather than separate water reference, etc. files. Could you please help with more guidance?

27

Hi @z_ilchovska,

MRS data acquired on GE scanners should be exported as P-files (.7). The saved DICOM files are simply the sum of all the data, which is not what you want to use for data processing. I suggest you work with your MR technician/radiographer to re-export your data in the P-file format.

Mark

28

Hi @mmikkel, thank you for your reply. The reason I’ve resolved to the dicoms is because, due to system failure, we lost the P-files, and are not able to generate these post-scanning in our case. I was wondering whether there is any way around it with .nii files or anything else you might suggest as tools? Also, apologies if any question is self-explanatory, I’m very fresh to all this.

29

Unfortunately, P-files are what are needed to process GE MRS data.