Gannet on Siemens .dcm files

Hi,

I cannot figure out, is it possible to use Gannet if I only have Siemens .dcm files? That is one file for Water reference and e.g. 256 .dcm files for metabolites?

Hi @dace,

Yes, Gannet can process Siemens .dcm files. Let me know where you may be having issues running your data.

Mark

Thanks, Mark!
At GannetLoad, do I specify DICOM files as a folder or a list of all .dcm files? Nothing seems to work.

If I specify as a list of files, for each file I get this error message and also a popup window with an error (>200 popups)

Loading 1.3.12.2.1107.5.2.43.67035.2022100610260399972023693.dcm…
256 water-suppressed DCM files detected in [my folder name]
Warning: ********** An error occured while loading dataset:
‘[my folder name]\1.3.12.2.1107.5.2.43.67035.2022100610260399972023693.dcm’.
Check data. Skipping to next dataset in batch **********

In GannetLoad (line 712)
Warning: Escaped character ‘\d’ is not valid. See ‘doc sprintf’ for supported special characters.
In GannetLoad (line 713)

What version of Gannet are you using?

It is from the GitHub the latest (as of few days ago). 3.2.1
And Matlab 2020b (but the same was on 2018a)

Are you able to share your data with me for debugging? My email is mam4041@med.cornell.edu

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@dace, I’ve fixed the bug related to your issue. Please try using the development version of the upcoming Gannet release (v3.3.0-rc). Downloadable: GitHub - markmikkelsen/Gannet at dev

The syntax for loading your data is:

MRS = GannetLoad({metabfile_folder/one_dcm_file.dcm}, {waterfile_folder/one_dcm_file.dcm});

Thanks, Mark! I will try.

Regarding the syntax, I have 256 dcm files for metabolites, will it automatically then load all even if I only specify one of the files?

Yep, it will find all the files in the folder ending in *.dcm.

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It now worked without any problem. Thanks so much, Mark! :slight_smile:

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