Hi,

I'm new to Linux. I need to convert DICOM to Nifti filetype. I've downloaded Microgl and dcm2niix as executables, but I can't figure out how to launch them.

Thanks in advance!

- Raisa

I assume you downloaded the Linux version of the software from here (v1.2.20181114). You will want to extract the zip file. You will find inside an executable called "MRIcroGL" - you can double click it to run the program. Once the program is running, you can choose the menu Import/ConvertDICOMtoNIfTI - a new window named "dcm2niix" will appear. You can then drag and drop your folder with all the DICOM files onto the dcm2niix window. Note that when your file is converted, the window will show the command line call to dcm2niix that it used to convert your images - you can convert this to the terminal.

You can also run the executable "dcm2niix" from the terminal. It should either be in your system path, or if your  command line is in the same folder as the executable you can run "./dcm2niix". You can run the program without any inputs to see your options, however the simplest conversion would be dcm2niix /path/to/DICOM/folder"