Hello, I have 4D dynamic susceptibility contrast (DSC) dicom images (T2* with contrast agent) to analyze. I’ve noticed that I can convert NIFTI files to NRRD files, just by click “Save” in Slicer. However, I want to convert hundreds of NIFTI files to NRRD files, so I need to do it by command line…

All operations you perform on the GUI are accessible through Python scripting, too. Save/load functions are exposed using a convenient interface in slicer.util package . You can start a script directly from the command-line as described here .

Thank you so much. However, I don’t understand why the code below is not working. Could you please tell me what’s the problem? (e.g. option, syntax, etc.) 1. I just want to load 35000671_DSC.nii.gz and save as a NRRD file with the same basename (i.e. save/load problem for a single file). MRHead=…

You can get filename from full path or get all files in a folder using standard Python commands. You can easily find answers on Google search and StackOverflow.

Thank you so much for quick response! However, I think it’s not the problem of Python commands. I think it’s because there’s no “slicer.py” on my Slicer folder. I think I should “import slicer” or “import slicer.util” to use those functions such as loadVolume, getNode, and saveNode. But “import s…

Hi @Kyu_Sung_Choi - you need to use forward slashes for your paths in python: “d:/file” not “d:\file” HTH, Steve

Thank you for your quick response! However, both ways are seemed to be not working. [image] Can anyone tell me where should I save my python file not to see the error msg saying “no modules named ‘slicer’”? I can’t find “slicer.py” or “slicerrc.py” in Slicer folder. Thank you in advance!

If you want to use Slicer from a Jupyter notebook, then you need to use the Slicer Jupyter kernel. See instructions here: https://github.com/Slicer/SlicerJupyter . Within Slicer’s Python interactor, slicer.util.loadVolume works well for me. Could you try to load a different image (e.g., download a S…

Thank you for your quick response! However, I’ve found that Python interactor works well on my workstation, not my desktop. [image] As you recommended, loading sample data (i.e. MRhead) and saving in NRRD file works well within Python interactor. [image] Now, let me put it in this way then, 1…

It does not matter where you put your .py file. However, it is important to run it using Slicer.exe and not using Python.exe. Some features work with PythonSlicer.exe, too. You can load volume using slicer.util.loadVolume(‘my filename.nrrd’)

Oh, I see. What a mistake! Refering below link, I wrote the code below and solve it by entering the below command in the command line. https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Load_volume_from_file import slicer [success, loadedVolumeNode] = slicer.util.loadVolume("/hom…

How can I convert NIFTI files to NRRD files in command lines?

Support

fedorov (Andrey Fedorov) August 3, 2018, 9:42pm 12

@Kyu_Sung_Choi please see this post for the answer to your last question: How can I import NIFTI files to DSCMRIAnalysis module?

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How can I convert NIFTI files to NRRD files in command lines?

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