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fedorov / MultiVolumeImporter

A 3D Slicer module to support import of multi-volume data from non-DICOM sources, and provide plugin for importing such data from images saved in DICOM.
http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/MultiVolumeImporter
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After import, multi-volume can only be saved as nrrd/nhdr, not other format #36

Open jenaflex opened 5 years ago

jenaflex commented 5 years ago

Slicer 4.10.0.

After importing 4D nifti using multi-volume importer, multi-volume can only be saved as nrrd/nhdr (attached screenshot), not other format. What I was trying to do is to import 4D nifti (diffusion MRI), crop them all together and save them as 4D nifti.

Thanks!

slicermultivolsave
fedorov commented 5 years ago

Saving of multivolumes is supported only into the nrrd format. We don't support nifti export for multivolumes.

jenaflex commented 5 years ago

OK. Can I request this feature? Is there a way around it as for now?

Thank you!

fedorov commented 5 years ago

Have you tried dcm2niix directly on the DICOM series?

Unfortunately, I do not currently have resources to work on new features for this module. Implementing this can be very involved and require changes to the Slicer core application, and so it is unlikely it will be added any time soon.

jenaflex commented 5 years ago

Thank you for your reply. Nifti files converted by dcm2niix cannot be read by MATLAB 2017b's niftiread.

BTW, I was wondering if you could help to give same example of how to make function call 'slicer.modules.cropvolume' in built-in Python console to crop 3D volumes with ROI (instead of using GUI, like attached screenshot). The documentation seems to be very limited. This way, I can write a recursive script to run 'crop volume' on all 3D volumes (extracted from 4D nifti)

Thanks! Harry Greeting from Washington University.

[image: CropScreenshot.PNG]

On Wed, Nov 28, 2018 at 2:38 PM Andrey Fedorov notifications@github.com wrote:

Have you tried dcm2niix directly on the DICOM series?

Unfortunately, I do not currently have resources to work on new features for this module. Implementing this can be very involved and require changes to the Slicer core application, and so it is unlikely it will be added any time soon.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/fedorov/MultiVolumeImporter/issues/36#issuecomment-442596112, or mute the thread https://github.com/notifications/unsubscribe-auth/ArVF-2eKjlkATfMaKfK-IJ6vw2fYvkvFks5uzvQ3gaJpZM4Y4Jn4 .

fedorov commented 5 years ago

Nifti files converted by dcm2niix cannot be read by MATLAB 2017b's niftiread

Sounds like you need to follow up with the maintainers of MATLAB 2017b's niftiread. I have no idea about what that function/package expects, and I would most definitely not standardize representation on what is expected by a Matlab implementation. In the Slicer community, we standardize on non-restrictive open source software and standards, and Matlab is not on that list.

BTW, I was wondering if you could help to give same example of how to make function call 'slicer.modules.cropvolume' in built-in Python console to crop 3D volumes with ROI

Please post your questions about Slicer on the Slicer forum here: https://discourse.slicer.org/.

jenaflex commented 5 years ago

Thank you Andrey,

This is very helpful!

Harry

On Wed, Dec 5, 2018 at 1:07 PM Andrey Fedorov notifications@github.com wrote:

Nifti files converted by dcm2niix cannot be read by MATLAB 2017b's niftiread

Sounds like you need to follow up with the maintainers of MATLAB 2017b's niftiread. I have no idea about what that function/package expects, and I would most definitely not standardize representation on what is expected by a Matlab implementation. In the Slicer community, we standardize on non-restrictive open source software and standards, and Matlab is not on that list.

BTW, I was wondering if you could help to give same example of how to make function call 'slicer.modules.cropvolume' in built-in Python console to crop 3D volumes with ROI

Please post your questions about Slicer on the Slicer forum here: https://discourse.slicer.org/.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/fedorov/MultiVolumeImporter/issues/36#issuecomment-444603757, or mute the thread https://github.com/notifications/unsubscribe-auth/ArVF-1DEbUbbgO45T5yO276ApCEu8ZPsks5u2BmGgaJpZM4Y4Jn4 .