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help > How to convert dicoms into just one comprssed NifTi using dcm2nii in mricron?
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Oct 11, 2018 01:10 PM | Fan Jiachen
How to convert dicoms into just one comprssed NifTi using dcm2nii in mricron?
Dear all ,
I am a graduate student from Southeast University .I found it difficult to convert Philips ingenia MRI dicom (EPI,DTI) into just one compressed Nifti.I used MRIConvert and mricron ( whcih has dcm2nii tool ) and I have also tried dcm2niix , which is inclued in mricrogl .However ,these tools were failed . I can't convert my dicoms into just one Nifti . For example ,when I convert my EPI dicoms (8275 images) into compressed FSL (4D NifTi nii) ,dcm2nii outputs 26 Niftis.It's ok to convert T1 3D dicoms into one NifTI .I hope you can give my some suggestions .Thank you.
Any help would be greatly appreciated !
Best,
Fan
I am a graduate student from Southeast University .I found it difficult to convert Philips ingenia MRI dicom (EPI,DTI) into just one compressed Nifti.I used MRIConvert and mricron ( whcih has dcm2nii tool ) and I have also tried dcm2niix , which is inclued in mricrogl .However ,these tools were failed . I can't convert my dicoms into just one Nifti . For example ,when I convert my EPI dicoms (8275 images) into compressed FSL (4D NifTi nii) ,dcm2nii outputs 26 Niftis.It's ok to convert T1 3D dicoms into one NifTI .I hope you can give my some suggestions .Thank you.
Any help would be greatly appreciated !
Best,
Fan
Oct 11, 2018 02:10 PM | Chris Rorden
RE: How to convert dicoms into just one comprssed NifTi using dcm2nii in mricron?
Hello,
I assume you are running the modern dcm2niix rather than the older dcm2nii. The DICOM standard has evolved a lot since dcm2niix replaced dcm2nii. I would reserve dcm2nii for archival analyses, in particular for proprietary formats that preceded the DICOM standard. I would heed the warning generated wheneve you run dcm2nii that you should consider moving to dcm2niix.
dcm2niix is provided with MRIcroGL
https://www.nitrc.org/frs/?group_id=889
or you can get it as a standalone program
https://github.com/rordenlab/dcm2niix/releases
If you do have problems, it would be helpful to know what version you are using - the is the first line displayed regarless of whether you use the graphical Import menu item from MRIcroGL or run the program from the command line:
Chris Rorden's dcm2niiX version v1.0.20180622 GCC6.1.0 (64-bit MacOS)
If your version is not the latest stable release (v1.0.20180622) please consider upgrading. You can also build a more recent developmental release (v1.0.20181009) by downloading and compiling the github code. If these do not work with your dataset, consider posting an issue on Github.
I assume you are running the modern dcm2niix rather than the older dcm2nii. The DICOM standard has evolved a lot since dcm2niix replaced dcm2nii. I would reserve dcm2nii for archival analyses, in particular for proprietary formats that preceded the DICOM standard. I would heed the warning generated wheneve you run dcm2nii that you should consider moving to dcm2niix.
dcm2niix is provided with MRIcroGL
https://www.nitrc.org/frs/?group_id=889
or you can get it as a standalone program
https://github.com/rordenlab/dcm2niix/releases
If you do have problems, it would be helpful to know what version you are using - the is the first line displayed regarless of whether you use the graphical Import menu item from MRIcroGL or run the program from the command line:
Chris Rorden's dcm2niiX version v1.0.20180622 GCC6.1.0 (64-bit MacOS)
If your version is not the latest stable release (v1.0.20180622) please consider upgrading. You can also build a more recent developmental release (v1.0.20181009) by downloading and compiling the github code. If these do not work with your dataset, consider posting an issue on Github.