[BIC-announce] Enhanced Dicom format conversion to nii and minc

[Ilana Ruth Leppert, Ms]

Dear BIC community,

This is a reminder that since our upgrade in September 2024 to the new software line on our 3T scanner (VE11c to XA30), the dicom images produced by the scanner are now in 'Enhanced Dicom' format (some info here https://sites.rutgers.edu/cahbir/siemens-enhanced-dicoms/).



As a result, it would be important to check that any software you use can correctly convert and handle this new format.



It looks as though the standard dcm2niix converter to nifti images is working properly, but please double-check for all modalities.



However, several users have noted issues with the conversion to minc (this includes the version that currently runs on the dicomserver and thus the images in /data/dicom/minc/). This can result in images not being converted at all or more subtle effects such as left-right flipping. As we work towards a more permanent solution to this issue, we are currently suggesting you convert the dicoms to nii (dcm2niix) and then back to mnc (nii2mnc). You might also consider adding a vitamin E pill next to all your participants' right temple, in order to control for any flipping.

Please note that any fixes to the dicom to minc conversion software will be done on a volunteer basis and will take time since there is no dedicated funding for minc development and maintenance available at this time. A notice to bic-announce will be made when the software is ready.

Best regards,

[neuro]

Ilana Leppert, MEng
MR Research Staff

McConnell Brain Imaging Center
The Neuro | #OpenScience
3801 University Street, Montreal, Quebec H3A 2B4

514-398-8547 theneuro.ca<http://www.theneuro.ca/>
Twitter<http://twitter.com/TheNeuro_MNI> | Facebook<https://www.facebook.com/TheNeuroMNI/> | Instagram<https://www.instagram.com/theneuro_mni/> | LinkedIn<https://ca.linkedin.com/company/the-montreal-neurological-institute> | YouTube<https://www.youtube.com/user/MontrealNeuro>
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