[Neuroimaging] EGAD ECAT!

[Galassi, Anthony (NIH/NIMH) [C]]

Hiya,

My co-worker reached out to Chris Markiewicz about ECAT’s and Nibabel and Chris recommended that I reach out to this email address with any questions or queries about that imaging format.

I’m currently working with OpenNeuro to integrate PET data into BIDS and our own database. Unfortunately, much (almost all) of the data that’s coming off of Siemens is in the dreaded form of ECAT. We have a handful (two) bespoke tools of our own creation that we’re using to convert some of this imaging data into nifti -> bids. But we would like to focus our efforts on better supporting libraries/packages such as Nibabel and Pybids since they’re widely adopted and well maintained already (and we’re avid users and fans).

I’m hoping that since this comment in nibabel’s ecat.py  was written something has changedr:

> There is very little documentation of the ECAT format, and many of the comments in this code come from a combination of trial and error and wild speculation.

If there are any wizend wizards about ECAT or PET we would be happy to receive any wisdom or advice they had to share. 

In the meantime we will use our limited knowledge and leet hacker skills to submit PR’s and bug fixes relating to ECAT and Nibabel as we collect and solve them.

Thank you,


Galassi, Anthony (NIH/NIMH) [C]
anthony.galassi at nih.gov
N4 Solutions, LLC