I’m trying to use bidskit to convert dicom data to bids format, and have an issue.
I installed bidskit with
sudo pip3 install bidskit
and then when I ran it, I got this message.
Check dcm2nixx version
dcm2niix v1.0.20211006 detected - please update to v1.0.20220720 or later
so I updated dcm2niix with
sudo apt-get install dcm2niix
dcm2niix is already the newest version (1.0.20211006-1build1).
0 upgraded, 0 newly installed, 0 to remove and 113 not upgraded.
So I installed the latest dcm2niix separately, but the error message from Bidskit didn’t change.
I’m using ubuntu on Windows.
Is there anyone exprience the same issue?
Thank you very much in advance!
Sounds like an environment issue. Is
bidskit installed in a certain environment, like with
conda? If so, you can update dcm2niix in that environment (probably with
pip as well). I am guessing that whatever is in your environment is superceeding the one you are installing with
Alternatively, maybe dcm2niix is installed in the Docker container Docker
Updating dcm2niix with pip worked!
You can always find the latest stable release of dcm2niix here, currently v1.0.20230411. Note that Debian systems tend to freeze software at the time of release. The BIDS, DICOM and manufacturers interpretation of DICOM are all evolving rapidly, so I would make sure you ensure you have the latest stable release (in particular if you have a Siemens scanner that was upgraded to XA).