Fmriprep MNI152 3mm missing (and issues running)

[wizofe]

I am replicating a paper which is using ABIDE data registered to 3mm isotropic MNI152 template space. Unfortunately, there’s no such option on fmriprep and is missing from templateflow. I tried adding a 3mm isotropic MNI152Lin template file (T1W, brain, mask) to ~/.cache/templateflow/tpl-MNI152Lin3mm and ask fmriprep to register to this template.

The result was a bit weird though, as the final pre-processed BOLD file was 3x3x4 (mm) even though the template file was correct 3x3x3 (mm). Is there anything I am missing?

If that is resolved I would like to add this template resolution to the existing MNI152Lin template. Is that possible to use the existing GitHub repository? I had a look on your contribution documentation but it says updating template is “in progress”. Thank you!

[bwinsto2]

hey were you able to figure this out and get a 3mm working?

[jsein]

This thread may be helpful:

Unable to use custom template fMRIPrep 22.1.1

Just as an example, here I’m mounting my existing MNI152NLin6Asym directory into the Docker image: $ docker run --rm -it \ -v /home/chris/.cache/templateflow/tpl-MNI152NLin6Asym:/home/fmriprep/.cache/templateflow/tpl-MNI152NLin6Asym3mm \ --entrypoint=bash nipreps/fmriprep:22.1.1 (base) root@035e86989976:/tmp# ls -l /home/fmriprep/.cache/templateflow total 236 drwxrwxrwx 1 root root 4096 Nov 30 20:26 tpl-Fischer344 drwxrwxrwx 1 root root 4096 Nov 30 20:26 tpl-MNI152Lin …

[wizofe]

Yes I managed and this is done the way @jsein describes. A better and more inclusive solution is to publish the 3mm template on the templateflow project (which I haven’t done)