Hello, I am trying to run FMRIPrep on a google colab notebook but can’t seem to figure out how, any advice would be very helpful.
Hi, this is an unsupported platform for fMRIPrep. I don’t know enough about Google colab to say whether it’s even possible, but I doubt it’s a good fit.
If someone does get it working, it might be an interesting write-up, but we won’t be able to provide any support for that effort. You might consider using platforms more targeted toward large data workflows like https://brainlife.io/. I know people have used fMRIPrep there.
The Neurodesk.org project enables to run neuroimaging applications (including fmriprep) on almost any platform, including google colab
Here is a little example that shows how to run fmriprep using Neurodesk in Google Colab: Google Colab
thanks so much for this, I was wondering if you had an example which worked in generating a preprocessed BOLD nii as well?
This example creates a preprocessed BOLD nii. You find the output in the subfolder: content/sub-08/func
(It worked on my colab test)
If you don’t have this folder your execution has been interrupted (most likely because the colab notebook timed out). If you can’t finish your analysis on the free google colab accounts, you could also run your analysis on Neurodesk Play - we allow longer sessions there (make sure to select the second option “start neurodesk lab” - this will save your homedirectory across sessions):
Here is a the example for Neurodesk play: