Fmriprep prepocessing not successful, file not gzip

Is sbp_env your datalad environment? Because in the screenshot above it indicated you were in base

While downloading I thought I would try using both, the miniconda environment as they suggest on the website (which is base) as well as sbp_env (which is created using: conda create -n sbp_env python=3.7 anaconda) but neither of them seem to work.

Do you get the same error in the other environment?

Yes, all the file sizes are too small to be nii.gz files.

I was more asking if the error message the same in both environments?

No error message here but just the fact that it hasn’t really downloaded

image

I wonder if it has to do with git not being configured, per the first screenshot.

If I run it the first time the output looks like this

(Right now I’ve done it for another file because I cleared the output)

Running it nth time:

But the file size is still 4K

Perhaps this is something you should ping the Templateflow and/or Datalad GitHub issues about.

Just so that I and everyone with the same issue can keep track, I have submitted two issues:

1 Like

The issue has been resolved for me. Here’s what I ran:

mkdir templateflow_installation/
cd templateflow_installation/
datalad clone https://github.com/templateflow/templateflow
cd templateflow/
datalad get -r tpl-Fischer344
datalad get -r tpl-MNI152Lin
datalad get -r tpl-MNI152NLin2009aAsym
datalad get -r tpl-MNI152NLin2009aSym
datalad get -r tpl-MNI152NLin2009bAsym
datalad get -r tpl-MNI152NLin2009bSym
datalad get -r tpl-MNI152NLin2009cAsym
datalad get -r tpl-MNI152NLin2009cSym
datalad get -r tpl-MNI152NLin6Asym
datalad get -r tpl-MNI152NLin6Sym
datalad get -r tpl-MNI305
datalad get -r tpl-MNIColin27
datalad get -r tpl-MNIInfant
datalad get -r tpl-MNIPediatricAsym
datalad get -r tpl-MouseIn
datalad get -r tpl-NKI
datalad get -r tpl-NMT31Sym
datalad get -r tpl-OASIS30ANTs
datalad get -r tpl-PNC
datalad get -r tpl-RESILIENT
datalad get -r tpl-UNCInfant
datalad get -r tpl-VALiDATe29
datalad get -r tpl-WHS
datalad get -r tpl-fsLR
datalad get -r tpl-fsaverage
cd ..
mv templateflow/ $HOME/.cache/

And in my slurm script I mentioned:

export SINGULARITYENV_TEMPLATEFLOW_HOME=$HOME/.cache/templateflow

The size of the files still seem the same (4K, 24K etc.) if you use ls -sh inside tpl-MNI152NLin6Asym.

image

I suggest you just run

cd  tpl-MNI152NLin6Asym
du -hs

to see the size of the entire folder:

image

And it seems fine so, just roll with it I guess.