FileNotFoundError: No such file or no access: 'sub-01_t1w_preproc.nii.gz'

[TamerGezici]

I am running the tutorial dockerfile and I ran into an issue like this at the example_preprocessing notebook.

While executing cell:

plotting.plot_epi(
    '/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz',
    title="T1", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');

FileNotFoundError: No such file or no access: '/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz'

The file is there, I checked.

[JohannesWiesner]

Did you ran introduction.ipynb before that? I think I stumpled upon the same FileNotFoundError but it's important to run this script before

[TamerGezici]

Did you ran introduction.ipynb before that? I think I stumpled upon the same FileNotFoundError but it's important to run this script before

Hi. Thanks a lot for your answer. I actually haven't so this could be why.

There is no single notebook called "introduction" but several with the prefix "introduction" is it the one called "introduction_dataset" that I should be running?

[JohannesWiesner]

Yes, you're right, I meant introduction_dataset.ipynb. Put please take this with a grain of salt I could also be wrong here (also trying out this tutorial for the first time). From the homepage it looks like one could directly start with example_preprocessing.ipynb but as you read the first lines of example_preprocessing.ipynbone already sees that introduction_dataset.ipynb has to be run before that (took me a while to find that out):

Preparation Before we can start with anything we first need to download the data (the other 9 subjects in the dataset). This can be done very quickly with the following datalad command.

Note: This might take a while, as datalad needs to download ~700MB of data

%%bash datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/preproc.nii.gz
/data/ds000114/sub-/ses-test/func/fingerfootlips