nipype_tutorial

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Binder doesn't set up the right environment

1

Hi, I wanted to complete the notebooks interactively using Binder. However, nipype don't seem to be installed in the environment as the module is not found when it should be...

celprov

I created a Singularity image with script provided in tutorial and started a jupyter-lab session on our remote research computing device. It has been working so far for many functions,...

Brainarea

I just wanted to ask if there is a specific reason why the nipype_tutorial container still runs on [SPM12 (v7219)](https://github.com/miykael/nipype_tutorial/blob/e78e3231e0fcaed6c763f35212e6d3ce064882e1/generate.sh#L14) instead of the [latest version 7771](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/)? If not, maybe this...

JohannesWiesner

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

3

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'); ```...

TamerGezici

I ran `introduction_dataset.ipynb` to download the `ds000114` dataset. Though I received some INFO messages here, the script seemed to have worked fine (or maybe this is where the bug begins?):...

JohannesWiesner

Hello all, I am trying to run example_preprocessing notebook to figure out whether if my installation is proper. I have datalad installed already. ``` %%bash datalad get -J 4 -d...

TamerGezici

BIDSDataGrabber/pybids not working as expected

1

Hi Michael, first of all - thanks for these really helpful tutorials! I managed to translate a lot of what you describe into my particular use case. Now I would...

loupl

Hi Miykael, I was going over [the basic_data_output tutorial](https://miykael.github.io/nipype_tutorial/notebooks/basic_data_output.html), and it seems like there's a mistake in the outputs of the notebook cells in the section "How to use Datasink"....

axiezai

Hi, I ran fmriprep on my own dataset, which is in BIDS format. So now have all of the preprocessing results on > derivatives/fmriprep/sub-00X/ folders. I want to use the...

orenpapers

Error with ANTS_registration.py

1

Hi Michael, Firstly, thank you for providing such a helpful guide to nipype, it is really excellent! I have been trying to use your script for ANTs registration but have...

JoffJones