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Pipeline for preprocessing of fMRI and structural MRI scans

Home Page: http://niak.simexp-lab.org/

License: Other

Python 1.67% MATLAB 93.97% Perl 0.53% JavaScript 1.43% CSS 0.52% HTML 1.74% Shell 0.06% Dockerfile 0.09%

bids bidsapp

niak's Introduction

This BIDS app is not longer maintained.

Niak

The neuroimaging analysis kit (NIAK) is a library of pipelines for the preprocessing and mining of large functional neuroimaging data, using GNU Octave or Matlab(r), and distributed under a MIT license. This includes but is not limited to the preprocessing pipeline implemented in this app. Essential documentation can be found on the NIAK website.

In this Bids-apps

This app implements a pipeline for preprocessing structural and functional MRI datasets. You can find the full description of the NIAK fmri preprocessing pipeline here.

This pipeline first aims at reducing various noise sources that compromise the interpretation of fMRI fluctuations, e.g. physiological and motion artefacts. The second major aim is to align the data acquired at different time points and imaging modalities for a single subject, sometimes separated by years, and also to establish some correspondence between the brains of different subjects, such that an inference on the role of a given brain area can be carried at the level of a group.

How to report errors and ask questions

If the problems seems to be related to the app itself, you can always create a new issue on our github page. If is seems to come from NIAK itself, please report you issues on the NIAK github page

Usage

To run NIAK Fmri preprocessing pipeline on your bids data set:

docker run -it --rm  \
    -v /path/to/bids_dataset:/bids_dataset:ro \
    -v path_to_result_dir:/outputs  \
    bids/niak /bids_dataset /outputs participant  \
    --participant_label "XXX-YYY"

docker run -it --rm  \
    -v /path/to/bids_dataset:/bids_dataset:ro \
    -v path_to_result_dir:/outputs  bids/niak \
    /bids_dataset /outputs group  \
    --participant_label "XXX-YYY"

For more details, type:

docker run  bids/niak --help

niak's People

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niak's Issues

doc

Write better/more usage example in doc

Lack of input validation

Inside the runscript please run bids-validator on the input dataset before everything else.

Incorrect argument order

According to the minimal BIDS App spec the analysis level should be the third positional argument instead of (currently) first.

caching in circleci

/cache/sample_test
Seems not cached properly in circleci

see: https://circleci.com/gh/BIDS-Apps/niak/73

incorrect subject labels (should fail)

In your circle.yml you pass "2" as --participant_label, yet your sample dataset features only subjects with labels "0274" and "0275". What's going on?

sample_test/
sample_test/sub-0274/
sample_test/sub-0274/ses-1/
sample_test/sub-0274/ses-1/func/
sample_test/sub-0274/ses-1/func/sub-0274_ses-1_task-rest_run-2_bold.nii.gz
sample_test/sub-0274/ses-1/func/sub-0274_ses-1_task-rest_run-1_bold.nii.gz
sample_test/sub-0274/ses-1/anat/
sample_test/sub-0274/ses-1/anat/sub-0274_ses-1_T1w.nii.gz
sample_test/sub-0275/
sample_test/sub-0275/ses-1/
sample_test/sub-0275/ses-1/func/
sample_test/sub-0275/ses-1/func/sub-0275_ses-1_task-rest_run-1_bold.nii.gz
sample_test/sub-0275/ses-1/anat/
sample_test/sub-0275/ses-1/anat/sub-0275_ses-1_T1w.nii.gz
sample_test/dataset_description.json

Push to Docker Hub deployment is missing

See: https://github.com/BIDS-Apps/example/blob/master/circle.yml#L45

source files are now missing for building image

see in circle Ci: https://app.circleci.com/pipelines/github/bids-apps/niak/5/workflows/ef367062-4569-4612-bbd3-eb4e3c3d0d1d/jobs/107

Step 17/37 : RUN wget --progress=dot:giga https://sites.google.com/site/bctnet/Home/functions/BCT.zip     && unzip BCT.zip     && rm BCT.zip     && wget --progress=dot:giga https://github.com/SIMEXP/psom/archive/v${PSOM_VERSION}.zip     && unzip v${PSOM_VERSION}.zip     && rm v${PSOM_VERSION}.zip     && cd /usr/local/bin     && ln -s ../niak/extensions/psom-${PSOM_VERSION}/psom_worker.py psom_worker.py     && ln -s ../niak/extensions/psom-${PSOM_VERSION}/container/psom_image_exec_redirection.sh psom_image_exec_redirection.sh     && ln -s ../niak/util/bin/niak_cmd.py niak_cmd.py     && mkdir /scratch
 ---> Running in 82b50f1cb8c1
--2023-01-04 12:12:36--  https://sites.google.com/site/bctnet/Home/functions/BCT.zip
Resolving sites.google.com (sites.google.com)... 172.217.12.238, 2607:f8b0:4004:c09::8a, 2607:f8b0:4004:c09::64, ...
Connecting to sites.google.com (sites.google.com)|172.217.12.238|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2023-01-04 12:12:36 ERROR 404: Not Found.

The command '/bin/sh -c wget --progress=dot:giga https://sites.google.com/site/bctnet/Home/functions/BCT.zip     && unzip BCT.zip     && rm BCT.zip     && wget --progress=dot:giga https://github.com/SIMEXP/psom/archive/v${PSOM_VERSION}.zip     && unzip v${PSOM_VERSION}.zip     && rm v${PSOM_VERSION}.zip     && cd /usr/local/bin     && ln -s ../niak/extensions/psom-${PSOM_VERSION}/psom_worker.py psom_worker.py     && ln -s ../niak/extensions/psom-${PSOM_VERSION}/container/psom_image_exec_redirection.sh psom_image_exec_redirection.sh     && ln -s ../niak/util/bin/niak_cmd.py niak_cmd.py     && mkdir /scratch' returned a non-zero code: 8

Exited with code exit status 8

log.txt

Tests need to run with --read-only

See: https://github.com/BIDS-Apps/example/blob/master/circle.yml#L27

pipeline prologue

Fitting the niak preprocessing pipelines into pure individual / group stages is pretty straightforward. There is however a small component of the pipeline that does not follow this logic. The pipeline starts by copying/resampling a number of templates at the resolution requested by the user. These templates are then fed in the individual pipelines. I see two ways to implement that:

BIDS apps have a "prologue" stage before individual analyses run.
I refactor my pipeline to duplicate the generation of templates for each subject. That is a bit inefficient, but not a big deal considering the amount of other outputs generated.

@chrisfilo let me know what you think.

Please fill in the README file

See the bids/example app. In particular please add the following sections:

Description
Documentation
Error reporting
Acknowledgements

git clone --depth 1 prom/niak not working as expected in circleci

It does not clone the tip of the branch! I am bemused.

Deployment issues

There are couple of issues with deployment:

'latest' tag is pushed to docker hub for every commit instead of every new tag
Tags do not seem to trigger a build on CircleCI (maybe something to do with the new 2.0 config you switched to?) https://circleci.com/gh/BIDS-Apps/niak

As a consequence 1.0 tag is not on Docker Hub https://hub.docker.com/r/bids/niak/tags/

Example command?

Hello NIAK Bids App Administrator,

So far, I have successfully tested Niak in a Jupyter Notebook and in a terminal using the test data I pulled with the "niak_wget('data_test_niak_nii')" command. Very promising app!

Now I am ready to test the pipeline on a BIDS-validated dataset, but there isn't enough documentation to figure out how to get started. Once I pull the bids docker image, I made my best guess and ran the following command:

docker run -i --rm -v /Users/David/tmp:/bids_dataset:ro -v /Users/David/tmp/outputs:/outputs bids/niak /bids_dataset /outputs participant --participant_label 01

This returns an error as shown below:

Traceback (most recent call last):
File "/code/run.py", line 15, in
import pyniak.load_pipeline
ImportError: No module named pyniak.load_pipeline

Any ideas? Please help. Thank you.