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View Code? Open in Web Editor NEWPipeline for preprocessing of fMRI and structural MRI scans
Home Page: http://niak.simexp-lab.org/
License: Other
Pipeline for preprocessing of fMRI and structural MRI scans
Home Page: http://niak.simexp-lab.org/
License: Other
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:
@chrisfilo let me know what you think.
Inside the runscript please run bids-validator on the input dataset before everything else.
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.
There are couple of issues with deployment:
As a consequence 1.0 tag is not on Docker Hub https://hub.docker.com/r/bids/niak/tags/
It does not clone the tip of the branch! I am bemused.
See the bids/example app. In particular please add the following sections:
Write better/more usage example in doc
/cache/sample_test
Seems not cached properly in circleci
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
According to the minimal BIDS App spec the analysis level should be the third positional argument instead of (currently) first.
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
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