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What would you like changed/added and why?

Pages https://github.com/nipreps and https://nipy.org/contribute.html contain a link to nipy.discourse.group.

This doesn't look like a valid DNS name.

Do you have any interest in helping improve the documentation?

Yes

Do you have any suggestions for the new documents?

Should I use the nipy tag on NeuroStars instead?

What would you like to see added in this software?

As discussed in the meeting of 02/21/2023.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

No response

What would you like to see added in this software?

See how to enable permalinks here - https://www.mkdocs.org/user-guide/writing-your-docs/

Then, make sure we have this set up for the news section.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

No response

My latest PR fails because the build image is no longer supported.
https://app.netlify.com/sites/vigorous-brahmagupta-fd6bf1/deploys/63ea4891d59e4200087702c1

The build image can upgraded to the latest build image in the Netlify UI under Site settings > Build & deploy > Continuous Deployment > Build image selection as described in https://answers.netlify.com/t/please-read-end-of-support-for-xenial-build-image-everything-you-need-to-know/68239.

cc/ @esavary

Open a new section in the documentation, that shows the guidelines and principles to contribute to fMRIPREP, and also gives finer detail on technical aspects of fmriprep.

In particular, and following @TimVanMourik's open review comment (http://preprint.space/openreviewers/0000-0002-8155-8641), fMRIPrep should describe its primarily features more clearly and in detail:

• Automatic data type recognition
• Rich support of data types
• Rich visual performance feedback
• Increased performance by best-in-breed approach.

Secure access to each project’s Roadmap document (as specified by the governance)

(cross-posted from templateflow org)

• Public profiles for reference of researchers
• Temporary profiles for peer-reviewers during the submission process of new templates

• Maintain a table of conference communications, educational materials, papers, etc)
• Make the index accessible on the NiPreps website.

Update the documentation about docker to include this issue, reported through the mailing list. The solution is:

service docker stop
dockerd --storage-opt dm.basesize=30G

• Implement a news and announcements section
• Ensure access from the main website to the documentation pages of every subproject
• Implement a new section about DEI
• Update the contributing guidelines with the new governance structure

• Approach: based on the experience organizing prior hackathons, and with the support of the new hire, the local organizers of ISBI 2023 will be contacted to secure a venue (e.g., a classroom in a nearby university) immediately before or after the event. Then the event will be announced with sufficient time for the conference attendees from abroad to arrange their travel (which will not be covered by this grant). The new engineer/manager will also be in charge of promoting the event through appropriate channels and establishing some participant registration process.
• Target audience: 15-20 graduate students, postdocs, and research engineers with a foundational knowledge of Python and interests in neuroscience, computer vision, or neuroimaging with a special focus on the latinx community, leveraging the geographic location of the conference.
• Expected outcomes: (i) engagement of new contributors to the NiPreps community; (ii) training of participants with git, Python, and neuroimaging software; (iii) targetted advances on the roadmap of NiPreps’ projects.

What would you like changed/added and why?

Hi
I needed to run mriqc on a cluster that does not allow an internet connection (OSLO university TSD)
However, the mriqc documentation does not provide any info (at least as far I could see) on how to do this or where to find relevant information.

The latter I found on: https://www.nipreps.org/apps/singularity/#templateflow-and-singularity

Maybe the documentation could have a subsection under "Running mriqc on HPC clusters", e.g., "running mriqc in singularity on clusters without or restricted internet connection," and link to https://www.nipreps.org/apps/singularity/#templateflow-and-singularity

In my case, the following steps did the trick:

1. get the templateflow data on a local cluster/computer

In terminal run:

export TEMPLATEFLOW_HOME=/path/to/keep/templateflow
python -m pip install -U templateflow # Install the client
python

import templateflow.api
templateflow.api.TF_S3_ROOT = 'http://templateflow.s3.amazonaws.com'
templateflow.api.get(‘MNI152NLin2009cAsym’)

2. create a tarfile

cd /path/to/keep
tar -cvf templateflow.tar templateflow/*

3. transfer tarfile to the remote cluster

4. untar tarfile

mkdir -p $HOME/.cache/
cp tarfile $HOME/.cache

tar xvf templateflow.tar

5. Example singularity setup.

export SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow

singularity run --cleanenv --contain
-B ${TEMPLATEFLOW_HOME:-$HOME/.cache/templateflow}:/templateflow
-B ${BIDS_DIR_TMP}/:/data_in
-B ${SCRIPTS_DIR}/:${SCRIPTS_DIR}
-B ${DERIV_DIR}/:/data_out
-B ${WORK_DIR}/:/work
-B /tmp:/tmp
${mriqc_sif}
/data_in
/data_out
participant
-w /work
--participant-label ${sub}
--mem_gb ${mem}
--float32
--nprocs ${SLURM_CPUS_PER_TASK}
--ants-nthreads ${SLURM_CPUS_PER_TASK}
--verbose-reports
--no-sub
-vv

Do you have any interest in helping improve the documentation?

No

Do you have any suggestions for the new documents?

Maybe add a subsection under "Running mriqc on HPC clusters", e.g., "running mriqc in singularity on clusters without or restricted internet connection," and link to https://www.nipreps.org/apps/singularity/#templateflow-and-singularity