1.4.3_23.0.1

What's Changed

Updated to latest current version of fMRIPrep 23.0.1

Fixes

• Set default of gear-log-to-file to true because even small data sets exceed log threshold and logs would be lost
• Fixed tests to work with new version of fMRIPrep

Enhancements

• Update fMRIPrep to 23.0.1

Impact On Gear Output

The logged output of fMRIPrep will no longer show up in the gear log because it is going to a file (log1.txt or log2.txt depending on how many times fMRIPrep was attempted).

1.4.2_20.2.7

What's Changed

Add ability to save output in two zip files instead of one. Fixed some bugs introduced by updating to newer libraries.

Fixes

• rm gear-keep-ouput config option which breaks gear because of too many outputs
• saving of resources used (metadata)
• tests to work with poetry in PyCharm debugger
• rm poetry from containers
• working on HPC again

Enhancements

• add gear-save-output-as-subfolders config and tests
• add python 3.8 for gear code, insulating gear environment from fMRIPrep environment

Impact On Gear Output

• format of output is changed if gear-save-output-as-subfolders is used

1.4.1_20.2.7

What's Changed

Created a new "main" branch to hold common gear code as multiple versions of fMRIPrep are being supported in ongoing branches.

Fixes

• Sorted manifest.json
• Tests now working in poetry
• Add new way of setting os_cpu_count using os.sched_getaffinity()
• black formatting

Enhancements

• Upgraded to fMRIPrep 20.2.7

Impact On Gear Output

None

1.2.14_20.2.6

What's Changed

Fixes

• properly returns 0 on success
• will not re-run if first run succeeded
• instantiates gtk_context twice (necessary for running on HPCs)

Enhancements

• add gear-log-to-file option: puts log into a file instead of streaming it. Excessive logging of long jobs can cause gear to fail.

Impact On Gear Output

None

1.3.2_21.0.1

fixed typo in manifest
testing docker build
Verified that tag is off main_v21.0.1 brach

1.2.8_20.2.6

What's Changed

Fixes

• no longer runs in /tmp unless /flywheel/v0 is not writable. In that case, runs in directory provided by new config option gear-writable-dir which must be set when running in Singularity.
• copies templateflow templates from default location to where the gear is running which is now guaranteed to be a writable directory even when running in Singularity. This is necessary for when templates need to be downloaded. Original attempt was to just link to the default templates, but that caused fMRIPrep to make templates zero length.
• added extra debugging output
• updated tests

Enhancements

• now re-tries running fMRIPrep on first failure
• bids-fmriprep can fail if it is run with insufficient or competition for hardware resources. The script notebooks/rerun-fmriprep.py will re-run a job that failed and by providing it with the results of the failed job, some of that work will not need to be repeated.

Impact On Gear Output

The output of the gear did not change. The gear now will not fail if a transitory resource failure has occurred. This gear should run more reliably in HPCs/Singularity.

1.2.4_20.2.6

What's Changed

Fixes

• Won't download TemplateFlow templates because they are already baked in to the Docker image

Impact On Gear Output

• No time/bandwidth wasted downloading templates

1.2.3_20.2.6

What's Changed

Fixes

• fs-subject-dir: subject directory gets put in proper place
• Name "bids-fmriprep" now appears in bids_tree.html properly

Enhancements

• Update to fMRIPrep 20.2.6
• Add bids-filter-file input
• Add previous-results input to provide previous output as input to run fMRIPrep incrementally
• Add code to handle --work-dir input, but didn't include that option in the manifest because it doesn't work yet
• Add running GNU "time" command and save resource usage as metadata
• Add and update tests for the new features

Impact On Gear Output

• Additional metadata on analysis container
• additional log output in debug mode

Full Changelog: 1.2.2_20.2.6...1.2.3_20.2.6

1.2.2_20.2.6

Fixes

• Fix how mem_mb is converted and passed to fmriprep

1.2.1_20.2.6

What’s Changed

Fixes

• no longer tries to remove previous runs which caused a permission error

Enhancements

• update to latest fMRIPrep version 20.2.6

• add --fs-subjects-dir

Impact On Gear Output

None (except for fixes due to using latest fMRIPrep)