1.2.1_7.2.0

Full Changelog: 1.1.2_7.2.0...1.2.1_7.2.0

• Changed "master" branch to "hpc" (still in development)
• Created "main" branch to be new default branch
• Bumped version so this will be the latest

Impact on gear function: none

1.1.2_7.2.0

What's Changed

• re-patch recon-all to avoid "Cannot find rh.white.H" race condition @AndysWorth (#11)

Impact On Gear Output

No changes to output except that there will be output instead of nothing sometimes

1.1.1_7.2.0

added fs version to release

1.1.1

Upgraded from Freesurfer 7.1 to 7.2, added Hyopthalmic Subunit segmentation option, added post-processing only option

What's Changed

• Runs FS v 7.2.0
• Has an option to run hypothalmic subunit segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits)
• Has an option to run post-processing only (if recon-all has already been run, the output .zip file can be passed in and any selected post-processing steps will be carried out)

Impact On Gear Output

• structure is the same, output will have additional files and metadata for hypothalmic subunits if selected.

1.1.0_7.1.1

What's Changed

ENH: Added option to perform Segmentation of thalamic nuclei after recon-all
ENH: Added ability to use the Expert Options File
FIX: for -parallel crash at the cortical ribbon mask stage
ENH: Add optional call to gtmseg
FIX: for "Cannot find rh.white.H" when used with -parallel option.

@AndysWorth (#7)

Impact On Gear Output

This release does not change existing outputs but it does add some extra outputs. See the README for a description of each option that was added.

1.0.0_7.1.1

What's Changed

• Merged 1.0.0 7.1.1 @AndysWorth (#3). Removed "_rc0" from the version
• Now using latest Flywheel SDK version 14.5.0.

Impact On Gear Output

None (gear function was not changed since the release candidate version).

1.0.0_7.1.1_rc0

Initial release candidate for Freesurfer recon-all version 7.1.1

What's Changed

This initial release duplicates the functionality of the old freesurfer-recon-all gear and adds:

• Retry on failure: using -parallel fails randomly and re-running recon-all should complete successfully.
• Volumes and areas from spreadsheets are now attached as metadata ("Custom Information" or "info") on the analysis container.

Impact On Gear Output

• Files are the same
• Now there is metadata for volumes and areas.

0.1.0_7.1.1_rc0

Initial release candidate for Freesurfer recon-all version 7.1.1

What's Changed

This initial release duplicates the functionality of the old freesurfer-recon-all gear and adds:

• Retry on failure: using -parallel fails randomly and re-running recon-all should complete successfully.
• Volumes and areas from spreadsheets are now attached as metadata ("Custom Information" or "info") on the analysis container.

Impact On Gear Output

• Files are the same
• Now there is metadata for volumes and areas.