0.4.1_6.0.1

This release has one change

• Update the Dockerfile to use FROM ubuntu:xenial instead of FROM ubuntu:trusty
• Ensures that Python 2.7.12 is used instead of Python 2.7.6
• Gives Freesurfer recon-all the python urllib3 (1.25.9) and requests (2.23.0) packages that works with Flywheel >= v12.0.0
• All top level files are shown to be exactly the same (md5 hash)
• Differences in the archive are primarily due to datestring differences between runs

0.3.1_6.0.1

UPDATES

• Upgrade FreeSurfer to v6.0.1

0.3.0

NEW

• Add support for multiple user-specified T1w input images.
• Add support for T2w input image. Note that providing a T2 input image will add -T2 <T2_ANAT_INPUT> -T2pial to the recon-all command.

0.2.0

NEW

• #16 Allows for previous output of freesurfer-recon-all gear to be used as input **, which allows a user to make some modifications, create a zip containing those modifications, and run the next stage in the processing pipeline using that zip as input***.
• Simplified license configuration. Now the key freesurfer_license can accept the license file contents, which means the user can simply copy/paste the license file content to this single field.

USAGE NOTES
** A freesurfer-recon-all gear output can be used as input, provided the filename is preserved from its initial output (e.g., freesurfer-recon-all_<subject_code>*.zip)
*** The exact stage of processing run can be configured by setting the reconall_options key within the config. For example, if you want to run autorecon3, you can modify the reconall_options key to -autorecon3.

0.1.4

FIXES

• exit status, e.g. when license information is invalid/does not exist (#14)

NEW

• no longer default to empty strings for license information
• no longer provide default subject code when a config file is present

0.1.3

NEW:

• Add cite key to manifest for citation information
• Modify ownership of $FREESURFER_HOME directory from the default ownership set in the MGH download to root:root.
• Prevent docker from doubling the size of the image as a result of ^

v0.1.2

NEW FEATURES:

• none

FIXES:

• #10 aparc stat file csv creation

FreeSurfer Recon-All v0.1.1

NEW FEATURES

• None

FIXES

• Issue #8 - spaces in input filenames and subject ids cause recon-all to crash. We now 'de-space' the input filenames and subject ID. Spaces are replaced with an underscore.

FreeSurfer Recon-All v0.1.0

NEW FEATURES

• FreeSurfer version 6.0.0
• DICOM support for input (archive or raw files)
• Matlab Compiler Runtime included (MCRv80) for optional FreeSurfer pipelines
• Configure default FreeSurfer license within manifest.json
• Hippocampal subfield processing (with results optionally exported to csv)
• Brainstem structure processing (with results optionally exported to csv)

FreeSurfer Recon-All v0.0.2

Add build-time estimate