This document describes the new features in Fsurf 2.0 and the differences from the 1.x versions.
Fsurf 2.0 adds a few new features:
- Support for running the recon-all workflow using multiple scans of the same subject. This allows FreeSurfer to correct errors in the scans due to subject movement.
- Support for running the recon-all workflow using a custom set of options. This allows users to run the recon-all workflow step by step using a specific options for each step.
- Better indications of workflow progress and information on completed workflows.
- Support for more FreeSurfer versions
Differences from Fsurf 1.x
Inputs for submission
Fsurf 2.0 changed how inputs are specified. When submitting a workflow, the inputs
must be specified using
--input. Previously, Fsurf required
that the input files have
[subject]_defaced.mri as their name. This is no longer
Fsurf 2.x and Fsurf 1.x also vary slightly in how workflow information is
displayed. Fsurf 2.x now shows the workflow progress when listing workflows.
Also when displaying information about a particular workflow (using the
command), Fsurf 2.x now gives information about workflow type, the parameters
used for that workflow, and resources used by that workflow.
Fsurf 2.x also changes a few of the terms to indicate the status of a workflow.
QUEUED instead of
UPLOADED when a workflow has been submitted.
Likewise, it uses
RUNNING instead of
PROCESSING to indicate a workflow that
is currently being run.
Support for more FreeSurfer versions
Fsurf 2.x now also supports processing workflows using FreeSurfer 5.1 and 6.0.
The default is set to FreeSurfer 5.3, but other versions can be specified using
--version=5.1.0 when submitting a workflow. E.g.
./fsurf submit --subject=MRN_3 --input=~/subjects/MRN_3_defaced.mgz --version 6.0.0