Overview

Note: this page covers Fsurf version 1.x and Fsurf version 2.x, places where the two versions differ are indicated through blockquotes like this or using inline text. Fsurf v1.x is the current production version and v2.x is currently in beta testing.

This page gives an overview of the commands and options that are supported by the fsurf utility. You can get general help by running ./fsurf --help and help on a specific command by running ./fsurf [command] --help. E.g. to get help on the submit command, you can run ./fsurf submit --help.

fsurf takes a single command (see below) followed by options for the command in any order. The commands that fsurf accepts are:

Command Operation
submit Submits MRI scans for processing
list Lists current and past workflows
status Gives the status of a specified workflow
output Downloads results or logs for a workflow
remove Removes an existing workflow
retry Retries a workflow that has failed
change-password Changes an user password


Command and Option summary

Command Function Required Switches Optional Switches
submit Upload and process scan --subject='[subject]'
  • --help
  • --user='[user name]'
  • --input='[path]' (Fsurf v2.x)
  • --freesurfer-options='[options]' (Fsurf v2.x)
  • --defaced
  • --deidentified
  • --dualcore
  • --version='[5.1
list List workflows submitted
  • --help
  • --user='[user name]'
  • --all-workflows
status List status of a given workflow --id='[workflow id]'
  • --help
  • --user='[user name]'
output Get output from completed workflow --id='[workflow id]'
  • --help
  • --user='[user name]'
  • --log-only
remove Remove specified workflow --id='workflow id]'
  • --help
  • --user='[user name]'
retry Retry a failed workflow --id='workflow id]'
  • --help
  • --user='[user name]'
change-password Change account password
  • --help
  • --user='[user name]'


Submit Options

Important note on data privacy: In order to protect the privacy of your participants’ scans, we request that you submit only defaced and fully deidentified scans for processing by fsurf. Images can be anonymized and deidentified before they are uploaded to OSG servers as described in the article on anonymizing images.

The submit command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--subject Name of subject to process.
--input (Fsurf v2.x) Path to input for workflow (subject directory or MRI scan).
--freesurfer-options (Fsurf v2.x) Options to pass to FreeSurfer. Arguments must be in quotes and be specifed as --freesurfer-options='-option1 -option2'.
--dualcore Use 2 cores rather than 8 for per hemisphere processing. This allow the processing to complete when 8 core systems are not available
--version Version of FreeSurfer to use for processing. Currently supports 5.1, 5.3, and 6.0 as options with 5.3 being the default.
--defaced Indicates that the scan is defaced
--deidentified Indicates that the scan is deidentified


List Options

The list command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--all-workflows List all workflows submitted rather than the workflows submitted in the last month


Status Options

The status command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--id ID of workflow to display


Output Options

The output command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--id ID of workflow to display
--log-only Only download log files for workflow


Remove Options

The remove command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--id ID of workflow to display


Retry Options

The retry command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command
--id ID of workflow to display


Change-password Options

The change-password command accepts the following options:

Option Description
--user Username to use when logging into the Fsurf service
--help Display help for command


 

This page was updated on May 21, 2018 at 01:45 from FsurfRemote/FsurfCommands.md.