Difference between revisions of "Freesurfer"

From UFRC
Jump to navigation Jump to search
 
(21 intermediate revisions by 5 users not shown)
Line 1: Line 1:
==Environment Variables==
+
[[Category:Software]][[Category:Bioinformatics]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
In order for Freesurfer to work, the followings environment variables need to be set:
+
{|<!--CONFIGURATION: REQUIRED-->
 +
|{{#vardefine:app|freesurfer}}
 +
|{{#vardefine:url|http://surfer.nmr.mgh.harvard.edu/}}
 +
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 +
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 +
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 +
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 +
|{{#vardefine:policy|}}        <!--POLICY-->
 +
|{{#vardefine:testing|}}      <!--PROFILING-->
 +
|{{#vardefine:faq|}}            <!--FAQ-->
 +
|{{#vardefine:citation|1}}      <!--CITATION-->
 +
|{{#vardefine:installation|}} <!--INSTALLATION-->
 +
|}
 +
<!--BODY-->
 +
<!--Description-->
 +
{{#if: {{#var: url}}|
 +
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
In bash:
+
Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.<!--Modules-->
<pre>
+
==Environment Modules==
$ export FREESURFER_HOME=/apps/freesurfer
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
+
==System Variables==
</pre>
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
In tcsh:
+
 
<pre>
+
<!--Configuration-->
$ setenv FREESURFER_HOME /apps/freesurfer
+
{{#if: {{#var: conf}}|==Configuration==
$ source $FREESURFER_HOME/SetUpFreeSurfer.csh
+
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
</pre>
+
|}}
 +
<!--Run-->
 +
{{#if: {{#var: exe}}|==Additional Information==
 +
Starting with freesurfer/6.0.0 the software is available as a Singularity container. To run any executable use the 'launch_freesurfer' wrapper after loading the module.
 +
 
 +
E.g.
 +
 
 +
launch_freesurfer dcmunpack
 +
 
 +
'''NOTE:'''
 +
 
 +
Freesurfer comes with Freeview software. Freeview is a completely separate software from Freesurfer and is used purely for data visualization. Freesurfer 6 includes Freeview 2.0.
 +
 
 +
|}}
 +
<!--PBS scripts-->
 +
{{#if: {{#var: pbs}}|==PBS Script Examples==
 +
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
 +
|}}
 +
<!--Policy-->
 +
{{#if: {{#var: policy}}|==Usage Policy==
 +
WRITE USAGE POLICY HERE (Licensing, usage, access).
 +
|}}
 +
<!--Performance-->
 +
{{#if: {{#var: testing}}|==Performance==
 +
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 +
|}}
 +
<!--Faq-->
 +
{{#if: {{#var: faq}}|==FAQ==
 +
*'''Q:''' **'''A:'''|}}
 +
<!--Citation-->
 +
{{#if: {{#var: citation}}|==Citation==
 +
If you publish research that uses {{#var:app}} you have to cite it as follows:
 +
 
 +
See [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation] in the Freesurfer wiki on how to correctly cite Freesurfer tools.
 +
|}}
 +
<!--Installation-->
 +
{{#if: {{#var: installation}}|==Installation==
 +
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 +
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 +
__NOTOC____NOEDITSECTION__

Latest revision as of 20:44, 10 June 2022

Description

freesurfer website  

Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

Environment Modules

Run module spider freesurfer to find out what environment modules are available for this application.

System Variables

  • HPC_FREESURFER_DIR - installation directory


Additional Information

Starting with freesurfer/6.0.0 the software is available as a Singularity container. To run any executable use the 'launch_freesurfer' wrapper after loading the module.

E.g.

launch_freesurfer dcmunpack

NOTE:

Freesurfer comes with Freeview software. Freeview is a completely separate software from Freesurfer and is used purely for data visualization. Freesurfer 6 includes Freeview 2.0.



Citation

If you publish research that uses freesurfer you have to cite it as follows:

See [1] in the Freesurfer wiki on how to correctly cite Freesurfer tools.