Diff for "FsTutorial/CourseLaptopSetup"

Differences between revisions 1 and 32 (spanning 31 versions)

FreeSurfer Course Setup

This purpose of this page is to describe how one would go about setting up laptops (or workstations) for a Freesurfer course.

Contents

FreeSurfer Course Setup
Hardware
Software
Tutorial Data
Startup Script
Testing

Hardware

Laptops/workstations should have hardware which meet or exceed the recommended System Requirements for running freesurfer.
Laptops/workstations should have internet access. (For following course tutorials and performing last minute updates of the data set)
In addition to the listed System Requirements, laptops should have 17" screens to facilitate viewing of images on the screen.

Software

Laptops/workstations should have the Development Version of freesurfer installed either locally, or via a central server.
Laptops/workstations should have a recent versions of FSL installed either locally, or via a central server. FSL is required for the Diffusion and TRACULA tutorials.
Optional: If the course is doing the FSFAST tutorial, than laptops should have the Matlab runtime installed (version 8.3, no license required). However, the commands requiring Matlab have been marked and can be skipped because the output data has already been provided. So Matlab is not an absolute requirement.

Tutorial Data

Laptops should have access to the "Lightweight" version of freesurfer tutorial data either downloaded locally, or via a central server, or external storage device (thumb drive, external hard drive, etc). Note that it is important for each laptop to have access its own sandboxed version of the data, with read/write access, because course participants will be creating files within their workspace.

Startup Script

The following lines should be added to a .bashrc file in the users home directory so that freesurfer is automatically sourced (and other environment variables set) whenever a terminal window is opened.

## Set location of tutorial location
export TUTORIAL_DATA=<location_of_tutorial_data>

## Set location of FSL (Required for Diffusion and TRACULA tutorials only)
export FSLDIR=<location_of_fsl_installation>

## Set location of Matlab and other Matlab/FSFAST related variables (Required for FSFAST tutorial only)
export FS_MCRROOT=<location_of_matlab_installation>
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/runtime/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/bin/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/sys/os/glnxa64" 
export FS_SPMREG_USE_BIN=1
export FS_MKCON_USE_BIN=1
export FS_SXA3_USE_BIN=1

## Source freesurfer
export FREESURFER_HOME=<location_of_freesurfer_installation>
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Testing

Once the steps above have been taken, the best an most reliable way to test your setup is simply to run thru one or more of the tutorials.
A more automated way to test your setup is to run the test_tutorials.sh script. This script comes with freesurfer and can be run in the following ways:

  ## Run a quick test  
  $> test_tutorials.sh -quick
  
  ## If the above command runs to completion without crashing than your probably all set.

  ## Run the Multi-Modal Integration tutorial
  $> test_tutorials.sh -multimodal

  ## Run the TRACULA tutorial
  $> test_tutorials.sh -tracula

  ## Display help and other options
  $> test_tutorials.sh -help

-  ⇤ ← Revision 1 as of 2016-04-21 13:58:08 → 
  Size: 1815
  Editor: ZekeKaufman
  Comment:
+   ← Revision 32 as of 2016-04-21 17:03:23 → ⇥
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  Editor: ZekeKaufman
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-Describe FsTutorial/CourseSetup_easy here.
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+Line 2:
-Notes on how to do the physical setup of the computers and stuff for the course.  Also see [[FreesurferCourseAdminNotes]]
+This purpose of this page is to describe how one would go about setting up laptops (or workstations) for a Freesurfer course.
-Line 8:
+Line 6:
-=== Laptop Setup ===
 * Laptops should meet or exceed the recommended [[SystemRequirements|system requirements]].
 * Laptops should have internet access. (For following course tutorials and performing last minute updates of the data set)
 * Laptops should have the [[Download|"Development Version"]] of freesurfer installed either locally, or via a central server.
+== Hardware ==
 * Laptops/workstations should have hardware which meet or exceed the recommended [[SystemRequirements|System Requirements]] for running freesurfer.
 * Laptops/workstations should have internet access. (For following course tutorials and performing last minute updates of the data set)
 * In addition to the listed System Requirements, laptops should have 17" screens to facilitate viewing of images on the screen.
-Line 13:
+Line 11:
-=== Tutorial Data ===
 * Laptops should have the "Leightweight" version of freesurfer [[Data|tutorial data]] installed either locally or via a central server. Note that it is important for each laptop to have access its own sandboxed version of the data, with read/write access, because course participants will be creating files within their workspace.
+== Software ==
 * Laptops/workstations should have the [[Download|Development Version]] of freesurfer installed either locally, or via a central server.
 * Laptops/workstations should have a recent versions of [[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation|FSL]] installed either locally, or via a central server. FSL is required for the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion|Diffusion]] and [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula|TRACULA]] tutorials.
 * ''Optional:'' If the course is doing the [[FsFastTutorial|FSFAST]] tutorial, than laptops should have the [[http://www.mathworks.com/products/compiler/mcr/|Matlab runtime]] installed (version 8.3, no license required). However, the commands requiring Matlab have been marked and can be skipped because the output data has already been provided. So Matlab is not an absolute requirement.
 Line 17:
- * Equipment consists of:
  * 4-5 boxes of laptops, 19 laptops in total, each with a power-supply, and mouse (plus USB hard disk if old setup).
    * Laptops nmrclass7-18, external hard-disks, mice, power-supplies and wireless router are kept in the 'Savoy' cabinet in south central.
    * Laptops nmrclass 19-27 are found in the storage closet at the end of the 2nd floor hall past the brain map room (these laptops are 'owned' and maintained by the Fischl group, while Stacey maintains the laptops7-18, which are 'owned' by R. Savoy).
  * box of ethernet cables, and white wireless router box, and 8 port switch, and 5 and 4 port ethernet hubs.
  * box containing two 24 port ethernet switches, and 'suez': the mac mini for streaming data.
  * box of power cables and outlet strips (note: there are some extra surge protector strips at nicks desk).
+== Tutorial Data ==
 * Laptops should have access to the "Lightweight" version of freesurfer [[FsTutorial/Data|tutorial data]] either downloaded locally, or via a central server, or external storage device (thumb drive, external hard drive, etc). Note that it is important for each laptop to have access its own sandboxed version of the data, with read/write access, because course participants will be creating files within their workspace.

== Startup Script ==
 * The following lines should be added to a {{{.bashrc}}} file in the users home directory so that freesurfer is automatically sourced (and other environment variables set) whenever a terminal window is opened.

{{{

## Set location of tutorial location
export TUTORIAL_DATA=<location_of_tutorial_data>

## Set location of FSL (Required for Diffusion and TRACULA tutorials only)
export FSLDIR=<location_of_fsl_installation>

## Set location of Matlab and other Matlab/FSFAST related variables (Required for FSFAST tutorial only)
export FS_MCRROOT=<location_of_matlab_installation>
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/runtime/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/bin/glnxa64"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$FS_MCRROOT/sys/os/glnxa64" 
export FS_SPMREG_USE_BIN=1
export FS_MKCON_USE_BIN=1
export FS_SXA3_USE_BIN=1

## Source freesurfer
export FREESURFER_HOME=<location_of_freesurfer_installation>
source $FREESURFER_HOME/SetUpFreeSurfer.sh

}}}

== Testing ==
 * Once the steps above have been taken, the best an most reliable way to test your setup is simply to run thru one or more of the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|tutorials]].
 * A more automated way to test your setup is to run the {{{test_tutorials.sh}}} script. This script comes with freesurfer and can be run in the following ways:

{{{
  ## Run a quick test  
  $> test_tutorials.sh -quick
  
  ## If the above command runs to completion without crashing than your probably all set.

  ## Run the Multi-Modal Integration tutorial
  $> test_tutorials.sh -multimodal

  ## Run the TRACULA tutorial
  $> test_tutorials.sh -tracula

  ## Display help and other options
  $> test_tutorials.sh -help
}}}