Diff for "FsTutorial/CourseLaptopSetup"

Differences between revisions 11 and 12

Describe FsTutorial/CourseSetup_easy here.

FreeSurfer Course Setup

Notes on how to do the physical setup of the computers and stuff for the course. Also see FreesurferCourseAdminNotes

Contents

FreeSurfer Course Setup
Laptop Hardware
Laptop Software
Tutorial Data
Startup Script

Laptop Hardware

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

Laptop Software

Laptops should have the "Development Version" of freesurfer installed either locally, or via a central server.
Optional: If the course is doing the Diffusion tutorial, than laptops should have FSL installed.
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 file in the users home directory so that freesurfer is sourced automatically and other environment variable set properly.

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

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

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

## Set location of Matlab and other variable (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

-Deletions are marked like this.
+Additions are marked like this.
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  * 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.
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+== Startup Script ==

 * The following lines should be added to a {{{.bashrc}} file in the users home directory so that freesurfer is sourced automatically and other environment variable set properly.
-Line 23:
+Line 25:
- * 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).
+{{{

## Source freesurfer

export FREESURFER_HOME=<location_of_freesurfer_installation>

source $FREESURFER_HOME/SetUpFreeSurfer.sh



## Set location of tutorial location

export TUTORIAL_DATA=<location_of_tutorial_data>



## Set location of FSL (Required for Diffusion tutorial only)

export FSLDIR=<location_of_fsl_installation>



## Set location of Matlab and other variable (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

}}}