FreeSurfer - Revision history

Bhickson@uab.edu: /* Track status of job */

2016-11-18T17:29:52Z

Track status of job

← Older revision		Revision as of 17:29, 18 November 2016
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	==== Track status of job ====		==== Track status of job ====

	Check on the job status with ~~qstat~~.		Check on the job status with squeue.
	<pre>		<pre>
	~~qstat~~ -u $USER		squeue -u $USER
	</pre>		</pre>

Bhickson@uab.edu: /* SSH-key Config */

2016-11-18T17:19:33Z

SSH-key Config

← Older revision		Revision as of 17:19, 18 November 2016
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	[http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#SSH_Keys Configure putty] to connect to Cheaha with ssh-keys.		[http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#SSH_Keys Configure putty] to connect to Cheaha with ssh-keys.

	Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Linux this link] for ssh key config on ~~linux~~.		Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Linux this link] for ssh key config on Linux.

	Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Mac this link] for ssh key config on ~~mac~~.		Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Mac this link] for ssh key config on Mac.

	=== Environment Setup ===		=== Environment Setup ===

Bhickson@uab.edu: /* FreeSurfer on Cheaha */

2016-11-18T17:18:43Z

FreeSurfer on Cheaha

← Older revision		Revision as of 17:18, 18 November 2016
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	== FreeSurfer on Cheaha ==		== FreeSurfer on Cheaha ==
	~~FreeSurfer-4.5 and~~ FreeSurfer-5.3 ~~versions are~~ installed on Cheaha. ''module'' command can be used to find out the current(latest) installed version. For ~~Freesurfer~~, use		FreeSurfer-5.3 is installed on Cheaha. ''module'' command can be used to find out the current (latest) installed version. For FreeSurfer, use
	<pre>		<pre>
	module whatis ~~freesurfer~~		module whatis FreeSurfer
	</pre>		</pre>

	FreeSurfer ~~run~~ its process in a non-parallel environment, so there won't be much benefit from a dual/quad/hex core machine for a single case analysis. However a number of FreeSurfer recon-all processes can be started in the same machine, thereby, theoretically reducing the time to analyze a group of cases. Following is a tutorial to setup your ~~Freesurfer~~ environment and to run an example recon-all process on Cheaha.		FreeSurfer runs its process in a non-parallel environment, so there won't be much benefit from a dual/quad/hex core machine for a single case analysis. However, a number of FreeSurfer recon-all processes can be started in the same machine, thereby, theoretically reducing the time to analyze a group of cases. Following is a tutorial to setup your FreeSurfer environment and to run an example recon-all process on Cheaha.

	=== SSH-key Config ===		=== SSH-key Config ===
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	</pre>		</pre>

	A lot of environment variables are set up, when you load ~~freesurfer~~ module, such as:		A lot of environment variables are set up, when you load FreeSurfer module, such as:
	<pre>		<pre>
	FREESURFER_HOME=/share/apps/freesurfer/5.3.0		FREESURFER_HOME=/share/apps/freesurfer/5.3.0

Bhickson@uab.edu: /* Example recon_all */

2016-11-16T16:14:43Z

Example recon_all

← Older revision		Revision as of 16:14, 16 November 2016
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	<pre>		<pre>
	wget http://repo.~~uabgrid~~.uab.edu/files/freesurfer/example.nii.gz		wget http://repo.rc.uab.edu/files/freesurfer/example.nii.gz

	gunzip example.nii.gz		gunzip example.nii.gz

Bhickson@uab.edu: /* Environment Setup */

2016-10-28T18:32:23Z

Environment Setup

← Older revision		Revision as of 18:32, 28 October 2016
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	For setting up an environment to run FreeSurfer on Cheaha, you need to load it's module to your environment:		For setting up an environment to run FreeSurfer on Cheaha, you need to load it's module to your environment:
	<pre>		<pre>
	module load freesurfer/freesurfer-5.3.0		module load rc/freesurfer/freesurfer-5.3.0
	</pre>		</pre>

Ravi89@uab.edu: Updating version information

2016-06-30T16:53:54Z

Updating version information

← Older revision		Revision as of 16:53, 30 June 2016
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	# Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions.		# Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions.

	The [http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes latest version of Freesurfer available is 5.1.0]. The last update to this software was ~~24 May 2011~~.		The [http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes latest version of Freesurfer available is 5.3.0]. The last update to this software was 2 March 2013.

	== FreeSurfer on Cheaha ==		== FreeSurfer on Cheaha ==

Ravi89@uab.edu: Removing .bashrc portion and adding information about QA_Tools

2016-06-30T16:52:15Z

Removing .bashrc portion and adding information about QA_Tools

← Older revision		Revision as of 16:52, 30 June 2016
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	=== Environment Setup ===		=== Environment Setup ===

	~~Setting~~ up an environment to run FreeSurfer on Cheaha, ~~consists of defining FreeSurfer related variables and their installation paths. Steps 1 and 2 are a one-time set up, ie., the first time~~ you ~~login~~ to ~~Cheaha. Need not set up and source env variables defined in .bashrc from the next time you login~~ to ~~Cheaha (as at login bashrc is auto-sourced).~~		For setting up an environment to run FreeSurfer on Cheaha, you need to load it's module to your environment:

	~~1. To set up~~ your environment ~~on Cheaha, open $HOME/.bashrc with your favorite text editor such as vim, nano, emacs etc., and copy-paste the contents below~~:
	<pre>		<pre>
	~~export FREESURFER_HOME=/share/apps~~/freesurfer/4.5		module load freesurfer/freesurfer-5.3.0
	~~source $FREESURFER_HOME/SetUpFreeSurfer~~.sh
	~~export FSFAST_HOME=$FREESURFER_HOME/fsfast~~
	~~export FSF_OUTPUT_FORMAT=nii~~
	~~export MNI_DIR=$FREESURFER_HOME/mni~~
	~~export FSL_DIR=$HOME/fsl~~
	~~export PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$MNI_DIR/bin:$FSL_DIR/bin:$PATH~~
	</pre>		</pre>
	NOTE: In the above bashrc, FSL_DIR is also defined. FSL is not part of FreeSurfer, but is installed and available to all users on Cheaha. To start using FSL/bedpostx [http://docs.uabgrid.uab.edu/wiki/FSL see this documentation.]

	~~2. Source the above~~ environment variables.		A lot of environment variables are set up, when you load freesurfer module, such as:
	<pre>		<pre>
	~~source~~ $HOME/.~~bashrc~~		FREESURFER_HOME=/share/apps/freesurfer/5.3.0
			FSFAST_HOME=$FREESURFER_HOME/fsfast
			FUNCTIONALS_DIR=$FREESURFER_HOME/sessions
			FSF_OUTPUT_FORMAT=nii
			MNI_DIR=/share/apps/freesurfer/5.3.0/mni
			MINC_BIN_DIR=$FREESURFER_HOME/mni/bin
			MINC_LIB_DIR=$FREESURFER_HOME/mni/lib
			MNI_DATAPATH=$FREESURFER_HOME/mni/data
			FSL_DIR=$HOME/fsl
			PERL5LIB $FREESURFER_HOME/mni/lib/perl5/5.8.5
			FS_OVERRIDE 0
			FMRI_ANALYSIS_DIR $FREESURFER_HOME/fsfast
			PATH $FREESURFER_HOME/bin:$FREESURFER_HOME/fsfast/bin:$FREESURFER_HOME/mni/bin:/share/apps/freesurfer/QA_TOOLS
			QA_TOOLS /share/apps/freesurfer/QA_TOOLS
	</pre>		</pre>

			NOTE:
			* FSL_DIR is also defined when you load FreeSurfer module. FSL is not part of FreeSurfer, but is installed and available to all users on Cheaha. To start using FSL/bedpostx [http://docs.uabgrid.uab.edu/wiki/FSL see this documentation.]
			* QA_TOOLS are also included, which are intended to be used in assessing the quality of one or more FreeSurfer recons. To use QA_TOOLS [https://surfer.nmr.mgh.harvard.edu/fswiki/QATools see this documentation.]

	=== Example recon_all ===		=== Example recon_all ===

Ravi89@uab.edu: Updating this section to include v5.3 in thedocumentation as well

2016-06-30T16:31:03Z

Updating this section to include v5.3 in thedocumentation as well

← Older revision		Revision as of 16:31, 30 June 2016
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	== FreeSurfer on Cheaha ==		== FreeSurfer on Cheaha ==
	FreeSurfer-4.5 ~~version is~~ installed on Cheaha. ''module'' command can be used to find out the current installed version. For Freesurfer, use		FreeSurfer-4.5 and FreeSurfer-5.3 versions are installed on Cheaha. ''module'' command can be used to find out the current(latest) installed version. For Freesurfer, use
	<pre>		<pre>
	module whatis freesurfer		module whatis freesurfer

Mhanby@uab.edu: replaced all references to $UABGRID_SCRATCH with $USER_SCRATCH

2013-05-22T19:32:38Z

replaced all references to $UABGRID_SCRATCH with $USER_SCRATCH

← Older revision		Revision as of 19:32, 22 May 2013
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	==== Create job submission script ====		==== Create job submission script ====

	This is a simple SGE script to submit recon-all process. This script first copies your subjects directory from your $HOME containing the MRI data to Cheaha's high performance file system, $~~UABGRID_SCRATCH~~, so as to ramp the speed of recon-all process. The recon-all process is then executed on $~~UABGRID_SCRATCH~~.		This is a simple SGE script to submit recon-all process. This script first copies your subjects directory from your $HOME containing the MRI data to Cheaha's high performance file system, $USER_SCRATCH, so as to ramp the speed of recon-all process. The recon-all process is then executed on $USER_SCRATCH.

	NOTE: For the example run, we've created a subjects directory at $HOME to hold the example.nii image.		NOTE: For the example run, we've created a subjects directory at $HOME to hold the example.nii image.
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	#!/bin/bash		#!/bin/bash

	scratch=$~~UABGRID_SCRATCH~~		scratch=$USER_SCRATCH
	jobs=$scratch/jobs		jobs=$scratch/jobs
	sub=$scratch/subjects		sub=$scratch/subjects
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	After the completion of the recon-all process, copy the results and logs back to your $HOME and delete the contents from scratch		After the completion of the recon-all process, copy the results and logs back to your $HOME and delete the contents from scratch
	<pre>		<pre>
	cp -r $~~UABGRID_SCRATCH~~/subjects $HOME/subjects-results		cp -r $USER_SCRATCH/subjects $HOME/subjects-results

	cp -r $~~UABGRID_SCRATCH~~/jobs $HOME/jobs-results		cp -r $USER_SCRATCH/jobs $HOME/jobs-results

	rm -rf $~~UABGRID_SCRATCH~~/subjects		rm -rf $USER_SCRATCH/subjects

	rm -rf $~~UABGRID_SCRATCH~~/jobs		rm -rf $USER_SCRATCH/jobs
	</pre>		</pre>

Tanthony@uab.edu: added category Image processing

2012-04-04T15:08:57Z

added category Image processing

← Older revision		Revision as of 15:08, 4 April 2012
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	[[Category:Software]]		[[Category:Software]][[Category:Image Processing]]