User:Ryan Cabeen - Revision history

Ryan Cabeen: /* Software Tools */

2016-11-28T20:45:31Z

Software Tools

← Older revision		Revision as of 20:45, 28 November 2016
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	# set up Freesurfer		# set up Freesurfer
	export FREESURFER_HOME="${GFXHOME}/bin/freesurfer"		export FREESURFER_HOME="${GFXHOME}/bin/freesurfer"
			export PATH=${FREESURFER_HOME}/bin:${PATH}

	# set up FSL		# set up FSL

Ryan Cabeen at 00:47, 28 November 2016

2016-11-28T00:47:58Z

← Older revision		Revision as of 00:47, 28 November 2016
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	==Contact==		==Contact==

	My permanent email is [mailto:cabeen@gmail.com ~~cabeeen~~@gmail.com]. Please feel free to contact me with any questions!		My permanent email is [mailto:cabeen@gmail.com cabeen@gmail.com]. Please feel free to contact me with any questions!

Ryan Cabeen at 01:41, 24 August 2016

2016-08-24T01:41:05Z

← Older revision		Revision as of 01:41, 24 August 2016
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	export LD_LIBRARY_PATH=${FSLDIR}/bin${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}		export LD_LIBRARY_PATH=${FSLDIR}/bin${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

	# DTI-TK		# set up DTI-TK
	export DTITK_QSUB_QUEUE="-V -l short"		export DTITK_QSUB_QUEUE="-V -l short"
	export DTITK_USE_QSUB=1		export DTITK_USE_QSUB=1
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	<pre>/research/graphics/common0/documents/papers</pre>		<pre>/research/graphics/common0/documents/papers</pre>

	~~MRI~~ imaging datasets can be found here:		MR imaging datasets and results can be found here:

	<pre>/data/graphics/mri</pre>		<pre>/data/graphics/mri</pre>

Ryan Cabeen at 20:17, 23 August 2016

2016-08-23T20:17:50Z

← Older revision		Revision as of 20:17, 23 August 2016
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	[http://cs.brown.edu/people/cabeen/ ~~Homepage~~]		=Legacy Page=

			PhD Student from Fall 2010 - Spring 2016 and Postdoc Summer 2016. Worked on computational tools for modeling, visualization, and analysis of brain anatomy from diffusion MRI datasets. Below are pointers to various research artifacts.

			==Publications==

			My publications can be found at the following pages:
			* [http://vis.cs.brown.edu/organization/people/cabeen.html#PUBS Visweb]
			* [https://www.ncbi.nlm.nih.gov/pubmed/?term=ryan+cabeen PubMed]
			* [http://scholar.google.com/citations?user=R5Jr4-UAAAAJ Google Scholar]

			==Software Tools==

			Software can be checked out from a shared SVN repository with the following command:

			<pre>svn co --username vrluser --password goredsox https://www.brayns.com/tools/tag/LATEST tools</pre>

			The pipeline requires FSL, Freesurfer, and DTI-TK to be installed and available on the path. These are available on the Brown CS filesystem, and the following can be added to your bash profile to set them up:

			<pre>
			# set up qit
			export PATH=${PATH}:${WHERE_YOU_CHECKED_QIT_OUT}/tools/qit-install/bin
			export GFXHOME="/research/graphics/users/cabeen"

			# set up Freesurfer
			export FREESURFER_HOME="${GFXHOME}/bin/freesurfer"

			# set up FSL
			export FSLDIR="${GFXHOME}/bin/fsl/5.0"
			export FSL_DATA_DIR="${FSLDIR}/data"
			source ${FSLDIR}/etc/fslconf/fsl.sh
			export PATH=${FSLDIR}/bin:$PATH
			export LD_LIBRARY_PATH=${FSLDIR}/bin${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

			# DTI-TK
			export DTITK_QSUB_QUEUE="-V -l short"
			export DTITK_USE_QSUB=1
			export DTITK_ROOT="${GFXHOME}/bin/dtitk-2.3.1-Linux-x86_64"
			export PATH="$PATH:$DTITK_ROOT/bin:$DTITK_ROOT/utilities:$DTITK_ROOT/scripts"
			</pre>

			You can learn more about what's available by exploring the documentation included in the package. The following script also provides a regression test to validate the pipeline on a regular basis:

			<pre>/research/graphics/users/cabeen/testing/qregress.browncs.sh</pre>

			==Files and Data==

			Posters and presentation slides can be found here:

			<pre>/research/graphics/common/talks/cabeen</pre>

			Grant-related documents can be found here

			<pre>
			/map/gfx0/common0/documents/proposals/nih/bisti/irb/dtimri
			/pro/graphics/proposals/nih/paul16smart2
			</pre>

			Source files for papers can be found here:

			<pre>/research/graphics/common0/documents/papers</pre>

			MRI imaging datasets can be found here:

			<pre>/data/graphics/mri</pre>

			==Contact==

			My permanent email is [mailto:cabeen@gmail.com cabeeen@gmail.com]. Please feel free to contact me with any questions!

Ryan Cabeen at 03:59, 21 September 2012

2012-09-21T03:59:26Z

← Older revision		Revision as of 03:59, 21 September 2012
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	[[http://cs.brown.edu/people/cabeen/ Homepage]]		[http://cs.brown.edu/people/cabeen/ Homepage]

Ryan Cabeen at 03:59, 21 September 2012

2012-09-21T03:59:14Z

← Older revision		Revision as of 03:59, 21 September 2012
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	~~Computer Science PhD Graduate Student entering 2010~~		[[http://cs.brown.edu/people/cabeen/ Homepage]]

Jadrian Miles: Creating user page with biography of new user.

2010-08-31T19:59:08Z

Creating user page with biography of new user.

New page

Computer Science PhD Graduate Student entering 2010