User:Ryan Cabeen: Difference between revisions
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=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="${GFXHOME}/bin/freesurfer" | |||
export PATH=${FREESURFER_HOME}/bin:${PATH} | |||
# set up FSL | |||
export FSLDIR="${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}} | |||
# set up 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:$DTITK_ROOT/scripts" | |||
</pre> | |||
You can learn more about what's available by exploring the documentation included in the package. The following script also provides a regression test to validate the pipeline on a regular basis: | |||
<pre>/research/graphics/users/cabeen/testing/qregress.browncs.sh</pre> | |||
==Files and Data== | |||
Posters and presentation slides can be found here: | |||
<pre>/research/graphics/common/talks/cabeen</pre> | |||
Grant-related documents can be found here | |||
<pre> | |||
/map/gfx0/common0/documents/proposals/nih/bisti/irb/dtimri | |||
/pro/graphics/proposals/nih/paul16smart2 | |||
</pre> | |||
Source files for papers can be found here: | |||
<pre>/research/graphics/common0/documents/papers</pre> | |||
MR imaging datasets and results can be found here: | |||
<pre>/data/graphics/mri</pre> | |||
==Contact== | |||
My permanent email is [mailto:cabeen@gmail.com cabeen@gmail.com]. Please feel free to contact me with any questions! | |||
Latest revision as of 20:45, 28 November 2016
Legacy Page
PhD Student from Fall 2010 - Spring 2016 and Postdoc Summer 2016. Worked on computational tools for modeling, visualization, and analysis of brain anatomy from diffusion MRI datasets. Below are pointers to various research artifacts.
Publications
My publications can be found at the following pages:
Software Tools
Software can be checked out from a shared SVN repository with the following command:
svn co --username vrluser --password goredsox https://www.brayns.com/tools/tag/LATEST tools
The pipeline requires FSL, Freesurfer, and DTI-TK to be installed and available on the path. These are available on the Brown CS filesystem, and the following can be added to your bash profile to set them up:
# set up qit
export PATH=${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"
export PATH=${FREESURFER_HOME}/bin:${PATH}
# 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}}
# set up 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"
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:
/research/graphics/users/cabeen/testing/qregress.browncs.sh
Files and Data
Posters and presentation slides can be found here:
/research/graphics/common/talks/cabeen
Grant-related documents can be found here
/map/gfx0/common0/documents/proposals/nih/bisti/irb/dtimri /pro/graphics/proposals/nih/paul16smart2
Source files for papers can be found here:
/research/graphics/common0/documents/papers
MR imaging datasets and results can be found here:
/data/graphics/mri
Contact
My permanent email is cabeen@gmail.com. Please feel free to contact me with any questions!