ON_MR_sheath_segmentation¶
- What does it do?
Estimates the radius of the optic nerve and surrounding subarachnoid cerebrospinal fluid at each slice which contains optic nerve labels.
- Requirements
NLSS resource from a version of ON_MR_segmentation
masimatlab utils
Trained random forest from matlab’s TreeBagger to transform parameter space to radius space
ANTS registration (used for resampling)
- Resources *
OUTLOG - STDOUT and STDERR from the process on the grid
PBS - The DRMAA compliant batch script to run the job
PDF - The output PDF file for determining QA status
SNAPSHOTS - Thumbnail of the first page of the PDF resource for viewing on XNAT
RADII - Contains the measured radii for each slice and the centroids
MATLAB - Matlab script used to run the estimation
- References
Harrigan, Robert L., et al. “Disambiguating the optic nerve from the surrounding cerebrospinal fluid: Application to MS‐related atrophy.” Magnetic resonance in medicine 75.1 (2016): 414-422.
- Version History
<revision> <name> <date> <lines changed>
- r3167 | robharrigan | 2015-08-11 13:13:30 -0500 (Tue, 11 Aug 2015) | 3 lines
- fixed difference in centroid naming
- r3166 | robharrigan | 2015-08-11 11:08:51 -0500 (Tue, 11 Aug 2015) | 1 line
- fixed what ben broke
- r3165 | robharrigan | 2015-08-11 10:14:57 -0500 (Tue, 11 Aug 2015) | 1 line
- switched to better pdf for sheath
- r3032 | robharrigan | 2015-07-16 08:13:40 -0500 (Thu, 16 Jul 2015) | 1 line
- fixed bug created by argparse magic
- r2960 | bdb | 2015-07-06 10:34:37 -0500 (Mon, 06 Jul 2015) | 1 line
- Add suffix_proc option for dax 0.3.1, also change vX.X.X to vX_X_X
- r2854 | masispider | 2015-06-10 09:05:24 -0500 (Wed, 10 Jun 2015) | 1 line
- fixed pdf call in sheath spider
- r2823 | robharrigan | 2015-06-08 14:08:15 -0500 (Mon, 08 Jun 2015) | 1 line
- updating pdf call
- r2655 | yben | 2015-05-11 09:02:40 -0500 (Mon, 11 May 2015) | 1 line
- Switching Modules/Processors/spiders for the version 0.3.0 of dax package (generic functions build in dax)
- r2196 | parvatp | 2015-02-09 13:58:24 -0600 (Mon, 09 Feb 2015) | 1 line
- string comparison fix SMD
- r2194 | robharrigan | 2015-02-09 12:03:06 -0600 (Mon, 09 Feb 2015) | 1 line
- saving centroids
- r1992 | yben | 2014-10-16 12:46:53 -0500 (Thu, 16 Oct 2014) | 2 lines
- Removing MASIMATLAB_PATH called from dax and instead getting path from VUIIS_path_settings.py in processors/ Adding all the path to processors/VUIIS_path_settings.py for each imaging software used.
- r1979 | yben | 2014-10-10 15:07:51 -0500 (Fri, 10 Oct 2014) | 2 lines
- Adding “-singleCompThread” to every matlab called from regular spiders. Fixing bedpost problem (using fa.nii instead of dti)
- r1932 | robharrigan | 2014-09-15 15:33:51 -0500 (Mon, 15 Sep 2014) | 1 line
- finally fixed verbose behavior
- r1931 | robharrigan | 2014-09-15 15:29:46 -0500 (Mon, 15 Sep 2014) | 1 line
- fixed pdf verbosity
- r1930 | robharrigan | 2014-09-15 15:28:49 -0500 (Mon, 15 Sep 2014) | 1 line
- fixing output
- r1929 | robharrigan | 2014-09-15 15:11:19 -0500 (Mon, 15 Sep 2014) | 2 lines
- fixed verbosity option
- r1928 | robharrigan | 2014-09-15 15:04:11 -0500 (Mon, 15 Sep 2014) | 2 lines
- fixed verbosity option
- r1927 | robharrigan | 2014-09-15 14:55:57 -0500 (Mon, 15 Sep 2014) | 1 line
- updated subprocess call
- r1926 | masispider | 2014-09-15 14:32:53 -0500 (Mon, 15 Sep 2014) | 1 line
- updated sheath segmentation to get stdout
- r1903 | yben | 2014-08-15 11:42:56 -0500 (Fri, 15 Aug 2014) | 2 lines
- Final commit to work with the new package dax. Fix some imports for modules/spiders/processors/Xnat_tools (fs)
- r1901 | yben | 2014-08-15 09:05:31 -0500 (Fri, 15 Aug 2014) | 4 lines
- Important Commit: 1) Adding new spiders using the new template 2) Switching old spiders to new template 3) Using new package dax
- r1836 | robharrigan | 2014-06-13 09:15:52 -0500 (Fri, 13 Jun 2014) | 1 line
- turned off smoothing on interp
- r1832 | robharrigan | 2014-06-12 15:57:50 -0500 (Thu, 12 Jun 2014) | 1 line
- fixed ants stuff
- r1831 | robharrigan | 2014-06-12 15:51:25 -0500 (Thu, 12 Jun 2014) | 1 line
- added resampling to spider
- r1824 | yben | 2014-06-10 11:39:24 -0500 (Tue, 10 Jun 2014) | 1 line
- Switching print to sys.stdout.write to see outlog from spider and matlab in the right order
- r1821 | robharrigan | 2014-06-10 09:45:45 -0500 (Tue, 10 Jun 2014) | 1 line
- updated version which saves all radius results
- r1790 | robharrigan | 2014-06-03 10:34:09 -0500 (Tue, 03 Jun 2014) | 1 line
- fixing bugs
- r1788 | robharrigan | 2014-06-03 10:22:29 -0500 (Tue, 03 Jun 2014) | 1 line
- minor fixes and verbosity
- r1784 | robharrigan | 2014-06-03 10:06:26 -0500 (Tue, 03 Jun 2014) | 1 line
- pdf path
- r1781 | robharrigan | 2014-06-03 09:49:59 -0500 (Tue, 03 Jun 2014) | 1 line
- added PDF to sheath seg
- r1779 | robharrigan | 2014-06-03 07:28:25 -0500 (Tue, 03 Jun 2014) | 1 line
- changed resource to RADII, lowered resources requested
- r1763 | robharrigan | 2014-05-29 13:03:55 -0500 (Thu, 29 May 2014) | 1 line
- fixed trees loading
- r1758 | robharrigan | 2014-05-28 11:09:17 -0500 (Wed, 28 May 2014) | 1 line
- added sheath spider
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