White_Matter_Stamper

• What does it do?
• Requirements
• 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

Intra_Session_Reg -

Peripheral_White_Matter_Labels -

WM_LABELS -

All_RAW_EVE_Labels -

STATS -

• References
• Version History

<revision> <name> <date> <lines changed>

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

r2682 | yben | 2015-05-13 10:58:49 -0500 (Wed, 13 May 2015) | 1 line

settinge verbose to true

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)

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)

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

r1688 | yben | 2014-04-15 08:56:58 -0500 (Tue, 15 Apr 2014) | 1 line

typo error

r1686 | plassaaj | 2014-04-14 13:50:56 -0500 (Mon, 14 Apr 2014) | 1 line r1502 | yben | 2014-02-19 08:44:06 -0600 (Wed, 19 Feb 2014) | 1 line

Error in the call of the function to add_file for EndOfSpider

r1416 | masispider | 2014-02-01 10:27:50 -0600 (Sat, 01 Feb 2014) | 1 line

Increase White Matter Stamper walltime to 10hours to be sure and Fix the last issues with spiders

r1415 | masispider | 2014-01-31 18:15:26 -0600 (Fri, 31 Jan 2014) | 1 line

Intra / nonrigid registration spider in fixing mode like EVE

r1401 | yben | 2014-01-30 11:21:11 -0600 (Thu, 30 Jan 2014) | 1 line

switching one os.path.isdir to os.path.isfile

r1400 | yben | 2014-01-30 11:19:42 -0600 (Thu, 30 Jan 2014) | 1 line

Find reg_aladin command in the folder if given or use the direct path if reg_aladin is a file (full path to reg_aladin software given in the options)

r1399 | yben | 2014-01-30 11:03:43 -0600 (Thu, 30 Jan 2014) | 1 line

Removing masi-fusion from the spider/processor for White Matter Stamper. Everything is in masimatlab.

r1392 | masispider | 2014-01-29 15:33:30 -0600 (Wed, 29 Jan 2014) | 1 line

Editing Spider nonrigid and WhiteMatter

r1383 | masispider | 2014-01-29 10:17:15 -0600 (Wed, 29 Jan 2014) | 1 line

Spider_intra_sess_reg fixed / working on nonrigid spider

r1375 | masispider | 2014-01-28 13:40:54 -0600 (Tue, 28 Jan 2014) | 1 line

Debugging WMS

r1371 | yben | 2014-01-28 11:43:05 -0600 (Tue, 28 Jan 2014) | 1 line

Debugging WMS

r1370 | masispider | 2014-01-28 10:28:23 -0600 (Tue, 28 Jan 2014) | 1 line

fixing EVE spider and processors

r1369 | masispider | 2014-01-27 16:16:58 -0600 (Mon, 27 Jan 2014) | 1 line

fixing more error on WMS spider

r1367 | yben | 2014-01-27 13:47:41 -0600 (Mon, 27 Jan 2014) | 1 line

Fixing some directory path error in WMS spider.

r1365 | masispider | 2014-01-27 10:03:16 -0600 (Mon, 27 Jan 2014) | 1 line

Fixing WM spider

r1364 | masispider | 2014-01-27 08:26:42 -0600 (Mon, 27 Jan 2014) | 1 line

fixing dtiqa saving the FA map

r1355 | yben | 2014-01-24 13:19:49 -0600 (Fri, 24 Jan 2014) | 1 line

Debugging White_Matter_Stamper to work on only one dtiqa and Multi Atlas per session (if several, set one to passed)

r1301 | yben | 2014-01-15 15:23:21 -0600 (Wed, 15 Jan 2014) | 1 line

Debugging ...

r1299 | yben | 2014-01-15 08:53:00 -0600 (Wed, 15 Jan 2014) | 1 line

Debugging ...

r1294 | yben | 2014-01-14 17:39:45 -0600 (Tue, 14 Jan 2014) | 3 lines

Changing tbss and tracula processor to check the passed in the status in lower case for both if someone set it to passed instead of Passed, it will still work. Working on WMStamper processor to make it work for any dtiqa complete with a FA and one multi_Atlas working.

r1259 | plassaaj | 2014-01-09 08:41:15 -0600 (Thu, 09 Jan 2014) | 2 lines

updated white matter spider

r1258 | plassaaj | 2014-01-09 08:38:55 -0600 (Thu, 09 Jan 2014) | 2 lines

updated white matter spider

r1234 | plassaaj | 2013-12-20 16:16:02 -0600 (Fri, 20 Dec 2013) | 1 line

Updated white matter spider to work

r1231 | plassaaj | 2013-12-20 15:59:16 -0600 (Fri, 20 Dec 2013) | 1 line

Updated White Matter Spider

r1119 | plassaaj | 2013-12-02 12:23:43 -0600 (Mon, 02 Dec 2013) | 1 line

Added White Matter Processors

Current Contact Person <date> <name> <email / URL> August 2016 Andrew Plassard email / MASI