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IDProjectCategoryView StatusLast Update
0002435Slicer4Module EMSegmentpublic2014-03-06 04:51
Reporternicole Assigned Tonicole  
PrioritynormalSeveritymajorReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.0.1 
Target VersionSlicer 4.2.0Fixed in VersionSlicer 4.1.0 
Summary0002435: Missing labels in color file used for EM Segmenter
Description

From Ron:
the label map has "holes". E.g. cingulate gyrus on the sagittal and
axial. Is it possible that the segmentationresults are displayed with
the wrong LUT?

Additional Information

From Kilian:
I am using the LUT with the name SPL-BrainAtlas-2009-ColorFile.
[...]
The list of labels are
2002, 2026,2034
but I do not know the structure names

TagsNo tags attached.

Activities

nicole

nicole

2012-08-27 08:54

administrator   ~0005799

Last edited: 2012-08-27 08:54

Marianna and I took a closer look at the SPL-BrainAtlas-2009-ColorFile and found that there were a few errors:

  • one structure name appeared twice, a copy/paste error between left and right brain structures
  • some structures weren't mirrrored right/left, and need to be added with sensible colors

Due to the first point, a new color table was decided as the way to go, since a label name was being changed.

nicole

nicole

2012-08-27 09:02

administrator   ~0005800

On 8/21/10, Marianna and I came up with these necessary changes to SPL-BrainAtlas-2009-ColorFile.txt, to be integrated into a new file named SPL-BrainAtlas-2012-ColorFile.txt:

1034 left_transverse_temporal_gyri -> right_transverse_temporal_gyri
And three colors added:
2002 right_cingulategyrus(1) 125 100 160 255
2026 right_cingulategyrus(3) 80 20 140 255
2034 right_transverse_temporal_gyri 150 150 200 255

nicole

nicole

2012-08-27 10:18

administrator   ~0005808

From Marianna:
per Ron's request I have changed some of the colors based on the colors of the Generic Anatomy Colors LUT.

nicole

nicole

2012-08-27 10:54

administrator   ~0005809

svn 20871 adds in the new color file SPL-BrainAtlas-2012-ColorFile.txt

nicole

nicole

2012-08-29 07:24

administrator   ~0005851

svn 20891 tweaks the white_matter_of_right_cerebral_hemisphere to differentiate it from the left, per request from Ron/Kilian/Marianna.

jcfr

jcfr

2014-03-06 04:50

administrator   ~0010722

Closing resolved issues that have not been updated in more than 3 months

Issue History

Date Modified Username Field Change
2012-08-27 08:52 nicole New Issue
2012-08-27 08:52 nicole Status new => assigned
2012-08-27 08:52 nicole Assigned To => nicole
2012-08-27 08:54 nicole Note Added: 0005799
2012-08-27 08:54 nicole Note Edited: 0005799
2012-08-27 09:02 nicole Note Added: 0005800
2012-08-27 10:18 nicole Note Added: 0005808
2012-08-27 10:54 nicole Note Added: 0005809
2012-08-27 10:54 nicole Status assigned => resolved
2012-08-27 10:54 nicole Fixed in Version => Slicer 4.1.0
2012-08-27 10:54 nicole Resolution open => fixed
2012-08-29 07:24 nicole Note Added: 0005851
2014-03-06 04:50 jcfr Note Added: 0010722
2014-03-06 04:51 jcfr Status resolved => closed