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IDProjectCategoryView StatusDate SubmittedLast Update
0002861Slicer4Module Annotationspublic2013-01-09 03:582013-08-28 06:03
ReporterLauraKoenders Assigned Tonicole  
PrioritynormalSeveritycrashReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.1.0 
Target VersionSlicer 4.3.0Fixed in VersionSlicer 4.3.0 
Summary0002861: loading FreeSurfer parcellation data (aparc.annot)
Description

Dear Slicer-people,

I have a problem uploading the FreeSurfer output in 3D Slicer.
First, let me explain what I am trying to do. We have a list with cortical and subcortical grey matter areas that were significantly different between our patient and control group. I want to make one picture showing all these areas, and the 3D model with a part of the surface 'clipped out' would be perfect.

I tried to do this by loading the surfaces and parcellation map in Slicer. I could successfully load the volumes (mri.mgz, aseg.mgz) and the surfaces (lh.pial and rh.pial). But when I load the parcellation map (aparc.annot) as a scalar overlay for the already loaded model, slicer crashes.

I found this problem on the helpdesk, however the solutions offer there do not work for me and Slicer keeps crashing. In addition, I tried to get round it by creating a surface model using modelmaker. However, the surfacemodel I get cannot be 'clipped', is this correct?

My question is: is there a way to fix this problem, and if not; is there another way to get the type of picture I want?

I really hope you can help me, thanks in advance!

Kind regards,
Laura

Additional Information

I tried this in different versions of Slicer (4.1.0, 4.0.1 and 4.2.2) on Windows, Linux and Mac. All versions crash every time I try this.

TagsNo tags attached.

Relationships

related to 0002837 closednicole program closes when loading freesurfer .annot files 

Activities

nicole

nicole

2013-01-09 06:47

administrator   ~0007634

Please attach lh.pial and aparc.annot that are causing your crash.

2013-01-17 05:20

 

rh.pial (4,442,802 bytes)

2013-01-17 05:21

 

lh.pial (4,435,530 bytes)

2013-01-17 05:21

 

lh.aparc.annot (986,946 bytes)

2013-01-17 05:21

 

rh.aparc.annot (988,562 bytes)
LauraKoenders

LauraKoenders

2013-01-17 05:22

reporter   ~0007691

Hi Nicole,

I am sorry, I only now see your question. I have uploaded the files you requested!

Kind regards, Laura
nicole

nicole

2013-01-17 06:13

administrator   ~0007694

Hi Laura,

Thanks for the data, I've reproduced the crashes (it fails on adding both the rh and the lh.aparc.annot to their respective surface models), debugging now.

For clipping, with any model you should be able to turn it on in the Models module: click on the model in the Scene tree, then open upthe Display panel. Turn on clipping for that model by checking the Clip box. Then open up the Clipping panel and select which 2D volume slice you want to use as a clipping plane. As you slide the slice offset slider for that 2d Viewer, you should see the model get clipped.
nicole

nicole

2013-01-17 09:15

administrator   ~0007696

svn 21608 [1] fixes this problem, the next Slicer 4 nightly build should work for you. The overlay file was valid but not all labels were assigned and Slicer was treating that as an error.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21608
nicole

nicole

2013-01-17 09:16

administrator   ~0007697

Please close the bug after testing to make sure it works for you on the next nightly build.
LauraKoenders

LauraKoenders

2013-01-24 03:42

reporter   ~0007728

Dear Nicole,
Thank you! The nightly build version available on download.slicer.org right now does not open on my computer, but I guess I have to wait on the next version? When do you think its coming online? Anyway, thank you for your help!
Regards, Laura
nicole

nicole

2013-01-29 09:43

administrator   ~0007755

There were some problems with the nightly builds that are getting resolved this week. We have no firm plans for the next release version, so just check on the download page for the next nightly version.
pieper

pieper

2013-08-27 11:40

administrator   ~0009631

Is this issue resolved now? Can we close it?
LauraKoenders

LauraKoenders

2013-08-27 17:50

reporter   ~0009657

The new version did work better but I believe the issue wasn't completely resolved. I decided to use a table instead of a figure in my paper so I stopped trying to figure it out. The thread can be closed though, thanks for your help!
nicole

nicole

2013-08-28 06:03

administrator   ~0009659

Closing this thread, and you can open a new bug if you find another crash case.

Issue History

Date Modified Username Field Change
2013-01-09 03:58 LauraKoenders New Issue
2013-01-09 03:58 LauraKoenders Status new => assigned
2013-01-09 03:58 LauraKoenders Assigned To => nicole
2013-01-09 06:47 nicole Note Added: 0007634
2013-01-09 06:49 nicole Relationship added related to 0002837
2013-01-17 05:20 LauraKoenders File Added: rh.pial
2013-01-17 05:21 LauraKoenders File Added: lh.pial
2013-01-17 05:21 LauraKoenders File Added: lh.aparc.annot
2013-01-17 05:21 LauraKoenders File Added: rh.aparc.annot
2013-01-17 05:22 LauraKoenders Note Added: 0007691
2013-01-17 06:13 nicole Note Added: 0007694
2013-01-17 09:15 nicole Note Added: 0007696
2013-01-17 09:16 nicole Note Added: 0007697
2013-01-17 09:16 nicole Status assigned => resolved
2013-01-17 09:16 nicole Fixed in Version => Slicer 4.3.0
2013-01-17 09:16 nicole Resolution open => fixed
2013-01-24 03:42 LauraKoenders Note Added: 0007728
2013-01-24 03:42 LauraKoenders Status resolved => feedback
2013-01-24 03:42 LauraKoenders Resolution fixed => reopened
2013-01-29 09:43 nicole Note Added: 0007755
2013-08-27 11:40 pieper Note Added: 0009631
2013-08-27 11:40 pieper Target Version => Slicer 4.3.0
2013-08-27 17:50 LauraKoenders Note Added: 0009657
2013-08-28 06:03 nicole Note Added: 0009659
2013-08-28 06:03 nicole Status feedback => closed
2013-08-28 06:03 nicole Resolution reopened => fixed