View Issue Details

IDProjectCategoryView StatusLast Update
0001899Slicer4Core: Usabilitypublic2017-06-14 21:34
ReportersidneiAssigned To 
PrioritylowSeveritymajorReproducibilityalways
Status acknowledgedResolutionopen 
Product VersionSlicer 4.0.1 
Target VersionFixed in Version 
Summary0001899: Cannot save and reopen color images as .nrrd file
Description

Slicer 4.0.1 r19033

I loaded a stack composed of several bmp images into Slicer. I then saved it as a .nrrd file and quit Slicer.

Once I reopen Slicer and try to load the .nrrd file with the "Add Data" command, Slicer crashes with the following message:

"Volume" Reader has successfully read the file "/mnt/galia/linux/lpdi/staff/sidnei/Alpha/sidnei/3D/Dentes/Dente36/Higido1/higido.nrrd"
error: [/mnt/galia/linux/64/local/src/Slicer-4.0.1-linux-amd64/./bin/SlicerQT-real] exit abnormally - Report the problem.

Additional Information

We are not sure if this is related to above mentioned crash, but during the session the following errors were also displayed before the crash:

...
Loading module "DiffusionTensorEstimation"
Loading module "ComputeSUVBodyWeight"
Loading module "GrayscaleModelMaker"
Number of loaded modules: 93
qSlicerDataDialogPrivate::selectedFiles - row: 0
ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageRGBToHSI.cxx, line 136
vtkImageRGBToHSI (0x4f8fc90): Input has too few components

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageRGBToHSI.cxx, line 136
vtkImageRGBToHSI (0x4f8fc90): Input has too few components

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageRGBToHSI.cxx, line 136
vtkImageRGBToHSI (0x4f8fc90): Input has too few components

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageRGBToHSI.cxx, line 136
vtkImageRGBToHSI (0x4f8fc90): Input has too few components

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x4ed6580): Execute: Component 2 is not in input.

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x4ed6580): Execute: Component 2 is not in input.

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x4ed6580): Execute: Component 2 is not in input.

ERROR: In /home/kitware/Dashboards/Package/Slicer-package/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x4ed6580): Execute: Component 2 is not in input.

TagsNo tags attached.

Relationships

has duplicate 0002241 closeddemian Crash reading a stack of PNG images 

Activities

jcfr

jcfr

2012-05-09 09:17

administrator   ~0004234

Can you reproduce the problem using a recent nightly builds ? See http://download.slicer.org

fedorov

fedorov

2012-07-31 13:02

developer   ~0005475

I confirmed this is still the issue. Steps to reproduce:

1) create a directory with a few identical PNG images with different names
2) Add data -> uncheck single file option
3) save the resulting loaded RGB volume (which should have multiple slices) as a NRRD volume
4) load it back -- slice viewers are completely green, and there are following error messages on the console

ERROR: In /Users/fedorov/github/Slicer-Superbuild-Release/VTK/Imaging/vtkImageRGBToHSI.cxx, line 136
vtkImageRGBToHSI (0x12d861480): Input has too few components

ERROR: In /Users/fedorov/github/Slicer-Superbuild-Release/VTK/Imaging/vtkImageExtractComponents.cxx, line 239
vtkImageExtractComponents (0x12d841a10): Execute: Component 2 is not in input.

pieper

pieper

2012-08-21 04:54

administrator   ~0005644

Looks like the issue is that the nrrd is saved as an RGBA and that's not currently handled.

pieper

pieper

2013-05-09 10:59

administrator   ~0008600

I can also confirm this happens with nrrd, but also that it does not happen if I save the data in .nii format. You may want to use .nii for now as a workaround.

I didn't try to debug more deeply, but I notice that the vtkImageData for an RGBA .nrrd file has a one-component scalar data and a three component vector data, so this is why the filters are complaining about missing components.

pieper

pieper

2013-07-02 10:58

administrator   ~0008818

Since there is a workaround we'll move this out of the critical path for the upcoming release.

pieper

pieper

2013-08-27 11:31

administrator   ~0009626

Nrrd is broken for this, but .nii works.

pieper

pieper

2014-03-07 05:32

administrator   ~0011316

This would be nice to fix - but we think it's low priority right now. Let us know if it is high priority for you (and if the workaround with .nii doesn't work right).

lassoan

lassoan

2017-06-10 00:43

developer   ~0014720

This is not a blocking issue, it has been open for years and there are workarounds.

Issue History

Date Modified Username Field Change
2012-04-12 08:43 sidnei New Issue
2012-05-09 09:16 jcfr Status new => assigned
2012-05-09 09:16 jcfr Assigned To => jcfr
2012-05-09 09:16 jcfr Target Version => Slicer 4.2.0 AHM Summer 2012
2012-05-09 09:17 jcfr Note Added: 0004234
2012-05-09 09:17 jcfr Status assigned => feedback
2012-07-31 12:56 fedorov Relationship added duplicate of 0002241
2012-07-31 13:01 fedorov Severity crash => block
2012-07-31 13:01 fedorov Status feedback => confirmed
2012-07-31 13:02 fedorov Note Added: 0005475
2012-07-31 13:03 fedorov Relationship deleted 0002241
2012-07-31 13:03 fedorov Relationship added has duplicate 0002241
2012-08-20 11:58 jcfr Status confirmed => assigned
2012-08-20 11:58 jcfr Assigned To jcfr => pieper
2012-08-20 11:58 jcfr Target Version Slicer 4.2.0 - Feature freeze Sept 1st 2012 => Slicer 4.2.5
2012-08-21 04:54 pieper Note Added: 0005644
2012-08-21 09:39 jcfr Target Version Slicer 4.2.5 => Slicer 4.3.0
2013-05-09 10:59 pieper Note Added: 0008600
2013-07-02 10:57 pieper Target Version Slicer 4.3.0 => Slicer 4.4.0
2013-07-02 10:58 pieper Note Added: 0008818
2013-08-27 11:31 pieper Note Added: 0009626
2013-08-27 11:31 pieper Status assigned => acknowledged
2014-03-07 05:32 pieper Note Added: 0011316
2014-03-07 05:32 pieper Assigned To pieper =>
2014-03-07 05:32 pieper Priority normal => low
2014-03-07 05:32 pieper Target Version Slicer 4.4.0 =>
2017-06-10 00:43 lassoan Severity block => major
2017-06-10 00:43 lassoan Note Added: 0014720
2017-06-14 21:34 lassoan Summary Saving and reopening .nrrd problem => Cannot save and reopen color images as .nrrd file