0001899: Cannot save and reopen color images as .nrrd file

ID	Project	Category	View Status	Date Submitted	Last Update

0001899	Slicer4	Core: Usability	public	2012-04-12 08:43	2018-05-30 00:38

Reporter	sidnei	Assigned To
Priority	low	Severity	major	Reproducibility	always
Status	acknowledged	Resolution	open
Product Version	Slicer 4.0.1
Target Version	backlog	Fixed in Version

Summary	0001899: 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.
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jcfr 2012-05-09 09:17 administrator ~0004234	Can you reproduce the problem using a recent nightly builds ? See http://download.slicer.org

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 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 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 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 2013-08-27 11:31 administrator ~0009626	Nrrd is broken for this, but .nii works.

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 2017-06-10 00:43 developer ~0014720	This is not a blocking issue, it has been open for years and there are workarounds.

lassoan 2018-05-30 00:38 developer ~0015808	Retarget stale issues to backlog.

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
2018-05-30 00:38	lassoan	Target Version	=> backlog
2018-05-30 00:38	lassoan	Note Added: 0015808

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