echo "STEP 1: Download any compressed nifti file"
curl http://slicer.kitware.com/midas3/download/bitstream/9847/ANON0006_20_T1_sag_twisted.nii.gz -o test.nii.gz

echo "STEP 2: Load file in slicer"
/scratch/johnsonhj/src/Slicer-build/Slicer-build/Slicer test.nii.gz

echo "STEP 3: Save mrml scene"
<<< [File][Save], Then save the MRML scene >>>

echo "STEP 4: Load mrml scene"
/scratch/johnsonhj/src/Slicer-build/Slicer-build/Slicer 2013-07-11-Scene.mrml

echo "STEP 5: scratch head as to why the scene looks wrong"

ERROR: In /scratch/johnsonhj/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
vtkMRMLVolumeArchetypeStorageNode (0x7fa9cba0da70): ReadData: Cannot read file as a volume of type Volume[fullName = /scratch/test.gz]
Number of files listed in the node = 0.
File reader says it was able to read 0 files.
File reader used the archetype file name of /scratch/test.gz []

echo "STEP 5: Notice file name is wrong: '/scratch/test.gz' instead of '/scratch/test.nii.gz'"

I'll bet it's related to this change [1] that was an attempt to fix [2]. I could believe it because QFileInfo::suffix probably doesn't understand .nii.gz.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Base/QTGUI/qSlicerSaveDataDialog.cxx?r1=22004&amp;r2=22003&amp;pathrev=22004

[2] http://na-mic.org/Bug/view.php?id=2326

The file path is ...nii.gz until the save data dialog is open. it then becomes .gz

Function "completeSuffix" should probably be used.
See http://qt-project.org/doc/qt-4.7/qfileinfo.html#id-df803c53-a727-4600-bed4-c3479ab29152

@Hans: did it ever work in slicer4 to open a .nii.gz file and save the scene with a reference to it? I'm just trying to get a sense of how extensive the changes need to be. I don't think my recent changes related to 0002326 are the only thing going on here.

Never mind - I see now. The behavior is different because now the volume is selected for saving by default, whereas previously the filename was wrong (test.nii.nrrd) but wasn't being used. You can ignore the question in comment 9273.

Thanks for looking into this. It has been a major source of frustration for our lab.

Hans

Please try r22246.

Number of instantiated modules: 125
2013-07-30 14:22:43.592 Slicer[49821:707] invalid drawable
2013-07-30 14:22:43.594 Slicer[49821:707] invalid drawable
Number of loaded modules: 125
Show module (name): "ViewControllers"
WARNING: qSlicerViewControllersModule ::helpText() is not implemented
ERROR: In /Users/johnsonhj/src/Slicer/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx, line 367
vtkMRMLVolumeArchetypeStorageNode (0x7f83513c9410): ReadData: Cannot read file as a volume of type Volume[fullName = /Volumes/Macintosh HD/scratch/HDNI_001/012366774/012366774_20110722_30/ANONRAW/012366774_012366774_20110722_30_T1-30_3.nii.nii.gz]
Number of files listed in the node = 0.
File reader says it was able to read 0 files.
File reader used the archetype file name of /Volumes/Macintosh HD/scratch/HDNI_001/012366774/012366774_20110722_30/ANONRAW/012366774_012366774_20110722_30_T1-30_3.nii.nii.gz []

The issue is still not fixed. now the file that is attempting to be read has ".nii.nii.gz" as the extension.

Okay I'll keep investigating.

Okay - I think I've got it this time. We could investigate other ways of managing default filenames but this should at least fix the regression. Try r22259

This is now working.

Hans