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IDProjectCategoryView StatusDate SubmittedLast Update
0001646Slicer4Core: CLI infrastructurepublic2012-01-05 07:362012-08-21 11:30
ReporterDMeier Assigned Topieper  
PrioritynormalSeveritycrashReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.0.0 
Target VersionSlicer 4.0.1Fixed in VersionSlicer 4.0.1 
Summary0001646: DicomToNrrdConverter converter crash
Description

Dicom image (simple structural DICOM from Siemens) does load properly in Slicer GUI (Add Volume)
but conversion of to NRRD fails:

call:
/Applications/Slicer.app/Contents/cli-modules/DicomToNrrdConverter --inputDicomDirectory BA1/BA1_2011_05_19/t2_tirm_tra_darkfluid_4 --outputVolume s4out.nrrd

yields:

ORIGINAL\PRIMARY\M\ND\NORM
Image acquired using a Siemens scanner
Siemens split format
=================== numberOfSlicesPerVolume:46
Dicom images are ordered in a volume interleaving way.
ImageOrientationPatient (0020:0037): LPS Orientation Matrix
0.999899 2.30203e-10 0.0142466
-0.00140677 0.995113 0.0987339
-0.014177 -0.0987439 0.995012

SpacingMatrix
0.976562 0 0
0 0.976562 0
0 0 3

NRRDSpaceDirection
0.976463 2.24808e-10 0.0427398
-0.0013738 0.97179 0.296202
-0.0138447 -0.0964296 2.98504

Slice 0: -122.9065954896-181.36021036298-35.584602555614
Slice 1: -122.86385562143-181.0640067497-32.599567612987
Slice order is IS
Row: 0.976463, -0.0013738, -0.0138447
Col: 2.24808e-10, 0.97179, -0.0964296
Sli: 0.0427398, 0.296202, 2.98504
2.98504
Number of Slices: 46
Number of Volume: 1
Number of Slices in each volume: 46

terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Abort trap

Additional Information

tried on Mac OS X 10.6.8

TagsNo tags attached.

Activities

2012-01-05 07:36

 

FLAIR_DICOM_Siemens.zip (3,414,746 bytes)
pieper

pieper

2012-01-26 10:47

administrator   ~0003557

Thanks for supplying the data.

This is fixed with the commit shown below.

Can you test this with DWI data from the same source to confirm that this change doesn't impact the diffusion converter?

svn commit -m "BUG: fix for crash reported in bug 1646" Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.cxx
Sending Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.cxx
Transmitting file data .
Committed revision 19139.
pieper

pieper

2012-02-27 02:46

administrator   ~0003732

Haven't heard back, so closing the issue. Re-open it if there's still a problem.

Issue History

Date Modified Username Field Change
2012-01-05 07:36 DMeier New Issue
2012-01-05 07:36 DMeier File Added: FLAIR_DICOM_Siemens.zip
2012-01-05 09:46 finetjul Status new => assigned
2012-01-05 09:46 finetjul Assigned To => pieper
2012-01-26 10:47 pieper Note Added: 0003557
2012-01-26 10:48 pieper Resolution open => fixed
2012-02-27 02:46 pieper Note Added: 0003732
2012-02-27 02:46 pieper Status assigned => closed
2012-08-21 11:30 jcfr Fixed in Version => Slicer 4.0.1
2012-08-21 11:30 jcfr Target Version => Slicer 4.0.1