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[SCIRUN-USERS] Some problems loading data from Seg3D to Seg3D2

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  • From: Ramón Casero Cañas <>
  • To: Mailing list SCIRun <>
  • Subject: [SCIRUN-USERS] Some problems loading data from Seg3D to Seg3D2
  • Date: Wed, 21 Sep 2011 12:25:51 +0100

Hi all,

I have created a segmentation in Seg3D v1.12.0 (with my patch for the Spline Tool), saved it to .mat, and opened it in Seg3D2. The application crashes with a segfault.

If I save a volume instead of a segmentation to .mat and try to open in Seg3D2, the segfault produces some output

$ *** glibc detected *** ./Seg3D2: corrupted double-linked list: 0x00007f880802e990 ***
======= Backtrace: =========
======= Memory map: ========
00400000-02556000 r-xp 00000000 08:0d 1065191 /home/scratch/ramc/comlab/Seg3D_2.1/bin/Seg3D2
02755000-02759000 r--p 02155000 08:0d 1065191 /home/scratch/ramc/comlab/Seg3D_2.1/bin/Seg3D2
02759000-027ff000 rw-p 02159000 08:0d 1065191 /home/scratch/ramc/comlab/Seg3D_2.1/bin/Seg3D2
027ff000-0282e000 rw-p 00000000 00:00 0
0356b000-08ad8000 rw-p 00000000 00:00 0 [heap]
4001c000-4001e000 r-xs 00000000 08:0b 110 /tmp/glu48OEI (deleted)
4006a000-400e1000 rw-p 00000000 00:00 0
400e1000-400e3000 r-xs 00000000 08:0b 152 /tmp/glYFXJyF (deleted)
400e3000-4015a000 rw-p 00000000 00:00 0
4015a000-4015c000 r-xs 00000000 08:0b 156 /tmp/glDytMvN (deleted)

From the export menu, it seems that currently, Seg3D2 can only export to NRRD, so maybe it cannot even read .mat files in the first place? Is this functionality going to be added at some point?

I have then saved a volume in Seg3D in .nrrd format, and opened it with Seg3D2. I get the following error:

ERROR: Could not read file '/home/ramc/elham/image-processing/ko-118-01-11-stack-seg-clean-smooth-lab.nrrd'.

Could not open file: /home/ramc/elham/image-processing/ko-118-01-11-stack-seg-clean-smooth-lab.nrrd : [nrrd] nrrdLoad: trouble reading "/home/ramc/elham/image-processing/ko-118-01-11-stack-seg-clean-smooth-lab.nrrd"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: trouble reading NRRD file
[nrrd] _nrrdFormatNRRD_read: trouble parsing spacings info "0.000000 0.000000 0.000001"
[nrrd] _nrrdReadNrrdParse_spacings: trouble
[nrrd] _nrrdFieldCheck_spacings: axis 0 spacing (0) invalid

Could this be because the resolution in my images is ~.5e-6, and Seg3D doesn't have enough precision when saving the data to a file?

I have been able to save a segmentation mask to .mha in Seg3D and open it with Seg3D2 without crashing.

Best regards,


Dr. Ramón Casero Cañas

Computational Biology
Department of Computer Science
University of Oxford
Wolfson Building, Parks Rd
Oxford OX1 3QD

tlf     +44 (0) 1865 610737

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