VipSkeleton error

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joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

VipSkeleton error

Post by joost »

Hi,

- version 4.2.1
- stamp: Linux neurojoost 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012 x86_64 GNU/Linux
- command: VipSkeleton -sk s -im a -gcs 2 -e 0.5 -i tmp_white.nii -so tmp_skel_1mm -g tmp_white
- terminal output:

Reading tmp_white.nii...
===============
SKELETONIZATION
===============
Initialization...
loop: 0, just killed: 0, total immortals: 51
Front size: 59001
loop: 1.1, total killed: 19292, total immortals: 932
loop: 1.2, total killed: 37450, total immortals: 2887
loop: 1.3, total killed: 54055, total immortals: 5213
loop: 1.4, total killed: 68090, total immortals: 7936
loop: 1.5, total killed: 80526, total immortals: 10033
loop: 1.6, total killed: 91144, total immortals: 11961
Front size: 33481
loop: 2.1, total killed: 9212, total immortals: 13361
loop: 2.2, total killed: 18928, total immortals: 15690
loop: 2.3, total killed: 26583, total immortals: 16964
loop: 2.4, total killed: 33371, total immortals: 18079
loop: 2.5, total killed: 40076, total immortals: 19719
loop: 2.6, total killed: 45279, total immortals: 20970
Front size: 18801
loop: 3.1, total killed: 5507, total immortals: 21831
loop: 3.2, total killed: 10511, total immortals: 22649
loop: 3.3, total killed: 13957, total immortals: 23543
loop: 3.4, total killed: 17014, total immortals: 24223
loop: 3.5, total killed: 20558, total immortals: 24996
loop: 3.6, total killed: 22671, total immortals: 25474
Front size: 11883
loop: 4.1, total killed: 3776, total immortals: 25857
loop: 4.2, total killed: 6502, total immortals: 26322
loop: 4.3, total killed: 9812, total immortals: 26714
loop: 4.4, total killed: 12935, total immortals: 27208
loop: 4.5, total killed: 15002, total immortals: 27535
loop: 4.6, total killed: 16329, total immortals: 27787
Front size: 8231
loop: 5.1, total killed: 2744, total immortals: 28066
loop: 5.2, total killed: 4337, total immortals: 28352
loop: 5.3, total killed: 5303, total immortals: 28542
loop: 5.4, total killed: 6706, total immortals: 28729
loop: 5.5, total killed: 7864, total immortals: 28946
loop: 5.6, total killed: 9035, total immortals: 29088
Front size: 6273
loop: 6.1, total killed: 2232, total immortals: 29341
loop: 6.2, total killed: 2886, total immortals: 29449
loop: 6.3, total killed: 3812, total immortals: 29617
loop: 6.4, total killed: 5645, total immortals: 29958
loop: 6.5, total killed: 6483, total immortals: 30089
loop: 6.6, total killed: 7210, total immortals: 30240
Front size: 4407
loop: 7.1, total killed: 1516, total immortals: 30449
loop: 7.2, total killed: 2788, total immortals: 30663
loop: 7.3, total killed: 3971, total immortals: 30841
loop: 7.4, total killed: 4426, total immortals: 30954
loop: 7.5, total killed: 4817, total immortals: 31064
loop: 7.6, total killed: 5151, total immortals: 31127
Front size: 2817
loop: 8.1, total killed: 883, total immortals: 31346
loop: 8.2, total killed: 1171, total immortals: 31458
loop: 8.3, total killed: 1467, total immortals: 31543
loop: 8.4, total killed: 2045, total immortals: 31710
loop: 8.5, total killed: 2217, total immortals: 31788
loop: 8.6, total killed: 2353, total immortals: 31835
Front size: 1495
loop: 9.1, total killed: 342, total immortals: 31901
loop: 9.2, total killed: 427, total immortals: 31932
loop: 9.3, total killed: 506, total immortals: 31966
loop: 9.4, total killed: 786, total immortals: 32011
loop: 9.5, total killed: 833, total immortals: 32028
loop: 9.6, total killed: 873, total immortals: 32047
Front size: 1026
loop: 10.1, total killed: 192, total immortals: 32160
loop: 10.2, total killed: 215, total immortals: 32175
loop: 10.3, total killed: 232, total immortals: 32191
loop: 10.4, total killed: 248, total immortals: 32205
loop: 10.5, total killed: 284, total immortals: 32243
loop: 10.6, total killed: 285, total immortals: 32243
Front size: 618
loop: 11.1, total killed: 0, total immortals: 32243
loop: 11.2, total killed: 1, total immortals: 32243
loop: 11.3, total killed: 3, total immortals: 32245
loop: 11.4, total killed: 3, total immortals: 32245
loop: 11.5, total killed: 3, total immortals: 32245
loop: 11.6, total killed: 3, total immortals: 32245
Front size: 613
loop: 12.1, total killed: 0, total immortals: 32245
loop: 12.2, total killed: 0, total immortals: 32245
loop: 12.3, total killed: 0, total immortals: 32245
loop: 12.4, total killed: 0, total immortals: 32245
loop: 12.5, total killed: 0, total immortals: 32245
loop: 12.6, total killed: 5, total immortals: 32245
Front size: 608
loop: 13.1, total killed: 0, total immortals: 32245
loop: 13.2, total killed: 0, total immortals: 32245
loop: 13.3, total killed: 0, total immortals: 32245
loop: 13.4, total killed: 0, total immortals: 32245
loop: 13.5, total killed: 0, total immortals: 32245
loop: 13.6, total killed: 0, total immortals: 32245
---------------------------------------
Pruning 3D curves of the skeleton...
---------------------------------------
Initialization...
Topological classification...
Initial front : 546 points
Deleted points: 512, 221, 132, 95, 68, 50, 44, 36, 31, 20, 17, 11, 10, 6, 4, 3, 1, 0
---------------------------------------
Pruning outside part of the skeleton...
---------------------------------------
Initialization...
Initial front : 0 points
Deleted points: 0
----------------------------------------------------
Topological Classification of the skeleton points...
----------------------------------------------------
Writing skeleton tmp_skel_1mm...
=======================
WATERSHED BASED VORONOI
=======================
Reading geometry image tmp_white...
-----------------------------------------------
Detecting saddle points of gray/white interface = pli de passage markers
-----------------------------------------------
Computing Gaussian smoothing (sigma 2.000000) of tmp_white...
Computing tmp_white isophote gaussian curvature...
Slice: 0
----------------------------------
Reading tmp_white.nii...
------------------------------------------------------------
Preprocessing for the watershed applied to geodesic depth...
------------------------------------------------------------
Computing geodesic distance map to outside...
dist: 0.0
Decreasing depth at the level of saddle points...
1753 saddle point marker found
Morphological filtering to reduce the number of extrema and the depth of sharp ones
Gray level opening (3x3x3 flat structuring element) is applied to the distance map...
Slice:256
Slice:256
Gray level closing (3x3x3 flat structuring element) is applied to the distance map...
Slice:256
Slice:256
Detecting local maxima which will represent sulcal roots...
Neighborhood size: 124
Slice:256

------------------------------
! VIP Warning:
Empty volume in VipGet3DConnex
------------------------------

------------------------------
! VIP Warning:
Nothing is left in VipConnexVolumeFilter
------------------------------
Initial number of seeds: 0

------------------------------
!! VIP Error:
Sorry, bad number of seeds
------------------------------

------------------------------
!! VIP Error:

Execution aborted in function '(morpho)VipComputeWatershedVoronoi'.

------------------------------

so, tmp_skel_1mm is written but should i be worried about the error? if so, what can i do to prevent it?

info on the input file (tmp_white.nii):
filename tmp_white.nii
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 256
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units Unknown
time_units Unknown
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.000000 0.000000 -0.000000 127.500000
qto_xyz:2 0.000000 0.000000 1.000000 -145.500000
qto_xyz:3 -0.000000 -1.000000 -0.000000 116.746002
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Superior-to-Inferior
qform_zorient Posterior-to-Anterior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FreeSurfer May 22 2011
aux_file

merci,
-joost
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Re: VipSkeleton error

Post by denghien »

And does the result seem right ?
Isa
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Re: VipSkeleton error

Post by denghien »

Could you please send us some snapshots of the result and the data ?
Thanks,
joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: VipSkeleton error

Post by joost »

Hi Isa,

can i send the complete input and output (zipped nifti format) file from my VipSkeleton command line to your (private) email address? that will give you the chance to replicate this error output.
you can send me an email (joost.janssen76@gmail.com) and i will reply with the input and output files attached.

ok?

merci,
-joost
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Re: VipSkeleton error

Post by denghien »

ok
I'm going to reply by email.
Isa
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: VipSkeleton error

Post by riviere »

Hi Joost,

I guess VipSkeleton doesn't work because you have provided the same input, a binary image, as -i and -g options. -g is expected to be a grey level image, used for saddle points extraction: here it is a binary image, so the saddle points are crap.

Did you get this command from the regular morphologist pipeline, or did you use it this way manually ?

If you don't have a grey level image to guide the skeletonization, you can remove the -g parameter, and disable the voronoi (-v n).

Denis
joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: VipSkeleton error

Post by joost »

Hi Denis,
riviere wrote:Hi Joost,

I guess VipSkeleton doesn't work because you have provided the same input, a binary image, as -i and -g options. -g is expected to be a grey level image, used for saddle points extraction: here it is a binary image, so the saddle points are crap.

Did you get this command from the regular morphologist pipeline, or did you use it this way manually ?

If you don't have a grey level image to guide the skeletonization, you can remove the -g parameter, and disable the voronoi (-v n).

Denis
ok, thanks. i use this command for non-morphologist related reasons. i removed the -g parameter and disabled the voronoi:
VipSkeleton -sk s -im a -gcs 2 -e 0.5 -i tmp_white.nii -so tmp_skel_1mm -v n

no more error output but the resulting output image (tmp_skel_1mm.nii) is the *same* as the output image from:
VipSkeleton -sk s -im a -gcs 2 -e 0.5 -i tmp_white.nii -so tmp_skel_1mm -g tmp_white

let me repeat that my goal is to modify "-e", i.e. i want to modify the erosion of the resulting skeleton image. with the current commands, no matter what value i put for "-e", i always get the same output skeleton image. the output skeleton image is not bad but i would like to see if i can improve it by modifying the "-e" value.

merci,
-joost
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