HistoAnalysis

Questions about BrainVisa usage and installation

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Dhalila
Posts: 6
Joined: Fri Jan 06, 2006 7:54 pm
Location: LIUPPA, Pau

HistoAnalysis

Post by Dhalila »

Hi again,
im trying the segmentation again, the vip bias correction works with a field rigidity 10 and regularization 1.0. The vip get brain works with a fast mode and erosion size 3.5. Error displayed with correction brain mask;i.e., can't open histo analysis file. Consequently i have excuted the vipHisto Analysis and this is the list of errors displayed. I can't understand how to adjust the scale.
VipHistoAnalysis

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! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 78 and localization 7
lost at iteration 0

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!! VIP Error:
Strange brain cascade for SPGR sequence
------------------------------

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

Execution aborted in function 'VipAnalyseCascadesSPGRSequence'.

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



in Vip Histogram analysis 4 RuntimeError: System command exited with non null value : 111



in Vip Histogram analysis 4 RuntimeError: System command exited with non null value : 111

neuroProcesses.py (1023) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (60) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullName(), '-o',self.histo_analysis.fullName(), '-S', 'y', '-m', 'a')
neuroProcessesGUI.py (637) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1102) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

VipHistoAnalysis
Command line
'VipHistoAnalysis' '-i' '/home/dhalila/Desktop/contusion/dicomimages/im1/anatomy/nobias_im1' '-o' '/home/dhalila/Desktop/contusion/dicomimages/im1/anatomy/nobias_im1' '-S' 'y' '-m' 'a'
Output

Reading volume...
Reading Tivoli/GIS image format...
No byte swapping
Volume geometry:
X size:512, Y size:512, Z size:36, T size:1
X voxsize:0.488mm, Y voxsize:0.488mm, Z voxsize:2.500mm, T voxsize:1.000s
Computing histogram
Writing histogram
Computing scale space singularities up to order three...
Undersampling histogram... (factor 64 )
Cutting range [41-43] in histogram right part (almost zero)
Cutting range [-34-0] in histogram left part
Detecting D1/D2 singularity matings and cascades...
Analysing histogram D1 and D2 singularities...
Main event scales: 95 14 13
Main cascade volumes: 668399 395999 219521
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! VIP Warning:
Strange: gap of more than 5 points along this trajectory (use smaller scale step)
------------------------------
Singularity steming from iteration 77 and localization 7
lost at iteration 0
------------------------------
!! VIP Error:
Strange brain cascade for SPGR sequence
------------------------------
------------------------------
!! VIP Error:
Execution aborted in function 'VipAnalyseCascadesSPGRSequence'.
------------------------------
Result
Value returned = 111
Sincere thanks
Regards.
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