help > Autoseg running problem!
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Jan 20, 2016  10:01 AM | lei shi
Autoseg running problem!
Autoseg is a really good software. I am now using the AutoSeg 3.2 to do registration process by using monkey data from the UNC.  I found that there are several problems:
When i run it they always report error like attachment error. Also the Autoseg parameter is the same lie before, my parameters are below:
// Automatic Segmentation Parameter File

// Atlases
Common Coordinate Image: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_skull/templateSkull.nrrd
Common Coordinate Image Type: T1
Tissue Segmentation Atlas Directory: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_skull
Tissue Segmentation Atlas Type: T1
// Loop
Loop: 1
Atlas Loop: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_stripped/
Loop - Number of iterations: 1
ROI Atlas File: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd
// Subcortical Structures
Subcortical Structure Segmentation: 0
Amygdala Left:
Amygdala Right:
Caudate Left:
Caudate Right:
Hippocampus Left:
Hippocampus Right:
Pallidus Left:
Pallidus Right:
Putamen Left:
Putamen Right:
Lateral Ventricle Left:
Lateral Ventricle Right:
// Generic ROI Maps
Generic ROI Segmentation: 1
ROI File 1: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/SubCortical.gipl.gz
ROI File 2:
ROI File 3:
ROI File 4:
ROI File 5:
// Parcellation Maps
Parcellation Map Segmentation: 1
Tissue Map: Hard
Parcellation File 1: /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/template_parc.gipl.gz
Parcellation File 2:
Parcellation File 3:
// Tissue Segmentation
EM Software: ABC
Filter Iterations: 10
Filter TimeStep: 0.01
Filter Method: Curvature flow
Max Bias Degree: 4
Initial Distribution Estimator: robust
Prior 1: 1.3
Prior 2: 1
Prior 3: 0.7
Prior 4: 1
Prior 5: 1
Fluid Atlas Warp: 1
Fluid Atlas Affine: 0
Fluid Atlas FATW: 0
Fluid Atlas Warp Iterations: 50
Fluid Atlas Warp Max Step: 0.1
Atlas Linear Mapping: affine
Image Linear Mapping: id
// Grid Template
Rigid Registration: 1
Is ROIAtlasGridTemplate: 1
GridTemplate SizeX: 0
GridTemplate SizeY: 0
GridTemplate SizeZ: 0
GridTemplate SpacingX: 0
GridTemplate SpacingY: 0
GridTemplate SpacingZ: 0
Registration Initialization: useCenterOfHeadAlign
Use T1 initial transform: 0
// Atlas Warping
Warping Method: BRAINSDemonWarp
// - Fluid Warping parameters
Alpha: 0.01
Beta: 0.01
Gamma: 0.001
Max Perturbation: 0.5
NumBasis: 0.01
Scale 4 - Number Of Iterations: 50
Scale 2 - Number Of Iterations: 25
Scale 1 - Number Of Iterations: 100
// - BRAINSDemonWarp parameters
Registration Filter Type: LogDemons
Deformation Field Smoothing Sigma: 2
Pyramid Levels: 5
Moving Shrink Factors: 16,16,16
Fixed Shrink Factors: 16,16,16
Iteration Count Pyramid Levels: 300,50,30,20,15
// - ANTS parameters
ANTS Iterations:
ANTS CC weight: 0
ANTS CC region radius: 0
ANTS MI weight: 0
ANTS MI bins: 0
ANTS MSQ weight: 0
ANTS Registration Type:
ANTS Registration Step:
ANTS Gaussian Smoothing: 0
ANTS Gaussian Sigma: 0
// Skull Stripping
Delete Vessels: 0
// Intensity Rescaling
Intensity Rescaling: Histogram quantile
// Regional histogram
Quantiles: 1,5,33,50,66,95,99
Point Spacing: 10
// N4 ITK Bias Field Correction
N4 ITK Bias Field Correction: 1
N4 Number of iterations: 50,40,30
N4 Spline distance: 0
N4 Shrink factor: 4
N4 Convergence threshold: 0.0001
N4 BSpline grid resolutions: 1,1,1
N4 BSpline alpha: 0
N4 BSpline beta: 0.5
N4 Histogram sharpening: 0
N4 BSpline order: 3
// Reorientation
Reorientation: 0
Input Orientation:
Output Orientation:
Does any one could give me some suggestions about Autoseg performance? Really appriciated any response!
best,
lei
Attachment: autoseg.tiff
Jan 21, 2016  07:01 AM | Martin Styner
RE: Autoseg running problem!
Hi Lei
There error you are getting is related to the atlas that you are using.
so
a)Is there a folder /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_skull/
b) Is there a folder /Users/shilei/Documents/MRI_Paper/MonkeyAtlas_used_forT1/ABC_stripped/ ?
c) do they contain correct ABC atlas data (files 1.mha, 2.mha etc and template.mha)

d) the tissue segmentation directory seems to be missing a "/" at the end. Can you add that and try again?

Martin
Jan 22, 2016  12:01 PM | lei shi
RE: Autoseg running problem!
Dear Martin,
Many thanks!
Now I could run the AutoSeg however the output is empty please see the attachment! It seems that the software does not start work!
Any response will be appreciated! I also attach AutoSeg paramters and AutoSeg.log files.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
starting BatchMake execution as Thread: /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg.bms
Error (55): 'No enough parameter for Set
Command: Set( ...)
*************************************************
MAIN COMPUTATION...
*************************************************
CHECKING FILES...

OrigT1CasesList: /scratch/kykwan_fluxm/leshi/MRI/test/20110807_KM02082_T1.nrrd
CHECKING FILES: DONE!
*************************************************
CHECKING IMAGE TYPE...
NRRD Format
CHECKING IMAGE TYPE: DONE!
T1 case List:: /scratch/kykwan_fluxm/leshi/MRI/test/20110807_KM02082_T1.nrrd
T1 show cases: /scratch/kykwan_fluxm/leshi/MRI/test/20110807_KM02082_T1.nrrd
*************************************************
WRITING PARAMETER FILES...
Status: Start cp /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg_Parameters.txt /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/
run: 'cp' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg_Parameters.txt' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/'
Status: Finish: Execution time 300ms
Status: Start cp /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg_Computation.txt /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/
run: 'cp' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg_Computation.txt' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/'
Status: Finish: Execution time 301ms
WRITING PARAMETER FILES: DONE!
***********************************************
*************************************************
N4 ITK Bias Field Correction...
Status: Start N4ITKBiasFieldCorrection /scratch/kykwan_fluxm/leshi/MRI/test/20110807_KM02082_T1.nrrd /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd --bsplineorder 3 --shrinkfactor 4 --splinedistance 0 --convergencethreshold 0.0001 --iterations 50,40,30 --meshresolution 1,1,1
run: 'N4ITKBiasFieldCorrection' '/scratch/kykwan_fluxm/leshi/MRI/test/20110807_KM02082_T1.nrrd' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd' '--bsplineorder' '3' '--shrinkfactor' '4' '--splinedistance' '0' '--convergencethreshold' '0.0001' '--iterations' '50,40,30' '--meshresolution' '1,1,1'
Status: Finish: Execution time 300ms
N4 ITK Bias Field Correction: DONE!
*************************************************
REGISTERING CASES TO A TEMPLATE...
T1 registration...
Case Number: 20110807_KM02082_T1
Computing rigid transformation T1 to Atlas ...
Status: Start BRAINSFit --fixedVolume /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/templateSkull.nrrd --movingVolume /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd --transformType Rigid --initializeTransformMode useCenterOfHeadAlign --outputTransform /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias.txt --outputVolume /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd --interpolationMode BSpline --outputVolumePixelType short
run: 'BRAINSFit' '--fixedVolume' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/templateSkull.nrrd' '--movingVolume' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd' '--transformType' 'Rigid' '--initializeTransformMode' 'useCenterOfHeadAlign' '--outputTransform' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias.txt' '--outputVolume' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd' '--interpolationMode' 'BSpline' '--outputVolumePixelType' 'short'
Status: Finish: Execution time 300ms
Applying rigid transformation...
Status: Start ResampleVolume2 /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd --transformationFile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias.txt -i bs --Reference /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/templateSkull.nrrd
run: 'ResampleVolume2' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Bias/20110807_KM02082_T1_Bias.nrrd' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd' '--transformationFile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias.txt' '-i' 'bs' '--Reference' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/templateSkull.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd -threshMask 0,1000000 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd' '-threshMask' '0,1000000' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd'
Status: Finish: Execution time 300ms
REGISTERING CASES TO A TEMPLATE: DONE!
*************************************************
TISSUE SEGMENTATION...
Case Number: 20110807_KM02082_T1
Status: Start ABC /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems/ABCparam.xml
run: 'ABC' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems/ABCparam.xml'
Status: Finish: Execution time 300ms
EMS SEGMENTATION: DONE!
*************************************************
SKULL STRIPPING...
Case Number: 20110807_KM02082_T1
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems/20110807_KM02082_T1_Bias_regAtlas_labels_EMS.nrrd -threshold 1,10000 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMStmp1.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems/20110807_KM02082_T1_Bias_regAtlas_labels_EMS.nrrd' '-threshold' '1,10000' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMStmp1.nrrd'
Status: Finish: Execution time 300ms
Status: Start SegPostProcessCLP /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMStmp1.nrrd /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd --skullstripping /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd --mask /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMS_mask.nrrd
run: 'SegPostProcessCLP' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMStmp1.nrrd' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd' '--skullstripping' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/atlasIso/20110807_KM02082_T1_Bias_regAtlas.nrrd' '--mask' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_labels_EMS_mask.nrrd'
Status: Finish: Execution time 301ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd -constOper 2,1 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd' '-constOper' '2,1' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS.nrrd'
Status: Finish: Execution time 300ms
SKULL STRIPPING: DONE!
*************************************************
TISSUE SEGMENTATION...
Case Number: 20110807_KM02082_T1
The Atlas is /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/ABC_stripped/
Status: Start ABC /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/ABCparam.xml
run: 'ABC' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/ABCparam.xml'
Status: Finish: Execution time 300ms
EMS SEGMENTATION: DONE!
*************************************************
SKULL STRIPPING...
Case Number: 20110807_KM02082_T1
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd -threshold 1,10000 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2tmp1.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd' '-threshold' '1,10000' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2tmp1.nrrd'
Status: Finish: Execution time 300ms
Status: Start SegPostProcessCLP /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2tmp1.nrrd /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd --skullstripping /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2//20110807_KM02082_T1_Bias_regAtlas_stripEMS_corrected_EMS_2.nrrd --mask /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2_mask.nrrd
run: 'SegPostProcessCLP' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2tmp1.nrrd' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '--skullstripping' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2//20110807_KM02082_T1_Bias_regAtlas_stripEMS_corrected_EMS_2.nrrd' '--mask' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2_mask.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -constOper 2,1 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-constOper' '2,1' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd'
Status: Finish: Execution time 300ms
SKULL STRIPPING: DONE!
*************************************************
INTENSITYCALIBRATION
Case Number: 20110807_KM02082_T1
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -matchHistogram /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-matchHistogram' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd'
Status: Finish: Execution time 301ms
INTENSITY CALIBRATION DONE!
*************************************************
AFFINE REGISTRATION...
Case Number: 20110807_KM02082_T1
Status: Start BRAINSFit --fixedVolume /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd --movingVolume /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd --transformType Rigid --initializeTransformMode useCenterOfHeadAlign --useAffine --outputVolume /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd --outputTransform /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_initializetransform.txt --interpolationMode BSpline --outputVolumePixelType short
run: 'BRAINSFit' '--fixedVolume' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd' '--movingVolume' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd' '--transformType' 'Rigid' '--initializeTransformMode' 'useCenterOfHeadAlign' '--useAffine' '--outputVolume' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd' '--outputTransform' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_initializetransform.txt' '--interpolationMode' 'BSpline' '--outputVolumePixelType' 'short'
Status: Finish: Execution time 300ms
AFFINE REGISTRATION: DONE!
*************************************************
WARPING COMPUTATION...
Case Number: 20110807_KM02082_T1
Error:No Skull Stripped File!
Computing transformation...
Status: Start BRAINSDemonWarp -f /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/ -m /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd --inputPixelType short --initializeWithTransform /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_initializetransform.txt -o /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd -O /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_transform.nrrd --outputPixelType short --registrationFilterType LogDemons -s 2 -n 5 --minimumMovingPyramid 16,16,16 --minimumFixedPyramid 16,16,16 -i 300,50,30,20,15 --interpolationMode BSpline
run: 'BRAINSDemonWarp' '-f' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/' '-m' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd' '--inputPixelType' 'short' '--initializeWithTransform' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasAffReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_initializetransform.txt' '-o' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd' '-O' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_transform.nrrd' '--outputPixelType' 'short' '--registrationFilterType' 'LogDemons' '-s' '2' '-n' '5' '--minimumMovingPyramid' '16,16,16' '--minimumFixedPyramid' '16,16,16' '-i' '300,50,30,20,15' '--interpolationMode' 'BSpline'
Status: Finish: Execution time 300ms
Status: Start ResampleVolume2 /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd --hfieldtype displacement -i bs -H /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_transform.nrrd --Reference /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/
run: 'ResampleVolume2' '/scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled.nrrd' '--hfieldtype' 'displacement' '-i' 'bs' '-H' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/AtlasWarpReg-20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped-irescaled_transform.nrrd' '--Reference' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/'
Status: Finish: Execution time 300ms
WARPING COMPUTATION: DONE!
*************************************************
ROI TRANSFORMATION...
Case Number: 20110807_KM02082_T1
Error:No Nrrd File!
ROI TRANSFORMATION DONE!
*************************************************
VOLUME COMPUTATION...
Tissue segmentation volume analysis:
Case Number: 20110807_KM02082_T1
Computing Volume information...
Status: Start ImageStat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -label /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd -volumeSummary -outbase /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2
run: 'ImageStat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-label' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd' '-volumeSummary' '-outbase' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2'
Status: Finish: Execution time 300ms
Gathering tissue volume information for the whole dataset...
Status: Start cat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2_volumeSummary.csv
run: 'cat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2_volumeSummary.csv'
Status: Finish: Execution time 300ms
Generic ROI map volume analysis:
GenericROIFile:SubCortical:
Case Number: 20110807_KM02082_T1
Computing Volume information...
Status: Start ImageStat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -label /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg.nrrd -volumeSummary -outbase /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg
run: 'ImageStat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-label' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg.nrrd' '-volumeSummary' '-outbase' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg'
Status: Finish: Execution time 300ms
Gathering volume information for the whole dataset...
Status: Start cat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg_volumeSummary.csv
run: 'cat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--SubCortical-WarpReg_volumeSummary.csv'
Status: Finish: Execution time 300ms
Parcellation map volume analysis:
Parcellation File: template_parc
Case Number: 20110807_KM02082_T1
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd -extractLabel 1 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_WM.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd' '-extractLabel' '1' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_WM.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd -mask /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_WM.nrrd -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd' '-mask' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_WM.nrrd' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageStat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -label /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM.nrrd -volumeSummary -outbase /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM
run: 'ImageStat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-label' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM.nrrd' '-volumeSummary' '-outbase' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM'
Status: Finish: Execution time 300ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd -extractLabel 2 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_GM.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd' '-extractLabel' '2' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_GM.nrrd'
Status: Finish: Execution time 301ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd -mask /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_GM.nrrd -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd' '-mask' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_GM.nrrd' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageStat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -label /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM.nrrd -volumeSummary -outbase /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM
run: 'ImageStat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-label' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM.nrrd' '-volumeSummary' '-outbase' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM'
Status: Finish: Execution time 300ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd -extractLabel 3 -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_CSF.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_labels_EMS_2.nrrd' '-extractLabel' '3' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_CSF.nrrd'
Status: Finish: Execution time 301ms
Status: Start ImageMath /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd -mask /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_CSF.nrrd -outfile /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF.nrrd
run: 'ImageMath' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg.nrrd' '-mask' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/ems_2/20110807_KM02082_T1_Bias_regAtlas_stripEMS_CSF.nrrd' '-outfile' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF.nrrd'
Status: Finish: Execution time 300ms
Status: Start ImageStat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd -label /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF.nrrd -volumeSummary -outbase /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF
run: 'ImageStat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/Stripped/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS-stripped.nrrd' '-label' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF.nrrd' '-volumeSummary' '-outbase' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF'
Status: Finish: Execution time 300ms
Gathering volume information for the whole dataset...
Status: Start cat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM_volumeSummary.csv
run: 'cat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_WM_volumeSummary.csv'
Status: Finish: Execution time 300ms
Status: Start cat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM_volumeSummary.csv
run: 'cat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_GM_volumeSummary.csv'
Status: Finish: Execution time 301ms
Status: Start cat /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF_volumeSummary.csv
run: 'cat' '/scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg/WarpROI/20110807_KM02082_T1_Bias_regAtlas_corrected_EMS--template_parc-WarpReg_CSF_volumeSummary.csv'
Status: Finish: Execution time 301ms
VOLUME COMPUTATION: DONE!
End of Automatic Segmentation!
finished with BatchMake execution: /scratch/kykwan_fluxm/leshi/MRI/test/AutoSeg.bms
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
best,
lei