Dear all,
I'm trying to troubleshoot an error that I'm getting when running v4.0
PreFreeSurferPipelineBatch. I initially thought the error arose as a result of
grandunwarp but I don't think that is the case anymore. This is the error I am
receiving:
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
and
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
are the same file
I have attached the full output to stdout. Any insights?
Kind regards,
Dinal Jayasekera<https://dinaljay.weebly.com/>
PhD Candidate | InSITE Fellow<https://www.insitefellows.org/>
Ammar Hawasli Lab<https://hawaslilab.weebly.com/>
Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx>
| Washington University in St. Louis<https://wustl.edu/>
_______________________________________________
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StudyFolder: /media/functionalspinelab/RAID/Data/Dinal/mystudy
Subjlist: NSI_21
EnvironmentScript:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/Examples/Scripts/SetUpHCPPipeline.sh
Run locally: TRUE
This script must be SOURCED to correctly setup the environment prior to running
any of the other HCP scripts contained here
NSI_21
Found 1 T1w Images for subject NSI_21
Found 1 T2w Images for subject NSI_21
About to run
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/PreFreeSurfer/PreFreeSurferPipeline.sh
PreFreeSurferPipeline.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
PreFreeSurferPipeline.sh: FSLDIR: /usr/local/fsl
PreFreeSurferPipeline.sh: HCPPIPEDIR_Global:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/scripts
PreFreeSurferPipeline.sh: HCPPIPEDIR_PreFS:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/PreFreeSurfer/scripts
Thu Jun 27 10:57:36 CDT 2019:PreFreeSurferPipeline.sh: Platform Information
Follows:
Linux fsl2 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux
Thu Jun 27 10:57:36 CDT 2019:PreFreeSurferPipeline.sh: Parsing Command Line
Options
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Finished Parsing Command
Line Options
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: StudyFolder:
/media/functionalspinelab/RAID/Data/Dinal/mystudy
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Subject: NSI_21
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wInputImages:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T1w_MPR1/NSI_21_3T_T1w_MPR1.nii.gz@
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wInputImages:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T2w_SPC1/NSI_21_3T_T2w_SPC1.nii.gz@
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplate:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplateBrain:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm_brain.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wTemplate2mm:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_2mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplate:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_0.7mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplateBrain:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_0.7mm_brain.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wTemplate2mm:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_2mm.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: TemplateMask:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Template2mmMask:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: BrainSize: 150
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: FNIRTConfig:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/T1_2_MNI152_2mm.cnf
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: MagnitudeInputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: PhaseInputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: GEB0InputName: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: TE: NONE
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh:
SpinEchoPhaseEncodeNegative:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T1w_MPR1/NSI_21_3T_SpinEchoFieldMap_AP.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh:
SpinEchoPhaseEncodePositive:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/unprocessed/3T/T1w_MPR1/NSI_21_3T_SpinEchoFieldMap_PA.nii.gz
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: SEEchoSpacing: 0.00056
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: SEUnwarpDir: y
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wSampleSpacing:
0.0000021
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wSampleSpacing:
0.0000021
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: UnwarpDir: z
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh:
GradientDistortionCoeffs:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/coeff_AS82_Prisma.grad
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: AvgrdcSTRING: TOPUP
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: TopupConfig:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/b02b0.cnf
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma:
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: UseJacobian: true
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: FSLDIR: /usr/local/fsl
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
========================================
DIRECTORY: /home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
PRODUCT: HCP Pipeline Scripts
VERSION: v4.0.0
========================================
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/scripts
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: HCPPIPEDIR_PreFS:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/PreFreeSurfer/scripts
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T1wFolder:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T1w
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: T2wFolder:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: AtlasSpaceFolder:
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/MNINonLinear
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T1w/xfms/
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/xfms/
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/MNINonLinear/xfms/
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: POSIXLY_CORRECT=
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Processing Modality: T1w
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: Performing Gradient
Nonlinearity Correction
Thu Jun 27 10:57:38 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T1w/T1w1_GradientDistortionUnwarp
GradientDistortionUnwarp.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 10:57:39 CDT 2019:GradientDistortionUnwarp.sh: START
gradunwarp-INFO: Parsing
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/coeff_AS82_Prisma.grad
for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . . .
. . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . .
. . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . .
150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . .
. . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 .
. . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . .
. 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . .
. . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320
gradunwarp-INFO: Writing output to trilinear.nii.gz
Thu Jun 27 11:01:07 CDT 2019:GradientDistortionUnwarp.sh: END
Thu Jun 27 11:01:07 CDT 2019:PreFreeSurferPipeline.sh: Not Averaging T1w Images
Thu Jun 27 11:01:07 CDT 2019:PreFreeSurferPipeline.sh: ONLY ONE AVERAGE FOUND:
COPYING
Thu Jun 27 11:01:08 CDT 2019:PreFreeSurferPipeline.sh: Aligning T1w image to
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T1_0.7mm.nii.gz
to create native volume space
Thu Jun 27 11:01:08 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T1w/ACPCAlignment
ACPCAlignment.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
ACPCAlignment.sh: FSLDIR: /usr/local/fsl
Thu Jun 27 11:01:08 CDT 2019:ACPCAlignment.sh: START
Final FOV is:
0.000000 208.000000 0.000000 300.000000 75.000000 188.000000
Thu Jun 27 11:02:23 CDT 2019:ACPCAlignment.sh: END
Thu Jun 27 11:02:23 CDT 2019:PreFreeSurferPipeline.sh: Performing Brain
Extraction using FNIRT-based Masking
Thu Jun 27 11:02:23 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T1w/BrainExtraction_FNIRTbased
BrainExtraction_FNIRTbased.sh: FSLDIR: /usr/local/fsl
BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates
BrainExtraction_FNIRTbased.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:02:23 CDT 2019:BrainExtraction_FNIRTbased.sh: START:
BrainExtraction_FNIRT
Thu Jun 27 11:11:14 CDT 2019:BrainExtraction_FNIRTbased.sh: END:
BrainExtraction_FNIRT
Thu Jun 27 11:11:14 CDT 2019:PreFreeSurferPipeline.sh: Processing Modality: T2w
Thu Jun 27 11:11:14 CDT 2019:PreFreeSurferPipeline.sh: Performing Gradient
Nonlinearity Correction
Thu Jun 27 11:11:14 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2w1_GradientDistortionUnwarp
GradientDistortionUnwarp.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:11:15 CDT 2019:GradientDistortionUnwarp.sh: START
gradunwarp-INFO: Parsing
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/coeff_AS82_Prisma.grad
for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70 . . . . . .
. . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . .
. . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . .
150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . .
. . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 .
. . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . .
. 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . .
. . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320
gradunwarp-INFO: Writing output to trilinear.nii.gz
Thu Jun 27 11:14:48 CDT 2019:GradientDistortionUnwarp.sh: END
Thu Jun 27 11:14:48 CDT 2019:PreFreeSurferPipeline.sh: Not Averaging T2w Images
Thu Jun 27 11:14:48 CDT 2019:PreFreeSurferPipeline.sh: ONLY ONE AVERAGE FOUND:
COPYING
Thu Jun 27 11:14:49 CDT 2019:PreFreeSurferPipeline.sh: Aligning T2w image to
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates/MNI152_T2_0.7mm.nii.gz
to create native volume space
Thu Jun 27 11:14:49 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/ACPCAlignment
ACPCAlignment.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
ACPCAlignment.sh: FSLDIR: /usr/local/fsl
Thu Jun 27 11:14:49 CDT 2019:ACPCAlignment.sh: START
Final FOV is:
0.000000 208.000000 0.000000 300.000000 74.000000 188.000000
Thu Jun 27 11:16:03 CDT 2019:ACPCAlignment.sh: END
Thu Jun 27 11:16:03 CDT 2019:PreFreeSurferPipeline.sh: Performing Brain
Extraction using FNIRT-based Masking
Thu Jun 27 11:16:03 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/BrainExtraction_FNIRTbased
BrainExtraction_FNIRTbased.sh: FSLDIR: /usr/local/fsl
BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/templates
BrainExtraction_FNIRTbased.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:16:03 CDT 2019:BrainExtraction_FNIRTbased.sh: START:
BrainExtraction_FNIRT
Thu Jun 27 11:26:16 CDT 2019:BrainExtraction_FNIRTbased.sh: END:
BrainExtraction_FNIRT
Thu Jun 27 11:26:16 CDT 2019:PreFreeSurferPipeline.sh: Performing TOPUP Readout
Distortion Correction
Thu Jun 27 11:26:16 CDT 2019:PreFreeSurferPipeline.sh: mkdir -p
/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg
T2wToT1wDistortionCorrectAndReg.sh: FSLDIR: /usr/local/fsl
T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR_Global:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/scripts
T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:26:18 CDT 2019:T2wToT1wDistortionCorrectAndReg.sh: START
TopupPreprocessingAll.sh: FSLDIR: /usr/local/fsl
TopupPreprocessingAll.sh: HCPPIPEDIR_Global:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/scripts
Thu Jun 27 11:26:18 CDT 2019:TopupPreprocessingAll.sh: START: Topup Field Map
Generation and Gradient Unwarping
GradientDistortionUnwarp.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:26:19 CDT 2019:GradientDistortionUnwarp.sh: START
gradunwarp-INFO: Parsing
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/coeff_AS82_Prisma.grad
for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60
gradunwarp-INFO: Writing output to trilinear.nii.gz
Thu Jun 27 11:26:43 CDT 2019:GradientDistortionUnwarp.sh: END
GradientDistortionUnwarp.sh: HCPPIPEDIR:
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0
Thu Jun 27 11:26:43 CDT 2019:GradientDistortionUnwarp.sh: START
gradunwarp-INFO: Parsing
/home/functionalspinelab/Desktop/Dinal/Pipelines_v4.0/global/config/coeff_AS82_Prisma.grad
for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . .
. 40 . . . . . . . . . 50 . . . . . . . . . 60
gradunwarp-INFO: Writing output to trilinear.nii.gz
Thu Jun 27 11:27:08 CDT 2019:GradientDistortionUnwarp.sh: END
SSD = 1587.05 n = 54180 Reg = 0 Cost = 1587.05
SSD = 1054.5 n = 54180 Reg = 78.2141 Cost = 1132.71
SSD = 811.752 n = 54180 Reg = 147.512 Cost = 959.264
SSD = 688.268 n = 54180 Reg = 185.675 Cost = 873.943
SSD = 631.747 n = 54178 Reg = 205.021 Cost = 836.768
SSD = 610.504 n = 54107 Reg = 213.569 Cost = 824.073
***Going to next resolution level***
SSD = 999.867 n = 54107 Reg = 100.321 Cost = 1100.19
SSD = 684.266 n = 54179 Reg = 139.32 Cost = 823.586
SSD = 580.459 n = 54180 Reg = 176.751 Cost = 757.21
SSD = 542.366 n = 54180 Reg = 192.955 Cost = 735.321
SSD = 525.868 n = 54180 Reg = 200.201 Cost = 726.07
SSD = 517.773 n = 54180 Reg = 203.838 Cost = 721.611
***Going to next resolution level***
SSD = 1156.36 n = 54180 Reg = 45.6667 Cost = 1202.02
SSD = 848.965 n = 54180 Reg = 94.4489 Cost = 943.414
SSD = 759.67 n = 54180 Reg = 125.756 Cost = 885.426
SSD = 730.958 n = 54180 Reg = 139.409 Cost = 870.368
SSD = 719.425 n = 54180 Reg = 145.29 Cost = 864.715
SSD = 713.598 n = 54180 Reg = 148.177 Cost = 861.775
***Going to next resolution level***
SSD = 850.62 n = 54180 Reg = 34.5196 Cost = 885.139
SSD = 511.517 n = 54180 Reg = 46 Cost = 557.517
SSD = 426.203 n = 54180 Reg = 64.2323 Cost = 490.435
SSD = 403.548 n = 54180 Reg = 71.8181 Cost = 475.366
SSD = 395.021 n = 54180 Reg = 74.6257 Cost = 469.647
SSD = 390.966 n = 54180 Reg = 75.7736 Cost = 466.74
***Going to next resolution level***
SSD = 391.061 n = 54180 Reg = 25.5055 Cost = 416.566
SSD = 367.516 n = 54180 Reg = 33.4853 Cost = 401.001
SSD = 357.073 n = 54180 Reg = 38.4386 Cost = 395.512
SSD = 353.157 n = 54180 Reg = 40.2906 Cost = 393.448
SSD = 351.478 n = 54180 Reg = 41.0309 Cost = 392.509
SSD = 350.628 n = 54180 Reg = 41.4 Cost = 392.028
***Going to next resolution level***
SSD = 1069.86 n = 456590 Reg = 132.784 Cost = 1202.64
SSD = 1028.13 n = 456590 Reg = 127.574 Cost = 1155.7
SSD = 971.942 n = 456590 Reg = 120.6 Cost = 1092.54
SSD = 904.34 n = 456590 Reg = 112.297 Cost = 1016.64
SSD = 830.519 n = 456590 Reg = 103.389 Cost = 933.908
SSD = 757.095 n = 456590 Reg = 94.8057 Cost = 851.901
SSD = 731.334 n = 456590 Reg = 91.9069 Cost = 823.241
SSD = 666.768 n = 456590 Reg = 85.1221 Cost = 751.89
SSD = 633.055 n = 456590 Reg = 81.9515 Cost = 715.007
SSD = 585.682 n = 456590 Reg = 78.6868 Cost = 664.369
SSD = 567.366 n = 456590 Reg = 77.5307 Cost = 644.897
***Going to next resolution level***
SSD = 675.132 n = 456590 Reg = 9.41072 Cost = 684.543
SSD = 671.149 n = 456590 Reg = 9.35675 Cost = 680.506
SSD = 667.033 n = 456590 Reg = 9.30306 Cost = 676.337
SSD = 661.509 n = 456590 Reg = 9.23567 Cost = 670.745
SSD = 652.503 n = 456590 Reg = 9.13286 Cost = 661.636
SSD = 643.772 n = 456590 Reg = 9.04755 Cost = 652.82
SSD = 632.619 n = 456590 Reg = 8.95052 Cost = 641.57
SSD = 615.019 n = 456590 Reg = 8.83614 Cost = 623.855
SSD = 597.37 n = 456590 Reg = 8.77801 Cost = 606.148
SSD = 571.299 n = 456590 Reg = 8.81522 Cost = 580.115
SSD = 554.934 n = 456590 Reg = 8.95964 Cost = 563.894
***Going to next resolution level***
SSD = 554.936 n = 456590 Reg = 0.0895967 Cost = 555.025
SSD = 552.563 n = 456590 Reg = 0.089247 Cost = 552.652
SSD = 550.536 n = 456590 Reg = 0.0889906 Cost = 550.625
SSD = 547.803 n = 456590 Reg = 0.0887222 Cost = 547.891
SSD = 543.758 n = 456590 Reg = 0.0883824 Cost = 543.846
SSD = 540.964 n = 456590 Reg = 0.0882202 Cost = 541.052
SSD = 535.121 n = 456590 Reg = 0.0879406 Cost = 535.209
SSD = 530.497 n = 456590 Reg = 0.087926 Cost = 530.585
SSD = 524.279 n = 456590 Reg = 0.088255 Cost = 524.367
SSD = 518.188 n = 456590 Reg = 0.0890173 Cost = 518.277
SSD = 509.321 n = 456590 Reg = 0.0907984 Cost = 509.411
SSD = 498.584 n = 456590 Reg = 0.0938552 Cost = 498.678
SSD = 487.853 n = 456590 Reg = 0.0984739 Cost = 487.952
SSD = 478.64 n = 456590 Reg = 0.104297 Cost = 478.744
SSD = 472.733 n = 456590 Reg = 0.109027 Cost = 472.842
SSD = 467.471 n = 456590 Reg = 0.113686 Cost = 467.584
SSD = 463.759 n = 456590 Reg = 0.116545 Cost = 463.875
SSD = 460.03 n = 456590 Reg = 0.119511 Cost = 460.149
SSD = 456.915 n = 456590 Reg = 0.121025 Cost = 457.036
SSD = 452.693 n = 456590 Reg = 0.123066 Cost = 452.816
SSD = 449.92 n = 456590 Reg = 0.124155 Cost = 450.044
***Going to next resolution level***
SSD = 449.92 n = 456590 Reg = 0.0024831 Cost = 449.922
SSD = 448.995 n = 456590 Reg = 0.00247745 Cost = 448.998
SSD = 448.099 n = 456590 Reg = 0.00247144 Cost = 448.102
SSD = 446.829 n = 456590 Reg = 0.00246202 Cost = 446.831
SSD = 444.677 n = 456590 Reg = 0.00244554 Cost = 444.679
SSD = 442.901 n = 456590 Reg = 0.0024307 Cost = 442.904
SSD = 439.978 n = 456590 Reg = 0.00240663 Cost = 439.981
SSD = 436.342 n = 456590 Reg = 0.00237433 Cost = 436.344
SSD = 432.707 n = 456590 Reg = 0.00233917 Cost = 432.71
SSD = 429.16 n = 456590 Reg = 0.00230074 Cost = 429.162
SSD = 426.154 n = 456590 Reg = 0.00226405 Cost = 426.156
SSD = 422.962 n = 456590 Reg = 0.00222144 Cost = 422.965
SSD = 420.7 n = 456590 Reg = 0.00218968 Cost = 420.703
SSD = 418.543 n = 456590 Reg = 0.00215936 Cost = 418.545
SSD = 417.325 n = 456590 Reg = 0.00214336 Cost = 417.327
SSD = 416.052 n = 456590 Reg = 0.0021282 Cost = 416.054
SSD = 415.448 n = 456590 Reg = 0.0021231 Cost = 415.45
SSD = 414.645 n = 456590 Reg = 0.00211969 Cost = 414.647
SSD = 414.106 n = 456590 Reg = 0.0021205 Cost = 414.108
SSD = 413.095 n = 456590 Reg = 0.0021281 Cost = 413.097
SSD = 412.327 n = 456590 Reg = 0.00213822 Cost = 412.329
SSD = 410.815 n = 456590 Reg = 0.00216687 Cost = 410.817
SSD = 409.509 n = 456590 Reg = 0.00219414 Cost = 409.511
SSD = 407.347 n = 456590 Reg = 0.00225114 Cost = 407.349
SSD = 406.078 n = 456590 Reg = 0.00229059 Cost = 406.081
SSD = 404.234 n = 456590 Reg = 0.00234816 Cost = 404.236
SSD = 402.83 n = 456590 Reg = 0.00239305 Cost = 402.833
SSD = 401.528 n = 456590 Reg = 0.00244107 Cost = 401.531
SSD = 400.084 n = 456590 Reg = 0.00249795 Cost = 400.086
SSD = 398.801 n = 456590 Reg = 0.00255172 Cost = 398.803
SSD = 397.378 n = 456590 Reg = 0.00261248 Cost = 397.38
SSD = 395.873 n = 456590 Reg = 0.00268396 Cost = 395.876
SSD = 394.422 n = 456590 Reg = 0.00275536 Cost = 394.425
SSD = 392.518 n = 456590 Reg = 0.00285208 Cost = 392.521
SSD = 391.233 n = 456590 Reg = 0.00291579 Cost = 391.236
SSD = 389.724 n = 456590 Reg = 0.0029927 Cost = 389.727
SSD = 388.584 n = 456590 Reg = 0.00305323 Cost = 388.587
SSD = 387.539 n = 456590 Reg = 0.00310945 Cost = 387.542
SSD = 386.548 n = 456590 Reg = 0.00316305 Cost = 386.551
SSD = 385.712 n = 456590 Reg = 0.00320746 Cost = 385.715
SSD = 384.58 n = 456590 Reg = 0.0032634 Cost = 384.583
SSD = 383.598 n = 456590 Reg = 0.00331248 Cost = 383.601
SSD = 382.74 n = 456590 Reg = 0.00335818 Cost = 382.743
SSD = 381.805 n = 456590 Reg = 0.00340617 Cost = 381.808
SSD = 380.869 n = 456590 Reg = 0.00344588 Cost = 380.872
SSD = 379.803 n = 456590 Reg = 0.00349079 Cost = 379.806
SSD = 379.156 n = 456590 Reg = 0.00351734 Cost = 379.159
SSD = 378.343 n = 456590 Reg = 0.00355093 Cost = 378.346
SSD = 377.696 n = 456590 Reg = 0.00357711 Cost = 377.7
SSD = 377.103 n = 456590 Reg = 0.00360054 Cost = 377.106
SSD = 376.457 n = 456590 Reg = 0.00362532 Cost = 376.461
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
and
'/media/functionalspinelab/RAID/Data/Dinal/mystudy/NSI_21/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/TopupField.nii.gz'
are the same file
