Wed May 8 15:57:09 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 16102552 16775280 0 639064 11191584 -/+ buffers/cache: 4271904 28605928 Swap: 67108848 22412 67086436 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-19:57:10-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-19:57:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-19:57:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-19:57:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-19:57:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-36 Linux compute-0-36 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 29360128 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 224391 total used free shared buffers cached Mem: 28741920 2665940 26075980 0 119748 123992 -/+ buffers/cache: 2422200 26319720 Swap: 67108856 120040 66988816 #------------------------------------- /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-preproc #------------------------------------- #@# Image corrections Wed May 8 15:57:22 EDT 2013 mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm... Getting Series No INFO: Found 81 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009 INFO: Scanning for Series Number 9 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 153605.779000 AcqTime 153231.872500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9970 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 995.3223 1152.7700 -67.0698 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 79), nframes = 70, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9970, TR = 9970 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#1 0.000000 1 1 ep_b0#2 0.000000 2 2 ep_b0#3 0.000000 3 3 ep_b0#4 0.000000 4 4 ep_b0#5 0.000000 5 5 ep_b0#6 0.000000 6 6 ep_b0#7 0.000000 7 7 ep_b0#8 0.000000 8 8 ep_b0#9 0.000000 9 9 ep_b0#10 0.000000 10 10 ep_b700#1 700.000000 1 11 ep_b700#2 700.000000 2 12 ep_b700#3 700.000000 3 13 ep_b700#4 700.000000 4 14 ep_b700#5 700.000000 5 15 ep_b700#6 700.000000 6 16 ep_b700#7 700.000000 7 17 ep_b700#8 700.000000 8 18 ep_b700#9 700.000000 9 19 ep_b700#10 700.000000 10 20 ep_b700#11 700.000000 11 21 ep_b700#12 700.000000 12 22 ep_b700#13 700.000000 13 23 ep_b700#14 700.000000 14 24 ep_b700#15 700.000000 15 25 ep_b700#16 700.000000 16 26 ep_b700#17 700.000000 17 27 ep_b700#18 700.000000 18 28 ep_b700#19 700.000000 19 29 ep_b700#20 700.000000 20 30 ep_b700#21 700.000000 21 31 ep_b700#22 700.000000 22 32 ep_b700#23 700.000000 23 33 ep_b700#24 700.000000 24 34 ep_b700#25 700.000000 25 35 ep_b700#26 700.000000 26 36 ep_b700#27 700.000000 27 37 ep_b700#28 700.000000 28 38 ep_b700#29 700.000000 29 39 ep_b700#30 700.000000 30 40 ep_b700#31 700.000000 31 41 ep_b700#32 700.000000 32 42 ep_b700#33 700.000000 33 43 ep_b700#34 700.000000 34 44 ep_b700#35 700.000000 35 45 ep_b700#36 700.000000 36 46 ep_b700#37 700.000000 37 47 ep_b700#38 700.000000 38 48 ep_b700#39 700.000000 39 49 ep_b700#40 700.000000 40 50 ep_b700#41 700.000000 41 51 ep_b700#42 700.000000 42 52 ep_b700#43 700.000000 43 53 ep_b700#44 700.000000 44 54 ep_b700#45 700.000000 45 55 ep_b700#46 700.000000 46 56 ep_b700#47 700.000000 47 57 ep_b700#48 700.000000 48 58 ep_b700#49 700.000000 49 59 ep_b700#50 700.000000 50 60 ep_b700#51 700.000000 51 61 ep_b700#52 700.000000 52 62 ep_b700#53 700.000000 53 63 ep_b700#54 700.000000 54 64 ep_b700#55 700.000000 55 65 ep_b700#56 700.000000 56 66 ep_b700#57 700.000000 57 67 ep_b700#58 700.000000 58 68 ep_b700#59 700.000000 59 69 ep_b700#60 700.000000 60 bValue = 700 nB0 = 10 nDir = 60 GradFile /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000070.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 153605.779000 AcqTime 154402.565000 Acquisition parameters PulseSeq ep_b700#60 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9970 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 8 SeriesNo 9 ImageNo 70 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 995.3223 1152.7700 -67.0698 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0.000209649 0.0208202 0.999783 INFO: no Siemens slice order reversal detected (good!). TR=9970.00, TE=84.00, TI=-1.00, flip angle=90.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mri_probedicom --i /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm > /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dcminfo.dat flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 6.34232 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.mghdti.bvecs /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.mghdti.bvals /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvals eddy_correct /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz 0 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0000 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0001 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0002 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0003 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0004 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0005 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0006 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0007 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0008 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0009 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0010 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0011 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0012 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0013 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0014 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0015 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0016 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0017 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0018 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0019 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0020 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0021 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0022 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0023 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0024 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0025 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0026 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0027 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0028 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0029 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0030 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0031 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0032 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0033 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0034 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0035 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0036 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0037 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0038 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0039 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0040 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0041 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0042 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0043 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0044 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0045 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0046 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0047 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0048 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0049 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0050 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0051 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0052 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0053 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0054 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0055 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0056 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0057 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0058 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0059 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0060 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0061 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0062 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0063 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0064 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0065 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0066 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0067 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0068 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0069 mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs.norot xfmrot /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.ecclog /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs.norot /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm... Getting Series No INFO: Found 50 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004 INFO: Scanning for Series Number 4 Scanning Directory INFO: found 47 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: ( 72 72 47), nframes = 1, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 151543.380000 AcqTime 151429.742500 Acquisition parameters PulseSeq fm2d2r Protocol field_mapping PhEncDir COL EchoNo 1 FlipAngle 55 EchoTime 4.24 InversionTime -1 RepetitionTime 500 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 72 NImageCols 72 NFrames 1 SliceArraylSize 47 IsMosaic 0 ImgPos 102.5377 131.2738 -50.6461 VolRes 3.0000 3.0000 3.0000 VolDim 72 72 47 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 1.9144 17.8490 22.2101 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=500.00, TE=4.24, TI=-1.00, flip angle=55.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz... flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 27 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm... Getting Series No INFO: Found 50 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 47 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. INFO: ( 72 72 47), nframes = 1, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 151543.662000 AcqTime 151430.245000 Acquisition parameters PulseSeq fm2d2r Protocol field_mapping PhEncDir COL EchoNo 2 FlipAngle 55 EchoTime 6.7 InversionTime -1 RepetitionTime 500 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 72 NImageCols 72 NFrames 1 SliceArraylSize 47 IsMosaic 0 ImgPos 102.5377 131.2738 -50.6461 VolRes 3.0000 3.0000 3.0000 VolDim 72 72 47 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 1.9144 17.8490 22.2101 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=500.00, TE=6.70, TI=-1.00, flip angle=55.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz... flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 27 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz mri_probedicom --i /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm > /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0info.dat fslroi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz 0 1 epidewarp.fsl --mag /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz --dph /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz --exf /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz --epi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz --tediff 2.46000000000000000000 --esp 0.51 --vsm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --epidw /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz FSLVersion 5.0.2.2 FSLVerMaj 5 FSL Version is 5.0.2.2, must be 3.X or 4.X Linux compute-0-36 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed May 8 16:22:43 EDT 2013 New invocation of trac-all Wed May 8 18:09:54 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -bedp -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 17462620 15415212 0 639168 12472240 -/+ buffers/cache: 4351212 28526620 Swap: 67108848 22412 67086436 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-22:09:55-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-22:09:58-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-22:09:58-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-22:09:58-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/08-22:09:59-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-all Wed May 8 22:49:27 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -path -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 17284588 15593244 0 639260 11908444 -/+ buffers/cache: 4736884 28140948 Swap: 67108848 22412 67086436 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-02:49:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-02:49:29-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-02:49:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-02:49:30-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-02:49:31-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-paths celine compute-0-53 Linux compute-0-53 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 29360128 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 5328792 27549044 0 202128 2938348 -/+ buffers/cache: 2188316 30689520 Swap: 67108856 94456 67014400 #------------------------------------- /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-paths #------------------------------------- #@# Path reconstruction Wed May 8 22:49:46 EDT 2013 rm -rf /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dpath/lh.cst_AS_avg33_cvs_bbr rm -rf /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dpath/rh.cst_AS_avg33_cvs_bbr /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/dmri_paths --outdir /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dpath/lh.cst_AS_avg33_cvs_bbr /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dpath/rh.cst_AS_avg33_cvs_bbr --dwi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz --grad /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs --bval /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvals --mask /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff/lowb_brain_mask.nii.gz --bpdir /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_end1_dil.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_end1_dil.nii.gz --roi2 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_end2_dil.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_end2_dil.nii.gz --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/diff2anatorig.bbr.mat --regnl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35.m3z --init /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff/lh.cst_AS_avg33_cvs_bbr_cpts_6.txt /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff/rh.cst_AS_avg33_cvs_bbr_cpts_6.txt --nprior /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_fsnnprior_all /autofs/cluster/mscat/users/caterina/3T/r! econs_fs v5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_fsnnids_all /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_fsnnprior_all /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_fsnnids_all --lprior /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_fsprior_all /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/lh.cst_AS_avg33_cvs_bbr_fsids_all /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_fsprior_all /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/rh.cst_AS_avg33_cvs_bbr_fsids_all --seg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/cvs/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff/lh.cst_AS_avg33_cvs_bbr_cpts_6_std.txt /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff/rh.cst_AS_avg33_cvs_bbr_cpts_6_std.txt Linux compute-0-53 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Wed May 8 22:49:47 EDT 2013 New invocation of trac-all Thu May 9 10:24:24 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 18731464 14146368 0 639876 13558800 -/+ buffers/cache: 4532788 28345044 Swap: 67108848 22412 67086436 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-14:24:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-14:24:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-14:24:27-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-14:24:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/09-14:24:28-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-99 Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 29360128 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 2908600 29969236 0 244864 478328 -/+ buffers/cache: 2185408 30692428 Swap: 67108856 107376 67001480 #------------------------------------- /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-preproc #------------------------------------- #@# Image corrections Thu May 9 10:25:17 EDT 2013 mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm... Getting Series No INFO: Found 81 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009 INFO: Scanning for Series Number 9 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 8 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 153605.779000 AcqTime 153231.872500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9970 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 8 SeriesNo 9 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 995.3223 1152.7700 -67.0698 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 79), nframes = 70, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9970, TR = 9970 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#1 0.000000 1 1 ep_b0#2 0.000000 2 2 ep_b0#3 0.000000 3 3 ep_b0#4 0.000000 4 4 ep_b0#5 0.000000 5 5 ep_b0#6 0.000000 6 6 ep_b0#7 0.000000 7 7 ep_b0#8 0.000000 8 8 ep_b0#9 0.000000 9 9 ep_b0#10 0.000000 10 10 ep_b700#1 700.000000 1 11 ep_b700#2 700.000000 2 12 ep_b700#3 700.000000 3 13 ep_b700#4 700.000000 4 14 ep_b700#5 700.000000 5 15 ep_b700#6 700.000000 6 16 ep_b700#7 700.000000 7 17 ep_b700#8 700.000000 8 18 ep_b700#9 700.000000 9 19 ep_b700#10 700.000000 10 20 ep_b700#11 700.000000 11 21 ep_b700#12 700.000000 12 22 ep_b700#13 700.000000 13 23 ep_b700#14 700.000000 14 24 ep_b700#15 700.000000 15 25 ep_b700#16 700.000000 16 26 ep_b700#17 700.000000 17 27 ep_b700#18 700.000000 18 28 ep_b700#19 700.000000 19 29 ep_b700#20 700.000000 20 30 ep_b700#21 700.000000 21 31 ep_b700#22 700.000000 22 32 ep_b700#23 700.000000 23 33 ep_b700#24 700.000000 24 34 ep_b700#25 700.000000 25 35 ep_b700#26 700.000000 26 36 ep_b700#27 700.000000 27 37 ep_b700#28 700.000000 28 38 ep_b700#29 700.000000 29 39 ep_b700#30 700.000000 30 40 ep_b700#31 700.000000 31 41 ep_b700#32 700.000000 32 42 ep_b700#33 700.000000 33 43 ep_b700#34 700.000000 34 44 ep_b700#35 700.000000 35 45 ep_b700#36 700.000000 36 46 ep_b700#37 700.000000 37 47 ep_b700#38 700.000000 38 48 ep_b700#39 700.000000 39 49 ep_b700#40 700.000000 40 50 ep_b700#41 700.000000 41 51 ep_b700#42 700.000000 42 52 ep_b700#43 700.000000 43 53 ep_b700#44 700.000000 44 54 ep_b700#45 700.000000 45 55 ep_b700#46 700.000000 46 56 ep_b700#47 700.000000 47 57 ep_b700#48 700.000000 48 58 ep_b700#49 700.000000 49 59 ep_b700#50 700.000000 50 60 ep_b700#51 700.000000 51 61 ep_b700#52 700.000000 52 62 ep_b700#53 700.000000 53 63 ep_b700#54 700.000000 54 64 ep_b700#55 700.000000 55 65 ep_b700#56 700.000000 56 66 ep_b700#57 700.000000 57 67 ep_b700#58 700.000000 58 68 ep_b700#59 700.000000 59 69 ep_b700#60 700.000000 60 bValue = 700 nB0 = 10 nDir = 60 GradFile /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/diffusion/mgh-dti-seqpack/gradient_mgh_dti60.gdt FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000070.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 153605.779000 AcqTime 154402.565000 Acquisition parameters PulseSeq ep_b700#60 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9970 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 8 SeriesNo 9 ImageNo 70 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 995.3223 1152.7700 -67.0698 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) sagrev = 0, correv =0, trarev = 0 Vs = -0.000209649 0.0208202 0.999783 INFO: no Siemens slice order reversal detected (good!). TR=9970.00, TE=84.00, TI=-1.00, flip angle=90.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mri_probedicom --i /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/DTI/009/928000-000009-000001.dcm > /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dcminfo.dat flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 6.34232 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.mghdti.bvecs /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.mghdti.bvals /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvals eddy_correct /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_orig_flip.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz 0 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0000 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0001 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0002 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0003 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0004 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0005 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0006 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0007 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0008 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0009 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0010 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0011 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0012 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0013 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0014 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0015 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0016 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0017 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0018 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0019 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0020 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0021 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0022 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0023 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0024 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0025 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0026 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0027 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0028 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0029 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0030 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0031 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0032 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0033 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0034 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0035 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0036 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0037 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0038 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0039 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0040 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0041 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0042 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0043 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0044 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0045 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0046 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0047 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0048 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0049 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0050 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0051 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0052 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0053 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0054 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0055 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0056 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0057 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0058 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0059 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0060 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0061 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0062 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0063 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0064 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0065 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0066 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0067 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0068 processing /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_tmp0069 mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs.norot xfmrot /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.ecclog /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs.norot /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/bvecs mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm... Getting Series No INFO: Found 50 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004 INFO: Scanning for Series Number 4 Scanning Directory INFO: found 47 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: ( 72 72 47), nframes = 1, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/004/928000-000004-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 151543.380000 AcqTime 151429.742500 Acquisition parameters PulseSeq fm2d2r Protocol field_mapping PhEncDir COL EchoNo 1 FlipAngle 55 EchoTime 4.24 InversionTime -1 RepetitionTime 500 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 72 NImageCols 72 NFrames 1 SliceArraylSize 47 IsMosaic 0 ImgPos 102.5377 131.2738 -50.6461 VolRes 3.0000 3.0000 3.0000 VolDim 72 72 47 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 1.9144 17.8490 22.2101 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=500.00, TE=4.24, TI=-1.00, flip angle=55.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz... flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 27 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm... Getting Series No INFO: Found 50 files in /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 47 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. INFO: ( 72 72 47), nframes = 1, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 -0.065 0.015 0.885; 0.066 0.969 -0.236 -14.711; 0.001 0.237 0.972 21.424; 0.000 0.000 0.000 1.000; FileName /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ms036_07072010_3T Date and time StudyDate 20100707 StudyTime 151018.928000 SeriesTime 151543.662000 AcqTime 151430.245000 Acquisition parameters PulseSeq fm2d2r Protocol field_mapping PhEncDir COL EchoNo 2 FlipAngle 55 EchoTime 6.7 InversionTime -1 RepetitionTime 500 PhEncFOV 216 ReadoutFOV 216 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 72 NImageCols 72 NFrames 1 SliceArraylSize 47 IsMosaic 0 ImgPos 102.5377 131.2738 -50.6461 VolRes 3.0000 3.0000 3.0000 VolDim 72 72 47 Vc -0.9978 -0.0662 0.0012 Vr 0.0662 -0.9976 0.0208 Vs -0.0002 0.0208 0.9998 VolCenter 1.9144 17.8490 22.2101 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=500.00, TE=6.70, TI=-1.00, flip angle=55.00 i_ras = (-0.997804, -0.0662335, 0.00117006) j_ras = (0.0662434, -0.997587, 0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz... flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 27 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz x -y z /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz mri_probedicom --i /autofs/cluster/mscat/users/caterina/3T/MS_pt36_07072010/field_mapping/005/928000-000005-000001.dcm > /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0info.dat fslroi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz 0 1 epidewarp.fsl --mag /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz --dph /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz --exf /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz --epi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz --tediff 2.46000000000000000000 --esp 0.51 --vsm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --epidw /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz FSLVersion 4.1.10 FSLVerMaj 4 Logfile is /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz.log FSLOUTPUTTYPE NIFTI_GZ Extension is nii.gz fslroi /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0mag.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/mag 0 1 bet /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/mag.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz -bin /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz -dilM /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz -dilM /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz -dilM /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/b0pha.nii.gz -sub 2047.5 -mul 0.00153435539 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/dph -odt float prelude -p /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/dph -a /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/mag.nii.gz -o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/dph -f -v -m /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/head.nii.gz Loading volumes Phase loaded Magnitude loaded Mask loaded Number of phase splits = 8 Calculating starting matrices (4455 by 4455) Finished connection_matrices 10858 constraints left 6319 constraints left 4614 constraints left 2524 constraints left 647 constraints left Did while loop 4454 times fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/dph -mul 0 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/ph.zeros.nii.gz fslmerge -t /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/ph.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/ph.zeros.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/dph Masking with /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/mag.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magdw.nii.gz -p /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/ph.nii.gz --dwell=0.51 --asym=2.46000000000000000000 --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz --saveshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz --smooth2=2 VSM Mean is -0.071563 fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz -sub -0.071563 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz fslmaths /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz -mul /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/mag.nii.gz -w /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz flirt.fsl -in /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw.nii.gz -ref /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz -out /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw-in-exf.nii.gz -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw-in-exf.fsl.mat -bins 256 -cost corratio -searchrx -10 10 -searchry -10 10 -searchrz -10 10 -dof 6 -interp trilinear flirt.fsl -in /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/vsmmag.nii.gz -ref /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz -out /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz -init /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw-in-exf.fsl.mat -applyxfm vsm-smooth --fwhm 10 --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz Thu May 9 10:51:57 EDT 2013 setenv SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 cd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/vsm-smooth --fwhm 10 --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 $Id: vsm-smooth,v 1.1.2.2 2011/08/18 14:59:29 greve Exp $ Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux mri_fwhm --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --o /scratch/tmpdir.vsm-smooth.2070/vsm.sm.nii --fwhm 10 --smooth-only voxelvolume 6.34232 mm3 Search region is 1294336 voxels = 8209099.226562 mm3 Smoothing input by fwhm=10.000000, gstd=4.246609 Saving to /scratch/tmpdir.vsm-smooth.2070/vsm.sm.nii SmoothOnly requested, so exiting now mri_binarize --abs --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --o /scratch/tmpdir.vsm-smooth.2070/notvsm.nii --min 1e-10 --inv $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 cmdline mri_binarize --abs --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --o /scratch/tmpdir.vsm-smooth.2070/notvsm.nii --min 1e-10 --inv sysname Linux hostname compute-0-99 machine x86_64 user celine input /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /scratch/tmpdir.vsm-smooth.2070/notvsm.nii Binarizing based on threshold min 1e-10 max +infinity binval 0 binvalnot 1 Removing sign from input Found 293950 values in range Counting number of voxels Found 293950 voxels in final mask mri_binarize done mri_mask /scratch/tmpdir.vsm-smooth.2070/vsm.sm.nii /scratch/tmpdir.vsm-smooth.2070/notvsm.nii /scratch/tmpdir.vsm-smooth.2070/vsm.sm.masked.nii DoAbs = 0 Found 1294336 voxels in mask Writing masked volume to /scratch/tmpdir.vsm-smooth.2070/vsm.sm.masked.nii...done. fscalc /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz add /scratch/tmpdir.vsm-smooth.2070/vsm.sm.masked.nii -o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz Thu May 9 10:52:03 EDT 2013 cd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/fscalc /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz add /scratch/tmpdir.vsm-smooth.2070/vsm.sm.masked.nii -o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh... ---------------------- mris_calc -o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh add /scratch/tmpdir.vsm-smooth.2070/vsm.sm.masked.nii Saving result to '/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh' (type = MGH ) [ ok ] ---------------------- mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmpdir.fscalc.2130/tmp.mgh... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208201, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz... Thu May 9 10:52:03 EDT 2013 vsm-smooth done flirt.fsl -in /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/brain.nii.gz -ref /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz -out /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz -init /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/magfw-in-exf.fsl.mat -applyxfm /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 fslsplit /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_eddy.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0000.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0000.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0001.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0001.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0002.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0002.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0003.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0003.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0004.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0004.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0005.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0005.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0006.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0006.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0007.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0007.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0008.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0008.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0009.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0009.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0010.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0010.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0011.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0011.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0012.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0012.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0013.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0013.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0014.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0014.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0015.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0015.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0016.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0016.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0017.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0017.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0018.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0018.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0019.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0019.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0020.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0020.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0021.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0021.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0022.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0022.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0023.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0023.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0024.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0024.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0025.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0025.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0026.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0026.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0027.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0027.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0028.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0028.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0029.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0029.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0030.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0030.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0031.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0031.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0032.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0032.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0033.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0033.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0034.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0034.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0035.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0035.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0036.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0036.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0037.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0037.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0038.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0038.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0039.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0039.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0040.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0040.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0041.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0041.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0042.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0042.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0043.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0043.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0044.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0044.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0045.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0045.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0046.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0046.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0047.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0047.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0048.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0048.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0049.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0049.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0050.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0050.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0051.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0051.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0052.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0052.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0053.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0053.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0054.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0054.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0055.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0055.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0056.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0056.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0057.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0057.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0058.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0058.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0059.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0059.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0060.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0060.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0061.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0061.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0062.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0062.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0063.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0063.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0064.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0064.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0065.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0065.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0066.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0066.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0067.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0067.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0068.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0068.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fugue -i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/vol0069.nii.gz -u /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0069.nii.gz --loadshift=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/vsm.nii.gz --mask=/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/maskexf.nii.gz fslmerge -t /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0000.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0001.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0002.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0003.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0004.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0005.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0006.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0007.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0008.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0009.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0010.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0011.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0012.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0013.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-! epidewar p.1857.fsl/epi-split/voldw0014.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0015.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0016.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0017.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0018.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0019.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0020.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0021.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0022.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0023.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0024.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0025.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0026.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0027.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0028.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0029.nii.gz /autofs/cluster/mscat! /users/c aterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0030.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0031.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0032.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0033.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0034.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0035.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0036.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0037.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0038.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0039.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0040.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0041.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0042.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0043.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0044.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-ep! idewarp. 1857.fsl/epi-split/voldw0045.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0046.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0047.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0048.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0049.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0050.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0051.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0052.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0053.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0054.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0055.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0056.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0057.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0058.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0059.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0060.nii.gz /autofs/cluster/mscat/u! sers/cat erina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0061.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0062.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0063.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0064.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0065.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0066.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0067.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0068.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl/epi-split/voldw0069.nii.gz Deleting tmp dir /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/tmp-epidewarp.1857.fsl Thu May 9 10:56:02 EDT 2013 epidewarp.fsl done ln -sf /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/data.nii.gz mri_convert --frame 0 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 0 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame0.nii.gz... mri_convert --frame 1 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame1.nii.gz mri_convert --frame 1 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 1 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame1.nii.gz... mri_convert --frame 2 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame2.nii.gz mri_convert --frame 2 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame2.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 2 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame2.nii.gz... mri_convert --frame 3 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame3.nii.gz mri_convert --frame 3 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame3.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 3 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame3.nii.gz... mri_convert --frame 4 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame4.nii.gz mri_convert --frame 4 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame4.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 4 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame4.nii.gz... mri_convert --frame 5 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame5.nii.gz mri_convert --frame 5 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame5.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 5 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame5.nii.gz... mri_convert --frame 6 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame6.nii.gz mri_convert --frame 6 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame6.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 6 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame6.nii.gz... mri_convert --frame 7 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame7.nii.gz mri_convert --frame 7 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame7.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 7 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame7.nii.gz... mri_convert --frame 8 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame8.nii.gz mri_convert --frame 8 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame8.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 8 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame8.nii.gz... mri_convert --frame 9 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame9.nii.gz mri_convert --frame 9 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame9.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 9 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame9.nii.gz... mri_concat --i /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame0.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame1.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame2.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame3.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame4.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame5.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame6.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame7.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame8.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi_frame9.nii.gz --mean --o /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz ninputs = 10 Checking inputs nframestot = 10 Allocing output Done allocing nframes = 10 Computing mean across frames Writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz bet /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb_brain.nii.gz -m -f 0.5 mv -f /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/lowb_brain_mask.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dlabel/diff #------------------------------------- #@# Intra-subject registration Thu May 9 10:57:51 EDT 2013 mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brain.mgz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brain.mgz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brain.mgz... TR=2530.00, TE=1.70, TI=1200.00, flip angle=7.00 i_ras = (-1, 0, 3.6375e-17) j_ras = (0, -1.68802e-09, -1) k_ras = (0, 1, 4.88217e-09) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz... flip4fsl /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz x z -y /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz fslorient -forceradiological /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz tkregister2 --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz --targ /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2anat.mat --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2anatorig.dat tkregister_tcl /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/tktools/tkregister2.tcl target volume /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz movable volume /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz reg file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 -0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 -0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2anatorig.mat -inverse /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2anat.mat Log file is /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat.log Thu May 9 10:57:58 EDT 2013 setenv SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 cd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/bbregister --s MS_pt36_recon --init-fsl --dti --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat --fslmat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii... fslregister --s MS_pt36_recon --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister --dof 6 --fsvol brainmask Log file is /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat.fslregister.log Thu May 9 10:58:12 EDT 2013 --s MS_pt36_recon --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ compute-0-99 Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brainmask.mgz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/refvol.fslregister.nii mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brainmask.mgz /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/brainmask.mgz... TR=2530.00, TE=1.70, TI=1200.00, flip angle=7.00 i_ras = (-1, 0, 3.6375e-17) j_ras = (0, -1.68802e-09, -1) k_ras = (0, 1, 4.88217e-09) writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997803, -0.0662335, 0.00117006) j_ras = (-0.0662434, 0.997587, -0.0207883) k_ras = (-0.000209649, 0.0208202, 0.999783) keeping frame 0 writing to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii... Mov determinant is -6.34232 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 tkregister2_cmdl --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/reg0.4093.dat --regheader --fslregout /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat.fsl.mat0 --s MS_pt36_recon --noedit tkregister_tcl /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii reg file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/reg0.4093.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.852 0.000 0.000 118.500; 0.000 0.000 1.850 -73.075; 0.000 -1.852 0.000 118.500; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.998 0.066 -0.001 -0.450; -0.000 0.021 1.000 -28.257; 0.066 -0.998 0.021 -1.308; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.066 -0.001 -0.450; -0.000 0.021 1.000 -28.257; 0.066 -0.998 0.021 -1.308; 0.000 0.000 0.000 1.000; Determinant 1 subject = MS_pt36_recon RegMat --------------------------- 0.998 0.066 -0.001 -0.450; -0.000 0.021 1.000 -28.257; 0.066 -0.998 0.021 -1.308; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -6.34232, ref det = -1 Thu May 9 10:58:23 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 flirt.fsl -ref /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/refvol.fslregister.nii -in /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/4.1.10/etc/flirtsch/xyztrans.sch -init /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat.fsl.mat0 Thu May 9 10:58:37 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 flirt.fsl -ref /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/refvol.fslregister.nii -in /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat.fsl.mat -init /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/fslregister/fslmat0.trans.mat -schedule /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s MS_pt36_recon --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --fslreg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat.fsl.mat --noedit tkregister_tcl /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.998 0.060 -0.003 1.749; -0.006 0.050 -0.999 167.560; -0.060 0.997 0.050 12.072; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii reg file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii Tmov: -------------------- -1.852 0.000 0.000 118.500; 0.000 0.000 1.850 -73.075; 0.000 -1.852 0.000 118.500; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -6.34232, ref det = -1 ---- Input registration matrix (computed) -------- 0.998 0.060 -0.006 -0.795; 0.003 0.050 0.999 -28.216; 0.060 -0.997 0.050 -2.742; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.060 -0.006 -0.795; 0.003 0.050 0.999 -28.216; 0.060 -0.997 0.050 -2.742; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = MS_pt36_recon RegMat --------------------------- 0.998 0.060 -0.006 -0.795; 0.003 0.050 0.999 -28.216; 0.060 -0.997 0.050 -2.742; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: M (standard_in) 1: illegal character: S (standard_in) 1: illegal character: _ (standard_in) 1: Error: multiple letter name - pt36_recon (standard_in) 2: Error: comparison in expression Started at Thu May 9 10:58:12 EDT 2013 Ended at Thu May 9 10:59:09 EDT 2013 fslregister Done To check results, run: tkregister2 --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --surf orig mri_segreg --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --init-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --out-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 cd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 mri_segreg --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --init-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat --out-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname compute-0-99 machine x86_64 user celine movvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii regfile /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.init.dat subject MS_pt36_recon dof 6 outregfile /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1368113442 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.060 -0.006 -0.795; 0.003 0.050 0.999 -28.216; 0.060 -0.997 0.050 -2.742; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.003209 1 -25.0 -25.0 25.0 1.058353 2 -25.0 25.0 -25.0 1.031087 3 -25.0 25.0 25.0 1.017660 4 25.0 -25.0 -25.0 0.983487 5 25.0 -25.0 25.0 1.045922 6 25.0 25.0 -25.0 0.992220 7 25.0 25.0 25.0 1.014322 REL: 8 0.302744 8.146261 1.018283 rel = 0.297308 Initial costs ---------------- Number of surface hits 2698 WM Intensity 345.9115 +/- 85.8322 Ctx Intensity 435.4784 +/- 119.9150 Pct Contrast 21.1222 +/- 26.7760 Cost 0.3027 RelCost 0.2973 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9215 0.9215 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9060 0.9060 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8082 0.8082 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8071 0.8071 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.7987 0.7987 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7711 0.7711 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6961 0.6961 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6670 0.6670 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3027 0.3027 0.0 Brute Force -------------------------- Min cost was 0.302744 Number of iterations 729 Search time 1.344000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 0.080 0.000 0.000 0.000 0.000 0.000 0.3017405590 8 0.098 0.000 0.000 0.000 0.000 0.000 0.3017033688 10 0.093 0.000 0.000 0.000 0.000 0.000 0.3016952253 23 0.093 -0.032 0.000 0.000 0.000 0.000 0.3011655478 24 0.093 -0.052 0.000 0.000 0.000 0.000 0.3011474125 25 0.093 -0.043 0.000 0.000 0.000 0.000 0.3010952049 29 0.093 -0.043 1.000 0.000 0.000 0.000 0.2979620494 33 0.093 -0.043 0.618 0.000 0.000 0.000 0.2877027326 34 0.093 -0.043 0.506 0.000 0.000 0.000 0.2869994285 35 0.093 -0.043 0.487 0.000 0.000 0.000 0.2869925445 36 0.093 -0.043 0.492 0.000 0.000 0.000 0.2869855876 37 0.093 -0.043 0.495 0.000 0.000 0.000 0.2869854135 39 0.093 -0.043 0.494 0.000 0.000 0.000 0.2869852759 44 0.093 -0.043 0.494 -0.618 0.000 0.000 0.2656704942 47 0.093 -0.043 0.494 -0.692 0.000 0.000 0.2647382850 48 0.093 -0.043 0.494 -0.691 0.000 0.000 0.2647282526 49 0.093 -0.043 0.494 -0.675 0.000 0.000 0.2646713758 51 0.093 -0.043 0.494 -0.678 0.000 0.000 0.2646683520 61 0.093 -0.043 0.494 -0.678 0.167 0.000 0.2596470668 63 0.093 -0.043 0.494 -0.678 0.147 0.000 0.2594684165 69 0.093 -0.043 0.494 -0.678 0.144 0.000 0.2594601954 80 0.093 -0.043 0.494 -0.678 0.144 -0.006 0.2594515700 81 0.093 -0.043 0.494 -0.678 0.144 -0.007 0.2594513306 92 0.083 -0.043 0.494 -0.678 0.144 -0.007 0.2594357536 93 0.086 -0.043 0.494 -0.678 0.144 -0.007 0.2594192915 94 0.087 -0.043 0.494 -0.678 0.144 -0.007 0.2594188628 102 0.087 -0.295 0.494 -0.678 0.144 -0.007 0.2518169109 105 0.087 -0.343 0.494 -0.678 0.144 -0.007 0.2515580214 106 0.087 -0.323 0.494 -0.678 0.144 -0.007 0.2512043168 107 0.087 -0.322 0.494 -0.678 0.144 -0.007 0.2512004390 108 0.087 -0.319 0.494 -0.678 0.144 -0.007 0.2511992342 111 0.087 -0.320 0.494 -0.678 0.144 -0.007 0.2511981534 118 0.087 -0.320 0.590 -0.678 0.144 -0.007 0.2499080020 119 0.087 -0.320 0.603 -0.678 0.144 -0.007 0.2498895251 120 0.087 -0.320 0.604 -0.678 0.144 -0.007 0.2498866497 123 0.087 -0.320 0.623 -0.678 0.144 -0.007 0.2498368436 124 0.087 -0.320 0.624 -0.678 0.144 -0.007 0.2498359818 126 0.087 -0.320 0.626 -0.678 0.144 -0.007 0.2498357035 145 0.087 -0.320 0.626 -0.678 0.237 -0.007 0.2479493231 147 0.087 -0.320 0.626 -0.678 0.240 -0.007 0.2479277091 148 0.087 -0.320 0.626 -0.678 0.245 -0.007 0.2479079204 159 0.087 -0.320 0.626 -0.678 0.245 0.020 0.2479033469 160 0.087 -0.320 0.626 -0.678 0.245 0.007 0.2477734139 173 0.093 -0.320 0.626 -0.678 0.245 0.007 0.2477451805 185 0.093 -0.291 0.626 -0.678 0.245 0.007 0.2476402991 186 0.093 -0.300 0.626 -0.678 0.245 0.007 0.2476125926 187 0.093 -0.299 0.626 -0.678 0.245 0.007 0.2476118394 196 0.093 -0.299 0.641 -0.678 0.245 0.007 0.2476102565 197 0.093 -0.299 0.634 -0.678 0.245 0.007 0.2476066200 199 0.093 -0.299 0.631 -0.678 0.245 0.007 0.2476057913 200 0.093 -0.299 0.632 -0.678 0.245 0.007 0.2476056464 208 0.093 -0.299 0.632 -0.713 0.245 0.007 0.2473666239 210 0.093 -0.299 0.632 -0.706 0.245 0.007 0.2473459400 222 0.093 -0.299 0.632 -0.706 0.238 0.007 0.2472913133 235 0.093 -0.299 0.632 -0.706 0.238 0.009 0.2472900525 247 0.085 -0.299 0.632 -0.706 0.238 0.009 0.2472689101 248 0.087 -0.299 0.632 -0.706 0.238 0.009 0.2472667479 258 0.087 -0.285 0.632 -0.706 0.238 0.009 0.2471282342 259 0.087 -0.283 0.632 -0.706 0.238 0.009 0.2471246069 270 0.087 -0.283 0.626 -0.706 0.238 0.009 0.2471123084 282 0.087 -0.283 0.626 -0.709 0.238 0.009 0.2471085130 294 0.087 -0.283 0.626 -0.709 0.226 0.009 0.2470917399 295 0.087 -0.283 0.626 -0.709 0.231 0.009 0.2470656176 307 0.087 -0.283 0.626 -0.709 0.231 0.004 0.2470491431 308 0.087 -0.283 0.626 -0.709 0.231 0.002 0.2470463721 310 0.087 -0.283 0.626 -0.709 0.231 0.001 0.2470457208 332 0.087 -0.278 0.626 -0.709 0.231 0.001 0.2470290163 344 0.087 -0.278 0.625 -0.709 0.231 0.001 0.2470278210 354 0.087 -0.278 0.625 -0.710 0.231 0.001 0.2470270373 365 0.087 -0.278 0.625 -0.710 0.230 0.001 0.2470265042 376 0.087 -0.278 0.625 -0.710 0.230 0.000 0.2470259712 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.005469 1 -25.0 -25.0 25.0 1.050936 2 -25.0 25.0 -25.0 1.036588 3 -25.0 25.0 25.0 1.002958 4 25.0 -25.0 -25.0 0.969388 5 25.0 -25.0 25.0 1.021951 6 25.0 25.0 -25.0 1.013441 7 25.0 25.0 25.0 1.029137 REL: 8 0.247026 8.129868 1.016234 rel = 0.24308 Number of iterations 4 Min cost was 0.247026 Number of FunctionCalls 378 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.671000 sec Parameters at optimum (transmm) 0.08731 -0.27782 0.62459 Parameters at optimum (rotdeg) -0.70965 0.22966 0.00023 Final costs ---------------- Number of surface hits 2698 WM Intensity 342.2931 +/- 87.4687 Ctx Intensity 436.8836 +/- 116.5850 Pct Contrast 22.8050 +/- 25.0675 Cost 0.2470 RelCost 0.2973 Reg at min cost was 0.998 0.056 -0.006 -0.718; 0.004 0.038 0.999 -28.526; 0.056 -0.998 0.037 -1.765; 0.000 0.000 0.000 1.000; Writing optimal reg to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat, type = 14 Original Reg 0.998 0.060 -0.006 -0.795; 0.003 0.050 0.999 -28.216; 0.060 -0.997 0.050 -2.742; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.004 -0.000 -0.078; -0.001 0.012 -0.001 0.310; 0.004 0.001 0.012 -0.977; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.936738 Computing change in rh position Surface RMS Diff (mm) 0.848144 1.581442 mri_segreg done mri_segreg --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --init-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat --out-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 cd /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 mri_segreg --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii --init-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat --out-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname compute-0-99 machine x86_64 user celine movvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/template.nii regfile /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/tmp.bbregister.4037/bbr.pass1.dat subject MS_pt36_recon dof 6 outregfile /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1368550379 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.998 0.056 -0.006 -0.718; 0.004 0.038 0.999 -28.526; 0.056 -0.998 0.037 -1.765; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.988799 1 -25.0 -25.0 25.0 1.020076 2 -25.0 25.0 -25.0 1.027067 3 -25.0 25.0 25.0 1.003484 4 25.0 -25.0 -25.0 1.016410 5 25.0 -25.0 25.0 0.997485 6 25.0 25.0 -25.0 1.017869 7 25.0 25.0 25.0 1.010422 REL: 8 0.265332 8.081612 1.010202 rel = 0.262653 Initial costs ---------------- Number of surface hits 269308 WM Intensity 344.4802 +/- 84.9095 Ctx Intensity 436.9890 +/- 115.9829 Pct Contrast 22.2457 +/- 25.8002 Cost 0.2653 RelCost 0.2627 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.2537 0.2537 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.2529 0.2529 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.2515 0.2515 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.2513 0.2513 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.2506 0.2506 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.2492 0.2492 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.2491 0.2491 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.2491 0.2491 0.0 124 -0.1000 0.0000 0.0000 0.0000 0.1000 0.0000 0.2484 0.2484 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2470 0.2470 0.0 Brute Force -------------------------- Min cost was 0.247026 Number of iterations 729 Search time 1.980000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 -0.106 0.000 0.000 0.000 0.000 0.000 0.2646131673 8 -0.091 0.000 0.000 0.000 0.000 0.000 0.2645867732 9 -0.089 0.000 0.000 0.000 0.000 0.000 0.2645859947 10 -0.087 0.000 0.000 0.000 0.000 0.000 0.2645859309 18 -0.087 -0.024 0.000 0.000 0.000 0.000 0.2644801966 19 -0.087 -0.039 0.000 0.000 0.000 0.000 0.2644481683 20 -0.087 -0.051 0.000 0.000 0.000 0.000 0.2644441631 21 -0.087 -0.048 0.000 0.000 0.000 0.000 0.2644433437 30 -0.087 -0.048 0.142 0.000 0.000 0.000 0.2632870217 31 -0.087 -0.048 0.141 0.000 0.000 0.000 0.2632860708 32 -0.087 -0.048 0.135 0.000 0.000 0.000 0.2632826060 42 -0.087 -0.048 0.135 0.037 0.000 0.000 0.2632312646 43 -0.087 -0.048 0.135 0.028 0.000 0.000 0.2632281253 46 -0.087 -0.048 0.135 0.027 0.000 0.000 0.2632279127 48 -0.087 -0.048 0.135 0.026 0.000 0.000 0.2632278428 56 -0.087 -0.048 0.135 0.026 -0.056 0.000 0.2629885218 59 -0.087 -0.048 0.135 0.026 -0.058 0.000 0.2629883008 67 -0.087 -0.048 0.135 0.026 -0.058 -0.031 0.2629288313 68 -0.087 -0.048 0.135 0.026 -0.058 -0.036 0.2629268015 69 -0.087 -0.048 0.135 0.026 -0.058 -0.039 0.2629265585 70 -0.087 -0.048 0.135 0.026 -0.058 -0.040 0.2629263625 85 -0.088 -0.048 0.135 0.026 -0.058 -0.040 0.2629262752 93 -0.088 -0.013 0.135 0.026 -0.058 -0.040 0.2628377837 95 -0.088 -0.007 0.135 0.026 -0.058 -0.040 0.2628349113 97 -0.088 -0.002 0.135 0.026 -0.058 -0.040 0.2628344353 98 -0.088 -0.003 0.135 0.026 -0.058 -0.040 0.2628342436 106 -0.088 -0.003 0.145 0.026 -0.058 -0.040 0.2628163913 107 -0.088 -0.003 0.154 0.026 -0.058 -0.040 0.2628120082 108 -0.088 -0.003 0.153 0.026 -0.058 -0.040 0.2628119577 116 -0.088 -0.003 0.153 0.051 -0.058 -0.040 0.2627644501 118 -0.088 -0.003 0.153 0.047 -0.058 -0.040 0.2627640906 121 -0.088 -0.003 0.153 0.048 -0.058 -0.040 0.2627638192 130 -0.088 -0.003 0.153 0.048 -0.046 -0.040 0.2627569533 132 -0.088 -0.003 0.153 0.048 -0.049 -0.040 0.2627566816 133 -0.088 -0.003 0.153 0.048 -0.048 -0.040 0.2627565763 152 -0.091 -0.003 0.153 0.048 -0.048 -0.039 0.2627562243 153 -0.090 -0.003 0.153 0.048 -0.048 -0.039 0.2627562028 161 -0.090 0.004 0.153 0.048 -0.048 -0.039 0.2627542414 163 -0.090 0.001 0.153 0.048 -0.048 -0.039 0.2627529129 172 -0.090 0.001 0.141 0.048 -0.048 -0.039 0.2627516981 173 -0.090 0.001 0.146 0.048 -0.048 -0.039 0.2627487369 222 -0.090 0.000 0.146 0.048 -0.048 -0.039 0.2627487198 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.989949 1 -25.0 -25.0 25.0 1.020576 2 -25.0 25.0 -25.0 1.027051 3 -25.0 25.0 25.0 1.003120 4 25.0 -25.0 -25.0 1.018106 5 25.0 -25.0 25.0 0.999641 6 25.0 25.0 -25.0 1.016935 7 25.0 25.0 25.0 1.011581 REL: 8 0.262749 8.086960 1.010870 rel = 0.259923 Number of iterations 4 Min cost was 0.262749 Number of FunctionCalls 318 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 37.374000 sec Parameters at optimum (transmm) -0.08975 0.00028 0.14595 Parameters at optimum (rotdeg) 0.04846 -0.04826 -0.03853 Final costs ---------------- Number of surface hits 269308 WM Intensity 344.4446 +/- 85.0381 Ctx Intensity 437.7182 +/- 116.6556 Pct Contrast 22.4070 +/- 25.8331 Cost 0.2627 RelCost 0.2627 Reg at min cost was 0.998 0.057 -0.006 -0.825; 0.003 0.038 0.999 -28.523; 0.057 -0.998 0.038 -1.644; 0.000 0.000 0.000 1.000; Writing optimal reg to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.998 0.056 -0.006 -0.718; 0.004 0.038 0.999 -28.526; 0.056 -0.998 0.037 -1.765; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.001 -0.001 0.107; 0.001 -0.001 0.000 -0.002; -0.001 -0.000 -0.001 -0.121; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.168093 Computing change in rh position Surface RMS Diff (mm) 0.185623 0.249223 mri_segreg done tkregister2_cmdl --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz reg file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.998 0.057 -0.006 -0.825; 0.003 0.038 0.999 -28.523; 0.057 -0.998 0.038 -1.644; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz Tmov: -------------------- -1.852 0.000 0.000 118.500; 0.000 0.000 1.850 -73.075; 0.000 -1.852 0.000 118.500; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.998 0.057 -0.006 -0.825; 0.003 0.038 0.999 -28.523; 0.057 -0.998 0.038 -1.644; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = MS_pt36_recon RegMat --------------------------- 0.998 0.057 -0.006 -0.825; 0.003 0.038 0.999 -28.523; 0.057 -0.998 0.038 -1.644; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -6.34232, ref det = -1 Cleaning up Started at Thu May 9 10:57:58 EDT 2013 Ended at Thu May 9 11:00:29 EDT 2013 BBR-Run-Time-Sec 151 bbregister Done To check results, run: tkregister2 --mov /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/dwi.nii.gz --reg /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.mat -inverse /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2diff.bbr.mat -concat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anatorig2diff.bbr.mat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2anatorig.mat convert_xfm -omat /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/diff2anat.bbr.mat -inverse /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Thu May 9 11:00:29 EDT 2013 ln -sfn /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/cvs/cvs_avg35 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs ln -s /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/subjects/cvs_avg35 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 mri_cvs_register --mov MS_pt36_recon --template cvs_avg35 --outdir /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs --cleanall The outdir: /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs Log file is /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/MS_pt36_recon_to_cvs_avg35.mri_cvs_register.1305091100.log Thu May 9 11:00:30 EDT 2013 --mov MS_pt36_recon --template cvs_avg35 --outdir /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs --cleanall $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ compute-0-99 Linux compute-0-99 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux asegfname aseg Using m3z type morph files. l_dist = 1.000 using inflated surface for initial alignment treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading surface from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/surf/lh.sphere... reading spherical surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/lh.sphere... computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/lh.inflated.H... curvature mean = -0.000, std = 1.000 computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/lh.sulc... computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/lh.smoothwm... curvature mean = -0.000, std = 0.591 curvature mean = -0.021, std = 0.263 MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 528 (210) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=1.000, l_dist=1.000 using quadratic fit line minimization -------------------- 0 Reading lh.inflated.H tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=0.333, l_dist=1.000 using quadratic fit line minimization curvature mean = 0.000, std = 1.000 curvature mean = 0.008, std = 0.915 curvature mean = 0.005, std = 0.922 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 84220.4, tmin=1.3794 d=32.00 min @ (0.00, 8.00, -8.00) sse = 74817.1, tmin=2.7561 d=16.00 min @ (4.00, 0.00, 4.00) sse = 66938.2, tmin=4.1015 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 66831.7, tmin=6.8585 d=2.00 min @ (0.50, 0.50, 0.00) sse = 66774.2, tmin=8.2175 d=1.00 min @ (0.00, -0.25, 0.25) sse = 66758.1, tmin=9.5786 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 66754.5, tmin=10.9274 MRISrigidBodyAlignGlobal() done 10.93 min curvature mean = 0.008, std = 0.962 curvature mean = 0.002, std = 0.971 curvature mean = 0.009, std = 0.977 curvature mean = 0.000, std = 0.989 curvature mean = 0.009, std = 0.983 curvature mean = -0.000, std = 0.996 1 Reading lh.sulc curvature mean = 0.000, std = 0.569 curvature mean = 0.013, std = 0.835 curvature mean = 0.024, std = 0.852 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, 0.00, -8.00) sse = 107766.5, tmin=2.5861 d=16.00 min @ (0.00, 0.00, 4.00) sse = 107401.2, tmin=3.8828 d=8.00 min @ (0.00, 0.00, -2.00) sse = 106874.4, tmin=5.1779 d=4.00 min @ (1.00, 0.00, 0.00) sse = 106680.4, tmin=6.4864 d=2.00 min @ (0.00, 0.00, 0.50) sse = 106671.5, tmin=7.7929 d=1.00 min @ (0.25, 0.25, 0.00) sse = 106671.3, tmin=9.1035 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 106659.6, tmin=10.4153 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=1.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 10.42 min curvature mean = -0.014, std = 0.898 curvature mean = 0.011, std = 0.935 curvature mean = -0.015, std = 0.926 curvature mean = 0.004, std = 0.971 curvature mean = -0.015, std = 0.937 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.031, std = 0.271 curvature mean = 0.035, std = 0.369 curvature mean = 0.057, std = 0.376 curvature mean = 0.039, std = 0.546 curvature mean = 0.021, std = 0.581 curvature mean = 0.041, std = 0.655 curvature mean = 0.011, std = 0.719 curvature mean = 0.043, std = 0.713 curvature mean = 0.004, std = 0.816 MRISregister() return, current seed 0 writing registered surface to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/surf/lh.cvs.tocvs_avg35.sphere.reg... expanding nbhd size to 1 l_dist = 1.000 using inflated surface for initial alignment treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading surface from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/surf/rh.sphere... reading spherical surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/rh.sphere... computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/rh.inflated.H... curvature mean = 0.000, std = 1.000 computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/rh.sulc... computing parameterization for surface /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf/rh.smoothwm... curvature mean = 0.000, std = 0.605 curvature mean = -0.020, std = 0.249 MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 528 (210) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=1.000, l_dist=1.000 using quadratic fit line minimization -------------------- 0 Reading rh.inflated.H tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=0.333, l_dist=1.000 using quadratic fit line minimization curvature mean = 0.000, std = 1.000 curvature mean = 0.004, std = 0.919 curvature mean = 0.008, std = 0.909 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, 0.00, -8.00) sse = 74497.2, tmin=2.5456 d=16.00 min @ (0.00, -4.00, 4.00) sse = 68617.7, tmin=3.8021 d=8.00 min @ (2.00, 2.00, 0.00) sse = 67416.5, tmin=5.1123 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 67347.5, tmin=7.8075 d=1.00 min @ (0.25, 0.00, -0.25) sse = 67318.8, tmin=9.1232 MRISrigidBodyAlignGlobal() done 10.44 min curvature mean = 0.015, std = 0.959 curvature mean = 0.003, std = 0.966 curvature mean = 0.016, std = 0.973 curvature mean = 0.001, std = 0.987 curvature mean = 0.016, std = 0.979 curvature mean = 0.000, std = 0.995 1 Reading rh.sulc curvature mean = -0.000, std = 0.570 curvature mean = 0.004, std = 0.836 curvature mean = 0.029, std = 0.848 Starting MRISrigidBodyAlignGlobal() d=16.00 min @ (0.00, 0.00, -4.00) sse = 93575.4, tmin=3.8285 d=8.00 min @ (0.00, 0.00, 2.00) sse = 93082.3, tmin=5.1139 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 92766.9, tmin=6.4019 d=2.00 min @ (0.50, 0.50, 0.00) sse = 92640.0, tmin=7.7314 d=0.50 min @ (0.00, 0.00, -0.12) sse = 92635.5, tmin=10.3173 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.100, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=1.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 10.32 min curvature mean = -0.022, std = 0.911 curvature mean = 0.012, std = 0.936 curvature mean = -0.023, std = 0.939 curvature mean = 0.005, std = 0.973 curvature mean = -0.024, std = 0.950 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.033, std = 0.267 curvature mean = 0.046, std = 0.379 curvature mean = 0.070, std = 0.378 curvature mean = 0.042, std = 0.554 curvature mean = 0.028, std = 0.587 curvature mean = 0.040, std = 0.664 curvature mean = 0.014, std = 0.733 curvature mean = 0.040, std = 0.724 curvature mean = 0.006, std = 0.833 MRISregister() return, current seed 0 writing registered surface to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/surf/rh.cvs.tocvs_avg35.sphere.reg... before reading annotation /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) trying to write annotation before reading annotation /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) trying to write annotation before reading annotation /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) trying to write annotation before reading annotation /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) trying to write annotation mri_cvs_register: Step 1 (spherical registration) took 5663 seconds No ASEG option present No field output option specified will use default value out_field.mgz will cache transform in file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/transform.txt reading fixed volume reading moving volume surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf//lh.white type = 0 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf//rh.white type = 0 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf//lh.pial type = 1 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/surf//rh.pial type = 1 processing APARC reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) label = unknown -> value = 0 label = corpuscallosum -> value = 4 ignored labels = 0 4 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) label = unknown -> value = 0 label = corpuscallosum -> value = 4 ignored labels = 0 4 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) label = unknown -> value = 0 label = corpuscallosum -> value = 4 ignored labels = 0 4 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) label = unknown -> value = 0 label = corpuscallosum -> value = 4 ignored labels = 0 4 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/lh.resample.white type = 0 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/rh.resample.white type = 0 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/lh.resample.pial type = 1 surface name = /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/rh.resample.pial type = 1 trying to read transform from /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/transform.txt Error opening file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/transform.txt to read transform reading transform failed -> applying Powell energy before calling Powell = 10.9418 energy after Powell = 6.51548 writing transform to cache file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/transform.txt done with Powell applying linear transform to MOVING surf pos. linear transform = 0.979246 -0.083492 0.0629272 0.0869953 1.02128 -0.127247 -0.0610869 0.115303 0.978866 2.60954 -0.914622 9.56844 linear transform = 0.979246 -0.083492 0.0629272 0.0869953 1.02128 -0.127247 -0.0610869 0.115303 0.978866 2.60954 -0.914622 9.56844 linear transform = 0.979246 -0.083492 0.0629272 0.0869953 1.02128 -0.127247 -0.0610869 0.115303 0.978866 2.60954 -0.914622 9.56844 linear transform = 0.979246 -0.083492 0.0629272 0.0869953 1.02128 -0.127247 -0.0610869 0.115303 0.978866 2.60954 -0.914622 9.56844 DONE direct min = 62.3002 45.1985 37.6148 direct max = 195.891 164.948 215.515 bounding box elts = min = 52.3002 35.1985 27.6148 max = 205.891 174.948 225.515 DIRTY value = 1 create BC container - ripCounter = 0 create BC container - ripCounter = 0 create BC container - ripCounter = 0 create BC container - ripCounter = 0 creating container for the mesher writing surface to file lh.dbg_surf.white writing surface to file rh.dbg_surf.white writing surface to file lh.dbg_surf.pial writing surface to file rh.dbg_surf.pial srcPoints size = 0 ====================== step = 17 =============== elt_vol= 10 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 14.48 Smoothing mesh. Smooth seconds: 0.82 Writing nodes. Writing elements. Writing faces. Output seconds: 0.1 Total running seconds: 15.4 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 121828 Mesh tetrahedra: 739056 Mesh faces: 1494319 Mesh subfaces: 32414 Mesh subsegments: 626 mesh nodes = 121828 mesh elts = 739056 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 InitializeOctantDeterminant count inserted = 100000 elapsed = 0.124 seconds element count = 800208 count inserted = 200000 elapsed = 0.259 seconds element count = 2422080 count inserted = 300000 elapsed = 0.253 seconds element count = 4013438 count inserted = 400000 elapsed = 0.222 seconds element count = 5467196 count inserted = 500000 elapsed = 0.215 seconds element count = 6883637 count inserted = 600000 elapsed = 0.207 seconds element count = 8299698 count inserted = 700000 elapsed = 0.202 seconds element count = 9718960 done building octree - total elements = 10276256 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 143223 Total BCs = 548640 no-eqs = 365484 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=365484, cols=365484 total: nonzeros=16883430, allocated nonzeros=16883727 using I-node routines: found 121844 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=365484, cols=365484 total: nonzeros=16883430, allocated nonzeros=16883727 using I-node routines: found 121844 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 101591 countInvalid = 0 general-count = 548640 Average of the error norm = 0.12406 Initial error = 0.38295 Average of the error norm conditional = 0.123616 Active Residual error = 0.0322719 Total error = 0.12406 c0324 time elapsed updating the sources (seconds) = 0 NO ORIENTATION PBs FOUND !!! compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 6.20792 Max after displacement = 29.5767 Error points = 0 ====================== step = 16 =============== elt_vol= 9.6875 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 14.86 Smoothing mesh. Smooth seconds: 0.85 Writing nodes. Writing elements. Writing faces. Output seconds: 0.1 Total running seconds: 15.82 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 125414 Mesh tetrahedra: 761432 Mesh faces: 1539405 Mesh subfaces: 33082 Mesh subsegments: 630 mesh nodes = 125414 mesh elts = 761432 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.135 seconds element count = 777689 count inserted = 200000 elapsed = 0.254 seconds element count = 2363228 count inserted = 300000 elapsed = 0.262 seconds element count = 3933296 count inserted = 400000 elapsed = 0.223 seconds element count = 5365337 count inserted = 500000 elapsed = 0.225 seconds element count = 6763367 count inserted = 600000 elapsed = 0.205 seconds element count = 8155457 count inserted = 700000 elapsed = 0.201 seconds element count = 9542076 done building octree - total elements = 10408660 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 143557 Total BCs = 548640 no-eqs = 376242 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=376242, cols=376242 total: nonzeros=17389050, allocated nonzeros=17389338 using I-node routines: found 125430 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=376242, cols=376242 total: nonzeros=17389050, allocated nonzeros=17389338 using I-node routines: found 125430 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 104560 countInvalid = 0 general-count = 548640 Average of the error norm = 0.130028 Initial error = 0.38799 Average of the error norm conditional = 0.129211 Active Residual error = 0.0338113 Total error = 0.130028 c0324 time elapsed updating the sources (seconds) = 0 NO ORIENTATION PBs FOUND !!! compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 5.9101 Max after displacement = 28.657 Error points = 0 ====================== step = 15 =============== elt_vol= 9.375 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 15.37 Smoothing mesh. Smooth seconds: 0.87 Writing nodes. Writing elements. Writing faces. Output seconds: 0.11 Total running seconds: 16.37 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 129545 Mesh tetrahedra: 786982 Mesh faces: 1590880 Mesh subfaces: 33832 Mesh subsegments: 637 mesh nodes = 129545 mesh elts = 786982 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.126 seconds element count = 761066 count inserted = 200000 elapsed = 0.242 seconds element count = 2310044 count inserted = 300000 elapsed = 0.253 seconds element count = 3851314 count inserted = 400000 elapsed = 0.219 seconds element count = 5261740 count inserted = 500000 elapsed = 0.214 seconds element count = 6633990 count inserted = 600000 elapsed = 0.198 seconds element count = 7994271 count inserted = 700000 elapsed = 0.198 seconds element count = 9357578 done building octree - total elements = 10553552 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 144073 Total BCs = 548640 no-eqs = 388635 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=388635, cols=388635 total: nonzeros=17967237, allocated nonzeros=17967525 using I-node routines: found 129561 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=388635, cols=388635 total: nonzeros=17967237, allocated nonzeros=17967525 using I-node routines: found 129561 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 106153 countInvalid = 0 general-count = 548640 Average of the error norm = 0.136203 Initial error = 0.394001 Average of the error norm conditional = 0.134958 Active Residual error = 0.0354421 Total error = 0.136203 c0324 time elapsed updating the sources (seconds) = 0 NO ORIENTATION PBs FOUND !!! compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 5.61421 Max after displacement = 27.6444 Error points = 0 ====================== step = 14 =============== elt_vol= 9.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 0.01 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 15.89 Smoothing mesh. Smooth seconds: 0.91 Writing nodes. Writing elements. Writing faces. Output seconds: 0.11 Total running seconds: 16.93 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 133841 Mesh tetrahedra: 814143 Mesh faces: 1645510 Mesh subfaces: 34448 Mesh subsegments: 647 mesh nodes = 133841 mesh elts = 814143 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.15 seconds element count = 744132 count inserted = 200000 elapsed = 0.261 seconds element count = 2254138 count inserted = 300000 elapsed = 0.262 seconds element count = 3763729 count inserted = 400000 elapsed = 0.227 seconds element count = 5152505 count inserted = 500000 elapsed = 0.224 seconds element count = 6505094 count inserted = 600000 elapsed = 0.205 seconds element count = 7838809 count inserted = 700000 elapsed = 0.2 seconds element count = 9172072 count inserted = 800000 elapsed = 0.195 seconds element count = 10521287 done building octree - total elements = 10713157 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 144525 Total BCs = 548640 no-eqs = 401523 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=401523, cols=401523 total: nonzeros=18577689, allocated nonzeros=18577968 using I-node routines: found 133857 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=401523, cols=401523 total: nonzeros=18577689, allocated nonzeros=18577968 using I-node routines: found 133857 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 112090 countInvalid = 0 general-count = 548640 Average of the error norm = 0.144117 Initial error = 0.401009 Average of the error norm conditional = 0.142748 Active Residual error = 0.0376053 Total error = 0.144117 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 179268 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 5.32151 Max after displacement = 26.5375 Error points = 0 ====================== step = 13 =============== elt_vol= 8.75 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.02 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 16.44 Smoothing mesh. Smooth seconds: 0.94 Writing nodes. Writing elements. Writing faces. Output seconds: 0.12 Total running seconds: 17.54 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 138646 Mesh tetrahedra: 843658 Mesh faces: 1704935 Mesh subfaces: 35238 Mesh subsegments: 650 mesh nodes = 138646 mesh elts = 843658 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.15 seconds element count = 719901 count inserted = 200000 elapsed = 0.26 seconds element count = 2196924 count inserted = 300000 elapsed = 0.257 seconds element count = 3672665 count inserted = 400000 elapsed = 0.225 seconds element count = 5039310 count inserted = 500000 elapsed = 0.221 seconds element count = 6364054 count inserted = 600000 elapsed = 0.2 seconds element count = 7664797 count inserted = 700000 elapsed = 0.2 seconds element count = 8974253 count inserted = 800000 elapsed = 0.19 seconds element count = 10289908 done building octree - total elements = 10868562 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 145441 Total BCs = 548640 no-eqs = 415938 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=415938, cols=415938 total: nonzeros=19245768, allocated nonzeros=19246065 using I-node routines: found 138662 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=415938, cols=415938 total: nonzeros=19245768, allocated nonzeros=19246065 using I-node routines: found 138662 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 116582 countInvalid = 0 general-count = 548640 Average of the error norm = 0.153356 Initial error = 0.409341 Average of the error norm conditional = 0.151028 Active Residual error = 0.0400387 Total error = 0.153356 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 139896 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 5.03187 Max after displacement = 25.4209 Error points = 0 ====================== step = 12 =============== elt_vol= 8.4375 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.02 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 17.05 Smoothing mesh. Smooth seconds: 0.98 Writing nodes. Writing elements. Writing faces. Output seconds: 0.12 Total running seconds: 18.19 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 143578 Mesh tetrahedra: 874299 Mesh faces: 1766701 Mesh subfaces: 36206 Mesh subsegments: 656 mesh nodes = 143578 mesh elts = 874299 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.151 seconds element count = 705319 count inserted = 200000 elapsed = 0.256 seconds element count = 2138835 count inserted = 300000 elapsed = 0.257 seconds element count = 3589369 count inserted = 400000 elapsed = 0.226 seconds element count = 4932323 count inserted = 500000 elapsed = 0.218 seconds element count = 6233011 count inserted = 600000 elapsed = 0.198 seconds element count = 7508878 count inserted = 700000 elapsed = 0.196 seconds element count = 8791377 count inserted = 800000 elapsed = 0.189 seconds element count = 10082029 done building octree - total elements = 11044422 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 146496 Total BCs = 548640 no-eqs = 430734 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=430734, cols=430734 total: nonzeros=19939182, allocated nonzeros=19939479 using I-node routines: found 143594 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=430734, cols=430734 total: nonzeros=19939182, allocated nonzeros=19939479 using I-node routines: found 143594 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 122204 countInvalid = 0 general-count = 548640 Average of the error norm = 0.163557 Initial error = 0.419316 Average of the error norm conditional = 0.160208 Active Residual error = 0.0427805 Total error = 0.163557 c0324 time elapsed updating the sources (seconds) = 0 NO ORIENTATION PBs FOUND !!! compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 4.74397 Max after displacement = 24.1386 Error points = 0 ====================== step = 11 =============== elt_vol= 8.125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.03 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 17.67 Smoothing mesh. Smooth seconds: 1.01 Writing nodes. Writing elements. Writing faces. Output seconds: 0.13 Total running seconds: 18.86 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 149030 Mesh tetrahedra: 908643 Mesh faces: 1835848 Mesh subfaces: 37124 Mesh subsegments: 663 mesh nodes = 149030 mesh elts = 908643 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.152 seconds element count = 684773 count inserted = 200000 elapsed = 0.254 seconds element count = 2080118 count inserted = 300000 elapsed = 0.256 seconds element count = 3502535 count inserted = 400000 elapsed = 0.225 seconds element count = 4823279 count inserted = 500000 elapsed = 0.213 seconds element count = 6093981 count inserted = 600000 elapsed = 0.197 seconds element count = 7344434 count inserted = 700000 elapsed = 0.192 seconds element count = 8600330 count inserted = 800000 elapsed = 0.187 seconds element count = 9852476 count inserted = 900000 elapsed = 0.178 seconds element count = 11119394 done building octree - total elements = 11229546 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 147302 Total BCs = 548640 no-eqs = 447090 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=447090, cols=447090 total: nonzeros=20712858, allocated nonzeros=20713146 using I-node routines: found 149046 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=447090, cols=447090 total: nonzeros=20712858, allocated nonzeros=20713146 using I-node routines: found 149046 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 129740 countInvalid = 1 general-count = 548639 Average of the error norm = 0.176174 Initial error = 0.431262 Average of the error norm conditional = 0.171932 Active Residual error = 0.0461672 Total error = 0.176177 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166297 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 4.4585 Max after displacement = 23.5052 Error points = 0 ====================== step = 10 =============== elt_vol= 7.8125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.04 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 18.38 Smoothing mesh. Smooth seconds: 1.06 Writing nodes. Writing elements. Writing faces. Output seconds: 0.13 Total running seconds: 19.63 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 154826 Mesh tetrahedra: 944379 Mesh faces: 1907819 Mesh subfaces: 38122 Mesh subsegments: 667 mesh nodes = 154826 mesh elts = 944379 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.153 seconds element count = 664880 count inserted = 200000 elapsed = 0.246 seconds element count = 2012211 count inserted = 300000 elapsed = 0.257 seconds element count = 3410334 count inserted = 400000 elapsed = 0.242 seconds element count = 4711853 count inserted = 500000 elapsed = 0.216 seconds element count = 5949651 count inserted = 600000 elapsed = 0.199 seconds element count = 7178811 count inserted = 700000 elapsed = 0.193 seconds element count = 8409641 count inserted = 800000 elapsed = 0.184 seconds element count = 9633048 count inserted = 900000 elapsed = 0.177 seconds element count = 10866951 done building octree - total elements = 11419070 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 148419 Total BCs = 548640 no-eqs = 464478 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=464478, cols=464478 total: nonzeros=21521562, allocated nonzeros=21521859 using I-node routines: found 154842 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=464478, cols=464478 total: nonzeros=21521562, allocated nonzeros=21521859 using I-node routines: found 154842 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 136117 countInvalid = 0 general-count = 548640 Average of the error norm = 0.190039 Initial error = 0.445843 Average of the error norm conditional = 0.1839 Active Residual error = 0.0497516 Total error = 0.190039 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 164271 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 4.17333 Max after displacement = 23.0274 Error points = 0 ====================== step = 9 =============== elt_vol= 7.5 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.04 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 19.13 Smoothing mesh. Smooth seconds: 1.1 Writing nodes. Writing elements. Writing faces. Output seconds: 0.14 Total running seconds: 20.43 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 161090 Mesh tetrahedra: 983422 Mesh faces: 1986452 Mesh subfaces: 39216 Mesh subsegments: 672 mesh nodes = 161090 mesh elts = 983422 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.15 seconds element count = 646614 count inserted = 200000 elapsed = 0.243 seconds element count = 1962807 count inserted = 300000 elapsed = 0.25 seconds element count = 3328011 count inserted = 400000 elapsed = 0.223 seconds element count = 4605475 count inserted = 500000 elapsed = 0.206 seconds element count = 5816937 count inserted = 600000 elapsed = 0.195 seconds element count = 7021117 count inserted = 700000 elapsed = 0.199 seconds element count = 8221554 count inserted = 800000 elapsed = 0.179 seconds element count = 9414930 count inserted = 900000 elapsed = 0.176 seconds element count = 10618043 done building octree - total elements = 11627886 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 150347 Total BCs = 548640 no-eqs = 483270 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=483270, cols=483270 total: nonzeros=22403274, allocated nonzeros=22403589 using I-node routines: found 161106 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=483270, cols=483270 total: nonzeros=22403274, allocated nonzeros=22403589 using I-node routines: found 161106 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 145507 countInvalid = 0 general-count = 548640 Average of the error norm = 0.207768 Initial error = 0.463696 Average of the error norm conditional = 0.199489 Active Residual error = 0.05467 Total error = 0.207768 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155586 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 129830 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 3.88936 Max after displacement = 22.72 Error points = 0 ====================== step = 8 =============== elt_vol= 7.1875 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.05 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 19.97 Smoothing mesh. Smooth seconds: 1.15 Writing nodes. Writing elements. Writing faces. Output seconds: 0.14 Total running seconds: 21.33 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 167900 Mesh tetrahedra: 1025838 Mesh faces: 2071897 Mesh subfaces: 40442 Mesh subsegments: 681 mesh nodes = 167900 mesh elts = 1025838 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.15 seconds element count = 626439 count inserted = 200000 elapsed = 0.237 seconds element count = 1900150 count inserted = 300000 elapsed = 0.252 seconds element count = 3235861 count inserted = 400000 elapsed = 0.22 seconds element count = 4488148 count inserted = 500000 elapsed = 0.206 seconds element count = 5675014 count inserted = 600000 elapsed = 0.189 seconds element count = 6850007 count inserted = 700000 elapsed = 0.186 seconds element count = 8020237 count inserted = 800000 elapsed = 0.18 seconds element count = 9189052 count inserted = 900000 elapsed = 0.17 seconds element count = 10361741 count inserted = 1000000 elapsed = 0.163 seconds element count = 11543327 done building octree - total elements = 11851384 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 152444 Total BCs = 548640 no-eqs = 503700 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=503700, cols=503700 total: nonzeros=23361666, allocated nonzeros=23361981 using I-node routines: found 167916 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=503700, cols=503700 total: nonzeros=23361666, allocated nonzeros=23361981 using I-node routines: found 167916 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 157088 countInvalid = 6 general-count = 548634 Average of the error norm = 0.229576 Initial error = 0.486155 Average of the error norm conditional = 0.218096 Active Residual error = 0.0606095 Total error = 0.229604 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 137876 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 438 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178285 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 144788 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172599 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 3.60571 Max after displacement = 22.5015 Error points = 0 ====================== step = 7 =============== elt_vol= 6.875 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.06 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 20.87 Smoothing mesh. Smooth seconds: 1.2 Writing nodes. Writing elements. Writing faces. Output seconds: 0.15 Total running seconds: 22.3 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 175381 Mesh tetrahedra: 1072657 Mesh faces: 2166120 Mesh subfaces: 41612 Mesh subsegments: 688 mesh nodes = 175381 mesh elts = 1072657 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.144 seconds element count = 604071 count inserted = 200000 elapsed = 0.23 seconds element count = 1842474 count inserted = 300000 elapsed = 0.248 seconds element count = 3143974 count inserted = 400000 elapsed = 0.227 seconds element count = 4371484 count inserted = 500000 elapsed = 0.205 seconds element count = 5532322 count inserted = 600000 elapsed = 0.184 seconds element count = 6679323 count inserted = 700000 elapsed = 0.191 seconds element count = 7818280 count inserted = 800000 elapsed = 0.178 seconds element count = 8959283 count inserted = 900000 elapsed = 0.165 seconds element count = 10100021 count inserted = 1000000 elapsed = 0.161 seconds element count = 11248357 done building octree - total elements = 12086420 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 154725 Total BCs = 548640 no-eqs = 526143 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=526143, cols=526143 total: nonzeros=24416925, allocated nonzeros=24417240 using I-node routines: found 175397 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=526143, cols=526143 total: nonzeros=24416925, allocated nonzeros=24417240 using I-node routines: found 175397 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 170111 countInvalid = 3 general-count = 548637 Average of the error norm = 0.256433 Initial error = 0.515092 Average of the error norm conditional = 0.242199 Active Residual error = 0.0683109 Total error = 0.256438 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 140594 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 489 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 170623 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 507 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156580 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 3.32046 Max after displacement = 22.1312 Error points = 0 ====================== step = 6 =============== elt_vol= 6.5625 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.06 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 21.86 Smoothing mesh. Smooth seconds: 1.25 Writing nodes. Writing elements. Writing faces. Output seconds: 0.17 Total running seconds: 23.36 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 183645 Mesh tetrahedra: 1124497 Mesh faces: 2270458 Mesh subfaces: 42928 Mesh subsegments: 695 mesh nodes = 183645 mesh elts = 1124497 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.143 seconds element count = 588289 count inserted = 200000 elapsed = 0.224 seconds element count = 1778445 count inserted = 300000 elapsed = 0.244 seconds element count = 3051210 count inserted = 400000 elapsed = 0.215 seconds element count = 4251215 count inserted = 500000 elapsed = 0.197 seconds element count = 5380094 count inserted = 600000 elapsed = 0.185 seconds element count = 6499178 count inserted = 700000 elapsed = 0.171 seconds element count = 7608227 count inserted = 800000 elapsed = 0.175 seconds element count = 8719552 count inserted = 900000 elapsed = 0.165 seconds element count = 9826828 count inserted = 1000000 elapsed = 0.158 seconds element count = 10948316 count inserted = 1100000 elapsed = 0.153 seconds element count = 12071774 done building octree - total elements = 12349419 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 157577 Total BCs = 548640 no-eqs = 550935 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=550935, cols=550935 total: nonzeros=25585053, allocated nonzeros=25585350 using I-node routines: found 183661 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=550935, cols=550935 total: nonzeros=25585053, allocated nonzeros=25585350 using I-node routines: found 183661 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 190159 countInvalid = 15 general-count = 548625 Average of the error norm = 0.291683 Initial error = 0.553381 Average of the error norm conditional = 0.272969 Active Residual error = 0.0784156 Total error = 0.291797 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166229 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 233874 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 696 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 273790 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 831 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168683 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 3.03303 Max after displacement = 21.7074 Error points = 0 ====================== step = 5 =============== elt_vol= 6.25 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.07 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 22.95 Smoothing mesh. Smooth seconds: 1.32 Writing nodes. Writing elements. Writing faces. Output seconds: 0.17 Total running seconds: 24.53 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 192554 Mesh tetrahedra: 1179748 Mesh faces: 2381735 Mesh subfaces: 44478 Mesh subsegments: 705 mesh nodes = 192554 mesh elts = 1179748 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.141 seconds element count = 568330 count inserted = 200000 elapsed = 0.221 seconds element count = 1722209 count inserted = 300000 elapsed = 0.238 seconds element count = 2963367 count inserted = 400000 elapsed = 0.255 seconds element count = 4137926 count inserted = 500000 elapsed = 0.233 seconds element count = 5235614 count inserted = 600000 elapsed = 0.223 seconds element count = 6329798 count inserted = 700000 elapsed = 0.271 seconds element count = 7410193 count inserted = 800000 elapsed = 0.236 seconds element count = 8494488 count inserted = 900000 elapsed = 0.257 seconds element count = 9570647 count inserted = 1000000 elapsed = 0.22 seconds element count = 10659089 count inserted = 1100000 elapsed = 0.262 seconds element count = 11748694 done building octree - total elements = 12628158 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 160760 Total BCs = 548640 no-eqs = 577662 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=577662, cols=577662 total: nonzeros=26834010, allocated nonzeros=26834334 using I-node routines: found 192570 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=577662, cols=577662 total: nonzeros=26834010, allocated nonzeros=26834334 using I-node routines: found 192570 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 215225 countInvalid = 7 general-count = 548633 Average of the error norm = 0.339438 Initial error = 0.60658 Average of the error norm conditional = 0.314411 Active Residual error = 0.0921399 Total error = 0.339505 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171955 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 531 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 165197 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 486 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173464 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155220 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172946 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175920 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 2.74052 Max after displacement = 21.4147 Error points = 0 ====================== step = 4 =============== elt_vol= 5.9375 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.07 Removing unwanted tetrahedra. Hole seconds: 0.01 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 24.16 Smoothing mesh. Smooth seconds: 1.41 Writing nodes. Writing elements. Writing faces. Output seconds: 0.18 Total running seconds: 25.85 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 202421 Mesh tetrahedra: 1241348 Mesh faces: 2505589 Mesh subfaces: 45786 Mesh subsegments: 710 mesh nodes = 202421 mesh elts = 1241348 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.137 seconds element count = 549086 count inserted = 200000 elapsed = 0.213 seconds element count = 1661149 count inserted = 300000 elapsed = 0.233 seconds element count = 2869465 count inserted = 400000 elapsed = 0.213 seconds element count = 4019943 count inserted = 500000 elapsed = 0.189 seconds element count = 5090754 count inserted = 600000 elapsed = 0.181 seconds element count = 6159634 count inserted = 700000 elapsed = 0.168 seconds element count = 7208349 count inserted = 800000 elapsed = 0.166 seconds element count = 8260804 count inserted = 900000 elapsed = 0.161 seconds element count = 9307778 count inserted = 1000000 elapsed = 0.152 seconds element count = 10364515 count inserted = 1100000 elapsed = 0.151 seconds element count = 11423090 count inserted = 1200000 elapsed = 0.142 seconds element count = 12489457 done building octree - total elements = 12930951 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 164776 Total BCs = 548640 no-eqs = 607263 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=607263, cols=607263 total: nonzeros=28220973, allocated nonzeros=28221306 using I-node routines: found 202437 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=607263, cols=607263 total: nonzeros=28220973, allocated nonzeros=28221306 using I-node routines: found 202437 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 249239 countInvalid = 10 general-count = 548630 Average of the error norm = 0.407286 Initial error = 0.685106 Average of the error norm conditional = 0.372597 Active Residual error = 0.111952 Total error = 0.407349 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 150889 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 456 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 179810 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 576 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 204916 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 579 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 144515 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 179593 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 486 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155533 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 237420 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 681 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 133264 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 417 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173614 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 570 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 157598 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 148459 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 190940 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 567 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156536 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 540 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 2.43802 Max after displacement = 21.2233 Error points = 0 ====================== step = 3 =============== elt_vol= 5.625 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.08 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 25.45 Smoothing mesh. Smooth seconds: 1.48 Writing nodes. Writing elements. Writing faces. Output seconds: 0.19 Total running seconds: 27.22 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 213446 Mesh tetrahedra: 1310649 Mesh faces: 2645078 Mesh subfaces: 47560 Mesh subsegments: 721 mesh nodes = 213446 mesh elts = 1310649 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.132 seconds element count = 531799 count inserted = 200000 elapsed = 0.207 seconds element count = 1608167 count inserted = 300000 elapsed = 0.227 seconds element count = 2779082 count inserted = 400000 elapsed = 0.209 seconds element count = 3904592 count inserted = 500000 elapsed = 0.184 seconds element count = 4949411 count inserted = 600000 elapsed = 0.176 seconds element count = 5988315 count inserted = 700000 elapsed = 0.164 seconds element count = 7008427 count inserted = 800000 elapsed = 0.158 seconds element count = 8026823 count inserted = 900000 elapsed = 0.158 seconds element count = 9043384 count inserted = 1000000 elapsed = 0.148 seconds element count = 10063611 count inserted = 1100000 elapsed = 0.146 seconds element count = 11095382 count inserted = 1200000 elapsed = 0.14 seconds element count = 12123004 count inserted = 1300000 elapsed = 0.137 seconds element count = 13162718 done building octree - total elements = 13273507 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 169671 Total BCs = 548640 no-eqs = 640338 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=640338, cols=640338 total: nonzeros=29782032, allocated nonzeros=29782365 using I-node routines: found 213462 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=640338, cols=640338 total: nonzeros=29782032, allocated nonzeros=29782365 using I-node routines: found 213462 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 301404 countInvalid = 31 general-count = 548609 Average of the error norm = 0.515326 Initial error = 0.812606 Average of the error norm conditional = 0.465737 Active Residual error = 0.144117 Total error = 0.515524 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 196316 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 192298 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 603 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 145142 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 159169 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175318 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 153033 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 180803 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 540 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 163949 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 540 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166961 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178704 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 555 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 283804 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 777 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156143 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169458 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 540 DirectSolverConvergence = ksp-converged-rtol Still having pbs after untangling btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 147369 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171321 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 531 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 248895 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 678 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 184064 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 579 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 160454 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155562 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 246324 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 774 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 145924 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178392 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 564 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 288085 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166514 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 165744 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168223 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 179746 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 170845 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 561 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166650 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after orientation pbs persisting initially 35 post = 1 new problems size = 1 DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_3 Initial transform name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 2.1176 Max after displacement = 20.6432 Error points = 0 ====================== step = 2 =============== elt_vol= 5.3125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0.01 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.07 Removing unwanted tetrahedra. Hole seconds: 0.01 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 26.94 Smoothing mesh. Smooth seconds: 1.56 Writing nodes. Writing elements. Writing faces. Output seconds: 0.2 Total running seconds: 28.81 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 225871 Mesh tetrahedra: 1388294 Mesh faces: 2801346 Mesh subfaces: 49516 Mesh subsegments: 733 mesh nodes = 225871 mesh elts = 1388294 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.121 seconds element count = 512017 count inserted = 200000 elapsed = 0.193 seconds element count = 1542727 count inserted = 300000 elapsed = 0.219 seconds element count = 2681732 count inserted = 400000 elapsed = 0.202 seconds element count = 3777121 count inserted = 500000 elapsed = 0.175 seconds element count = 4789270 count inserted = 600000 elapsed = 0.173 seconds element count = 5801065 count inserted = 700000 elapsed = 0.159 seconds element count = 6787831 count inserted = 800000 elapsed = 0.152 seconds element count = 7772714 count inserted = 900000 elapsed = 0.155 seconds element count = 8760316 count inserted = 1000000 elapsed = 0.143 seconds element count = 9745808 count inserted = 1100000 elapsed = 0.144 seconds element count = 10746529 count inserted = 1200000 elapsed = 0.14 seconds element count = 11744991 count inserted = 1300000 elapsed = 0.132 seconds element count = 12747989 done building octree - total elements = 13637723 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 175233 Total BCs = 548640 no-eqs = 677613 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=677613, cols=677613 total: nonzeros=31532685, allocated nonzeros=31533036 using I-node routines: found 225887 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=677613, cols=677613 total: nonzeros=31532685, allocated nonzeros=31533036 using I-node routines: found 225887 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 391817 countInvalid = 120 general-count = 548520 Average of the error norm = 0.722517 Initial error = 1.05857 Average of the error norm conditional = 0.644404 Active Residual error = 0.206724 Total error = 0.724156 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 194036 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 576 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 251603 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 774 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 295738 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 813 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155544 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 262831 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 310286 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 891 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 249651 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 828 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 372761 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1014 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 261521 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 759 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 157606 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 254965 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 711 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 285600 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 144476 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 489 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 266871 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 735 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 167392 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 224546 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 660 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 355558 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1029 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 188995 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 582 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 284442 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 903 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 249733 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 738 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 210184 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 648 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 157145 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 489 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 143921 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172560 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 287858 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 807 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 152106 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 354103 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1017 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166426 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 184315 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178583 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 561 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166214 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 314801 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 975 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 149581 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 441 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161713 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 152435 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 486 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171985 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 300382 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 873 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 165523 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 184716 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 585 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 196209 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 211643 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 645 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 141051 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 180130 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 555 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178898 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 185865 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 212561 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 651 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 136711 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174377 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 567 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 191550 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 594 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182224 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 272948 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 876 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 187545 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 147317 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182974 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 147098 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 157870 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 483 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173915 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156445 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 138489 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 139922 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 146154 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 213759 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 570 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 186027 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 606 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 183564 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 582 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168639 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 227789 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 660 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 158915 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 129349 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 154031 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 165658 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 145196 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 124360 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 456 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175848 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 594 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 113240 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 438 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178570 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 594 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 167769 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 141587 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_2 Initial transform name = compressed_step_3 Initial transform name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 1.76584 Max after displacement = 20.1897 Error points = 0 ====================== step = 1 =============== elt_vol= 5 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.08 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 28.64 Smoothing mesh. Smooth seconds: 1.67 Writing nodes. Writing elements. Writing faces. Output seconds: 0.22 Total running seconds: 30.64 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 239666 Mesh tetrahedra: 1474548 Mesh faces: 2974870 Mesh subfaces: 51548 Mesh subsegments: 740 mesh nodes = 239666 mesh elts = 1474548 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.114 seconds element count = 496390 count inserted = 200000 elapsed = 0.182 seconds element count = 1480616 count inserted = 300000 elapsed = 0.254 seconds element count = 2589887 count inserted = 400000 elapsed = 0.194 seconds element count = 3647989 count inserted = 500000 elapsed = 0.212 seconds element count = 4633660 count inserted = 600000 elapsed = 0.169 seconds element count = 5616640 count inserted = 700000 elapsed = 0.154 seconds element count = 6574088 count inserted = 800000 elapsed = 0.147 seconds element count = 7528554 count inserted = 900000 elapsed = 0.146 seconds element count = 8488861 count inserted = 1000000 elapsed = 0.142 seconds element count = 9441320 count inserted = 1100000 elapsed = 0.138 seconds element count = 10402373 count inserted = 1200000 elapsed = 0.147 seconds element count = 11373016 count inserted = 1300000 elapsed = 0.13 seconds element count = 12337708 count inserted = 1400000 elapsed = 0.128 seconds element count = 13312713 done building octree - total elements = 14042039 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 182367 Total BCs = 548640 no-eqs = 718998 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=718998, cols=718998 total: nonzeros=33476010, allocated nonzeros=33476361 using I-node routines: found 239682 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=718998, cols=718998 total: nonzeros=33476010, allocated nonzeros=33476361 using I-node routines: found 239682 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 647490 countInvalid = 1687 general-count = 546953 Average of the error norm = 1.30839 Initial error = 1.75766 Average of the error norm conditional = 1.14757 Active Residual error = 0.391448 Total error = 1.34024 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 160315 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 681736 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2196 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 271611 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 786 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 1291377 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 12750 DirectSolverConvergence = ksp-converged-rtol Still having pbs after untangling btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 532787 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2100 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 1299946 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 11529 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 904451 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 3156 DirectSolverConvergence = ksp-converged-rtol Still having pbs after untangling btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 259426 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 786 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171429 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 675960 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1857 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 606549 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1614 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 247225 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 732 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 288819 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 861 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 530514 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1818 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 216685 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 603 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 294831 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173191 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 413618 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1167 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 377273 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1185 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 162584 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 148166 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 284280 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 768 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 313203 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 930 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 176501 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 231082 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 657 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 158042 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 748615 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2409 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 396174 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1134 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 592945 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1947 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 504075 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1623 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 514946 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1743 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 340432 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 951 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 362975 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1086 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 282820 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 858 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 629634 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2136 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 177901 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 164277 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 531 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 432610 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1317 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 183577 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 213403 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 654 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 221833 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 705 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 828710 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2538 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 331520 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 924 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 303409 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 897 DirectSolverConvergence = ksp-converged-rtol Still having pbs after untangling btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 138223 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 362312 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1086 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156494 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 483 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 291421 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 885 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161288 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 159759 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 292183 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 870 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 146250 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182779 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 570 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 422710 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1425 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 251695 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 735 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 396302 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1101 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 233449 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 636 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 159475 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 334453 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1068 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 186537 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 636 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 138654 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 432 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 270291 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 765 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 214703 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 693 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174559 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 411462 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1209 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 532410 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1431 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 153001 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 483 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 218402 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 615 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 163976 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 434257 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1251 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169009 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 555 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 213545 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 705 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 146313 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 510 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182953 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 298922 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 903 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 150028 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 201308 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 555 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 170777 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168170 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 152769 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 139494 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 441 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 200833 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 591 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172648 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 170416 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 317803 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 873 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 204127 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 603 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 149859 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 375975 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1005 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 247388 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 741 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 318607 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 915 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 301146 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 957 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 255483 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 822 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156454 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 124842 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 140727 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 447 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 162370 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175531 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171507 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 151215 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155546 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 260876 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 849 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 238544 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 747 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 430742 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1221 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 194186 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 573 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155447 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172470 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169124 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182326 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 228448 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 639 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 279723 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 774 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 278820 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 936 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 254571 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 783 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 263002 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 813 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 138411 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 468 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 221612 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 663 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 190881 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 621 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 218842 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 663 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175985 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 251424 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 798 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 213640 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 714 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169102 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 213274 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 582 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169470 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 201915 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 582 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173945 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178209 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 311720 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 930 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 180601 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 186676 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 600 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 170278 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 162289 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 339876 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1029 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156753 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 228006 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 687 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 149279 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 486 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 159208 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 143775 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166536 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 237284 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 726 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182050 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 561 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156650 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 277256 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 723 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 201958 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 594 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 139598 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 510 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 154373 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182002 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 579 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 154132 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 158916 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 140334 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 468 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 214287 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 675 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 165958 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 187741 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 588 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 142530 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 489 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 176345 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 189350 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 163056 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168029 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174782 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 167150 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 136428 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after orientation pbs persisting initially 1129 post = 1 new problems size = 1 DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_1 Initial transform name = compressed_step_2 Initial transform name = compressed_step_3 Initial transform name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 1.35511 Max after displacement = 19.252 Error points = 0 ====================== step = 0 =============== elt_vol= 5 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.08 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0.01 Adding Steiner points to enforce quality. Quality seconds: 28.63 Smoothing mesh. Smooth seconds: 1.66 Writing nodes. Writing elements. Writing faces. Output seconds: 0.21 Total running seconds: 30.61 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 239666 Mesh tetrahedra: 1474548 Mesh faces: 2974870 Mesh subfaces: 51548 Mesh subsegments: 740 mesh nodes = 239666 mesh elts = 1474548 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.13 seconds element count = 496390 count inserted = 200000 elapsed = 0.197 seconds element count = 1480616 count inserted = 300000 elapsed = 0.213 seconds element count = 2589887 count inserted = 400000 elapsed = 0.196 seconds element count = 3647989 count inserted = 500000 elapsed = 0.175 seconds element count = 4633660 count inserted = 600000 elapsed = 0.171 seconds element count = 5616640 count inserted = 700000 elapsed = 0.156 seconds element count = 6574088 count inserted = 800000 elapsed = 0.147 seconds element count = 7528554 count inserted = 900000 elapsed = 0.146 seconds element count = 8488861 count inserted = 1000000 elapsed = 0.143 seconds element count = 9441320 count inserted = 1100000 elapsed = 0.138 seconds element count = 10402373 count inserted = 1200000 elapsed = 0.135 seconds element count = 11373016 count inserted = 1300000 elapsed = 0.13 seconds element count = 12337708 count inserted = 1400000 elapsed = 0.128 seconds element count = 13312713 done building octree - total elements = 14042039 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 185660 Total BCs = 548640 no-eqs = 718998 percentage done= 0 percentage done= 5 percentage done= 10 percentage done= 15 percentage done= 20 percentage done= 25 percentage done= 30 percentage done= 35 percentage done= 40 percentage done= 45 percentage done= 50 percentage done= 55 percentage done= 60 percentage done= 65 percentage done= 70 percentage done= 75 percentage done= 80 percentage done= 85 percentage done= 90 percentage done= 95 done_bc_natural size of container = 548640 after building the map LOAD size = 24 after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=718998, cols=718998 total: nonzeros=33476010, allocated nonzeros=33476361 using I-node routines: found 239682 nodes, limit used is 5 convergence reason = 4 KSP Object: type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-09, absolute=1e-50, divergence=10000 left preconditioning PC Object: type: jacobi linear system matrix = precond matrix: Matrix Object: type=seqaij, rows=718998, cols=718998 total: nonzeros=33476010, allocated nonzeros=33476361 using I-node routines: found 239682 nodes, limit used is 5 Iterations 1 Absolute-Norm of error = 439325 countInvalid = 453 general-count = 548187 Average of the error norm = 1.14665 Initial error = 1.3534 Average of the error norm conditional = 0.96152 Active Residual error = 0.327955 Total error = 1.15351 c0324 time elapsed updating the sources (seconds) = 0 orientation_pbs solving topology problems using old topology solver using Lame constants given by E = 1000 nu = 0.3 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173959 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 872243 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 3807 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 616703 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1887 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 281973 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 271140 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 846 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 190973 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 740665 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2106 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 343183 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 987 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 188739 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 600 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 621307 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2097 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 249355 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 693 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 317539 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 921 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 144231 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 447 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 632671 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2013 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161893 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 378887 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1179 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 659465 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 2154 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 503787 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1626 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161345 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 163439 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 179184 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 181191 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 383769 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1047 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 238405 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 666 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 371540 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1041 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 289811 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 852 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 313891 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 936 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 194760 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 570 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 216847 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 666 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 197798 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 660 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 148116 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 483 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 147925 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 334730 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 948 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 306142 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 906 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 287321 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 819 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 164489 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 133942 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 447 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172666 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 552 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 292294 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 849 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 172106 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 531 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 216265 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 732 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161288 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 149785 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 139157 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 444 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 175389 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 505921 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1590 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 302974 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 831 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174145 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 159475 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 474 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 460308 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1488 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 180906 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 573 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 401411 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1182 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 246850 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 678 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 314804 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 906 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 209504 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 624 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 195291 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 585 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182953 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 501 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 195957 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 618 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 140353 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174520 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 510 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173821 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 495 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 160358 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 177037 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 537 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 471922 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 1263 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 194875 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 124519 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 414 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 197625 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 609 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 183760 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 543 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 200681 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 137260 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 483 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 254568 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 762 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174460 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 162927 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 158548 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 555 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 147384 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 181967 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 567 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182744 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 576 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 156380 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 136910 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 204884 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 561 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168646 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 540 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 244067 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 756 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 183493 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 579 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 141902 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 441 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 256434 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 804 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 163258 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 154852 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 480 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 266630 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 801 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 190881 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 621 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 218842 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 663 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 142863 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 149346 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 143727 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 504 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 252610 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 720 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 178209 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 549 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 239525 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 777 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 127532 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 465 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 166143 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 513 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 155110 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 199833 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 570 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168686 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 609 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 143361 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 468 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 252178 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 714 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 143775 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 471 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 230677 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 660 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 180685 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 594 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 136755 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 468 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 153842 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 498 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173741 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 492 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 169450 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 519 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 262841 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 741 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 168231 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 171526 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 534 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 198755 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 576 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 182002 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 579 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 142319 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 462 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 161399 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 525 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 167019 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 477 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 188451 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 546 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 164355 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 528 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 154022 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 486 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 173716 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 531 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 205374 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 630 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 174782 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 516 DirectSolverConvergence = ksp-converged-rtol btest = 1 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 done building octree - total elements = 151533 solving cropped problem computing statistics for the displacement application error average norm of error in placement = 0 LOAD size = 522 DirectSolverConvergence = ksp-converged-rtol btest = 1 before after !!!! No residual problems. DONE compressing morph dcds mesh direct image = 0 0 1.23914e-312 dir img for computed transform = 6.95319e-310 6.95319e-310 6.55601e-315 dir img for compressed = 6.95319e-310 6.95319e-310 6.55601e-315 dcds total image for source point = 6.95319e-310 6.95319e-310 6.55601e-315 name = compressed_step_0 Initial transform name = compressed_step_1 Initial transform name = compressed_step_2 Initial transform name = compressed_step_3 Initial transform name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 6.51024 Final displacement = 1.16595 Max after displacement = 19.3968 Error points = 0 axe z = 0 z = 10 z = 20 z = 30 z = 40 z = 50 z = 60 z = 70 z = 80 z = 90 z = 100 z = 110 z = 120 z = 130 z = 140 z = 150 z = 160 z = 170 z = 180 z = 190 z = 200 z = 210 z = 220 z = 230 z = 240 z = 250 Invalid voxels = 12566350 Valid = 4210866 baly FEM error Initial displacement = 6.51024 Final displacement = 1.16595 Max after displacement = 19.3968 Error points = 0 will write volume morph in file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/el_reg_tocvs_avg35.tm3d saveTransform code writing transform size = 16 saveTransform code writing transform size = 18396509 saveTransform code writing transform size = 18181661 saveTransform code writing transform size = 17944266 saveTransform code writing transform size = 17726782 saveTransform code writing transform size = 17490409 saveTransform code writing transform size = 17252504 saveTransform code writing transform size = 17064747 saveTransform code writing transform size = 16879021 saveTransform code writing transform size = 16688385 saveTransform code writing transform size = 16526115 saveTransform code writing transform size = 16332926 saveTransform code writing transform size = 16135216 saveTransform code writing transform size = 16001226 saveTransform code writing transform size = 15930056 saveTransform code writing transform size = 15833523 saveTransform code writing transform size = 15915359 saveTransform code writing transform size = 17077610 saveTransform code writing transform size = 16402757 saveTransform code writing transform size = 71 writing morph to file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/el_reg_tocvs_avg35.tm3d z = 0 z = 10 z = 20 z = 30 z = 40 z = 50 z = 60 z = 70 z = 80 z = 90 z = 100 z = 110 z = 120 z = 130 z = 140 z = 150 z = 160 z = 170 z = 180 z = 190 z = 200 z = 210 z = 220 z = 230 z = 240 z = 250 Invalid voxels = 0 Valid = 15208561 releasing Petsc resources process performed in 23.0139 minutes mri_cvs_register: Step 2 (elastic registration) took 1382 seconds Template name:/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/mri//aseg.mgz After loading template Template name:/autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/mri//aseg.mgz After loading template extension = tm3d data size = 16 uilen = 3 loading transform id string = data size = 18396509 uilen = 24 loading transform id string = compressed_step_17 data size = 18181661 uilen = 24 loading transform id string = compressed_step_16 data size = 17944266 uilen = 24 loading transform id string = compressed_step_15 data size = 17726782 uilen = 24 loading transform id string = compressed_step_14 data size = 17490409 uilen = 24 loading transform id string = compressed_step_13 data size = 17252504 uilen = 24 loading transform id string = compressed_step_12 data size = 17064747 uilen = 24 loading transform id string = compressed_step_11 data size = 16879021 uilen = 24 loading transform id string = compressed_step_10 data size = 16688385 uilen = 23 loading transform id string = compressed_step_9 data size = 16526115 uilen = 23 loading transform id string = compressed_step_8 data size = 16332926 uilen = 23 loading transform id string = compressed_step_7 data size = 16135216 uilen = 23 loading transform id string = compressed_step_6 data size = 16001226 uilen = 23 loading transform id string = compressed_step_5 data size = 15930056 uilen = 23 loading transform id string = compressed_step_4 data size = 15833523 uilen = 23 loading transform id string = compressed_step_3 data size = 15915359 uilen = 23 loading transform id string = compressed_step_2 data size = 17077610 uilen = 23 loading transform id string = compressed_step_1 data size = 16402757 uilen = 23 loading transform id string = compressed_step_0 data size = 71 uilen = 7 loading transform id string = loaded transform executing filter on file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri//aseg.mgz z = 0 z = 10 z = 20 z = 30 z = 40 z = 50 z = 60 z = 70 z = 80 z = 90 z = 100 z = 110 z = 120 z = 130 z = 140 z = 150 z = 160 z = 170 z = 180 z = 190 z = 200 z = 210 z = 220 z = 230 z = 240 z = 250 Invalid voxels = 12566350 Valid = 4210866 done morphing - will write next done morph applied in 2.128 minutes ======= NUMBER OF OPENMP THREADS = 1 ======= not allowing temporary folds during numerical minimization integrating in 3 passes (default=3) not disabling zero image locations treating inputs as segmentations setting distance transform coefficient to 0.100 applying transform after registration using sigma=0.250 setting l_log_likelihood = 0.000 using optimal time-step integration using dt = 0.250 momentum = 0.25 reading transform from /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/id.xfm... converting ras xform to voxel xform initializing GCAM with vox->vox matrix: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; det(m_affine) = 1.00 (predicted orig area = 1.0) creating distance transform for Left_Thalamus_Proper, frame 0... creating distance transform for Right_Thalamus_Proper, frame 1... creating distance transform for Left_Putamen, frame 2... creating distance transform for Right_Putamen, frame 3... creating distance transform for Left_Pallidum, frame 4... creating distance transform for Right_Pallidum, frame 5... creating distance transform for Left_Lateral_Ventricle, frame 6... creating distance transform for Right_Lateral_Ventricle, frame 7... creating distance transform for Left_Caudate, frame 8... creating distance transform for Right_Caudate, frame 9... creating distance transform for Left_Cerebral_White_Matter, frame 10... creating distance transform for Right_Cerebral_White_Matter, frame 11... creating distance transform for Left_Hippocampus, frame 12... creating distance transform for Right_Hippocampus, frame 13... creating distance transform for Left_Amygdala, frame 14... creating distance transform for Right_Amygdala, frame 15... creating distance transform for Left_VentralDC, frame 16... creating distance transform for Right_VentralDC, frame 17... creating distance transform for Brain_Stem, frame 18... creating distance transform for Left_Inf_Lat_Vent, frame 19... creating distance transform for Right_Inf_Lat_Vent, frame 20... creating distance transform for Left_Cerebral_Cortex, frame 21... creating distance transform for Right_Cerebral_Cortex, frame 22... creating distance transform for Left_Cerebellum_White_Matter, frame 23... creating distance transform for Right_Cerebellum_White_Matter, frame 24... creating distance transform for Left_Cerebellum_Cortex, frame 25... creating distance transform for Right_Cerebellum_Cortex, frame 26... creating distance transform for Unknown, frame 27... **************** pass 1 of 3 ************************ setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=1.171, neg=0, invalid=1530 0001: dt=4.250000, rms=0.966 (17.520%), neg=0, invalid=1530 0002: dt=4.250000, rms=0.786 (18.600%), neg=0, invalid=1530 0003: dt=4.250000, rms=0.676 (13.938%), neg=0, invalid=1530 0004: dt=4.250000, rms=0.625 (7.606%), neg=0, invalid=1530 0005: dt=4.250000, rms=0.600 (4.011%), neg=0, invalid=1530 iter 0, gcam->neg = 1022 after 14 iterations, nbhd size=0, neg = 0 0006: dt=4.250000, rms=0.596 (0.592%), neg=0, invalid=1530 iter 0, gcam->neg = 4488 after 49 iterations, nbhd size=0, neg = 0 0007: dt=4.250000, rms=0.596 (-0.285%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.596, neg=0, invalid=1530 iter 0, gcam->neg = 4924 after 81 iterations, nbhd size=1, neg = 0 0008: dt=2.250000, rms=0.562 (5.717%), neg=0, invalid=1530 iter 0, gcam->neg = 4495 after 50 iterations, nbhd size=0, neg = 0 0009: dt=2.250000, rms=0.537 (4.447%), neg=0, invalid=1530 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0010: dt=2.250000, rms=0.514 (4.381%), neg=0, invalid=1530 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0011: dt=2.250000, rms=0.494 (3.883%), neg=0, invalid=1530 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0012: dt=2.250000, rms=0.480 (2.780%), neg=0, invalid=1530 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0013: dt=2.250000, rms=0.470 (2.129%), neg=0, invalid=1530 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0014: dt=2.250000, rms=0.467 (0.566%), neg=0, invalid=1530 iter 0, gcam->neg = 2784 after 50 iterations, nbhd size=0, neg = 0 0015: dt=2.250000, rms=0.456 (2.470%), neg=0, invalid=1530 iter 0, gcam->neg = 2147 after 28 iterations, nbhd size=1, neg = 0 0016: dt=2.250000, rms=0.456 (-2.491%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.456, neg=0, invalid=1530 iter 0, gcam->neg = 937 after 38 iterations, nbhd size=1, neg = 0 0017: dt=1.250000, rms=0.447 (1.986%), neg=0, invalid=1530 iter 0, gcam->neg = 467 after 26 iterations, nbhd size=1, neg = 0 0018: dt=1.250000, rms=0.435 (2.526%), neg=0, invalid=1530 iter 0, gcam->neg = 302 after 22 iterations, nbhd size=1, neg = 0 0019: dt=1.250000, rms=0.426 (2.102%), neg=0, invalid=1530 0020: dt=1.250000, rms=0.419 (1.622%), neg=0, invalid=1530 0021: dt=1.250000, rms=0.413 (1.455%), neg=0, invalid=1530 0022: dt=1.250000, rms=0.408 (1.222%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0023: dt=1.250000, rms=0.408 (-0.551%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.408, neg=0, invalid=1530 0024: dt=0.750000, rms=0.403 (1.241%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0025: dt=0.750000, rms=0.398 (1.360%), neg=0, invalid=1530 0026: dt=0.750000, rms=0.393 (1.192%), neg=0, invalid=1530 0027: dt=0.750000, rms=0.389 (0.996%), neg=0, invalid=1530 0028: dt=0.750000, rms=0.386 (0.805%), neg=0, invalid=1530 0029: dt=0.750000, rms=0.383 (0.709%), neg=0, invalid=1530 iter 0, gcam->neg = 38 after 0 iterations, nbhd size=0, neg = 0 0030: dt=0.750000, rms=0.381 (0.561%), neg=0, invalid=1530 0031: dt=0.750000, rms=0.380 (0.098%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.380, neg=0, invalid=1530 iter 0, gcam->neg = 29 after 14 iterations, nbhd size=1, neg = 0 0032: dt=0.500000, rms=0.380 (0.137%), neg=0, invalid=1530 iter 0, gcam->neg = 145 after 15 iterations, nbhd size=1, neg = 0 0033: dt=0.500000, rms=0.377 (0.744%), neg=0, invalid=1530 iter 0, gcam->neg = 224 after 13 iterations, nbhd size=1, neg = 0 0034: dt=0.500000, rms=0.374 (0.921%), neg=0, invalid=1530 iter 0, gcam->neg = 125 after 9 iterations, nbhd size=1, neg = 0 0035: dt=0.500000, rms=0.373 (0.214%), neg=0, invalid=1530 iter 0, gcam->neg = 76 after 3 iterations, nbhd size=0, neg = 0 0036: dt=0.500000, rms=0.372 (0.254%), neg=0, invalid=1530 iter 0, gcam->neg = 46 after 3 iterations, nbhd size=0, neg = 0 0037: dt=0.500000, rms=0.370 (0.445%), neg=0, invalid=1530 iter 0, gcam->neg = 32 after 3 iterations, nbhd size=0, neg = 0 0038: dt=0.500000, rms=0.370 (0.104%), neg=0, invalid=1530 iter 0, gcam->neg = 26 after 2 iterations, nbhd size=0, neg = 0 0039: dt=0.500000, rms=0.370 (0.013%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.370, neg=0, invalid=1530 iter 0, gcam->neg = 376 after 2 iterations, nbhd size=0, neg = 0 0040: dt=0.250000, rms=0.370 (-0.792%), neg=0, invalid=1530 **************** pass 2 of 3 ************************ setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.353, neg=0, invalid=1530 0041: dt=4.250000, rms=0.353 (-9.368%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.353, neg=0, invalid=1530 iter 0, gcam->neg = 21 after 0 iterations, nbhd size=0, neg = 0 0042: dt=2.250000, rms=0.353 (-3.597%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.353, neg=0, invalid=1530 iter 0, gcam->neg = 51 after 1 iterations, nbhd size=0, neg = 0 0043: dt=1.250000, rms=0.353 (-0.334%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.353, neg=0, invalid=1530 iter 0, gcam->neg = 161 after 3 iterations, nbhd size=0, neg = 0 0044: dt=0.750000, rms=0.348 (1.581%), neg=0, invalid=1530 iter 0, gcam->neg = 16 after 0 iterations, nbhd size=0, neg = 0 0045: dt=0.750000, rms=0.341 (1.910%), neg=0, invalid=1530 iter 0, gcam->neg = 14 after 0 iterations, nbhd size=0, neg = 0 0046: dt=0.750000, rms=0.335 (1.783%), neg=0, invalid=1530 0047: dt=0.750000, rms=0.330 (1.654%), neg=0, invalid=1530 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0048: dt=0.750000, rms=0.325 (1.488%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0049: dt=0.750000, rms=0.320 (1.402%), neg=0, invalid=1530 0050: dt=0.750000, rms=0.317 (1.003%), neg=0, invalid=1530 iter 0, gcam->neg = 82 after 2 iterations, nbhd size=0, neg = 0 0051: dt=0.750000, rms=0.313 (1.145%), neg=0, invalid=1530 iter 0, gcam->neg = 51 after 1 iterations, nbhd size=0, neg = 0 0052: dt=0.750000, rms=0.309 (1.210%), neg=0, invalid=1530 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0053: dt=0.750000, rms=0.307 (0.871%), neg=0, invalid=1530 0054: dt=0.750000, rms=0.304 (0.908%), neg=0, invalid=1530 iter 0, gcam->neg = 17 after 1 iterations, nbhd size=0, neg = 0 0055: dt=0.750000, rms=0.302 (0.618%), neg=0, invalid=1530 iter 0, gcam->neg = 62 after 2 iterations, nbhd size=0, neg = 0 0056: dt=0.750000, rms=0.300 (0.799%), neg=0, invalid=1530 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0057: dt=0.750000, rms=0.298 (0.502%), neg=0, invalid=1530 iter 0, gcam->neg = 48 after 2 iterations, nbhd size=0, neg = 0 0058: dt=0.750000, rms=0.296 (0.659%), neg=0, invalid=1530 iter 0, gcam->neg = 88 after 9 iterations, nbhd size=1, neg = 0 0059: dt=0.750000, rms=0.295 (0.243%), neg=0, invalid=1530 iter 0, gcam->neg = 55 after 8 iterations, nbhd size=1, neg = 0 0060: dt=0.750000, rms=0.293 (0.956%), neg=0, invalid=1530 iter 0, gcam->neg = 27 after 8 iterations, nbhd size=1, neg = 0 0061: dt=0.750000, rms=0.292 (0.127%), neg=0, invalid=1530 iter 0, gcam->neg = 41 after 10 iterations, nbhd size=1, neg = 0 0062: dt=0.750000, rms=0.290 (0.785%), neg=0, invalid=1530 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0063: dt=0.750000, rms=0.289 (0.349%), neg=0, invalid=1530 iter 0, gcam->neg = 27 after 1 iterations, nbhd size=0, neg = 0 0064: dt=0.750000, rms=0.288 (0.257%), neg=0, invalid=1530 iter 0, gcam->neg = 18 after 1 iterations, nbhd size=0, neg = 0 0065: dt=0.750000, rms=0.287 (0.522%), neg=0, invalid=1530 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0066: dt=0.750000, rms=0.286 (0.275%), neg=0, invalid=1530 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0067: dt=0.750000, rms=0.285 (0.187%), neg=0, invalid=1530 iter 0, gcam->neg = 142 after 2 iterations, nbhd size=0, neg = 0 0068: dt=0.750000, rms=0.285 (0.265%), neg=0, invalid=1530 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0069: dt=0.750000, rms=0.284 (0.164%), neg=0, invalid=1530 iter 0, gcam->neg = 20 after 1 iterations, nbhd size=0, neg = 0 0070: dt=0.750000, rms=0.284 (0.066%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.284, neg=0, invalid=1530 iter 0, gcam->neg = 77 after 14 iterations, nbhd size=1, neg = 0 0071: dt=0.500000, rms=0.282 (0.872%), neg=0, invalid=1530 iter 0, gcam->neg = 49 after 8 iterations, nbhd size=1, neg = 0 0072: dt=0.500000, rms=0.281 (0.080%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.281, neg=0, invalid=1530 iter 0, gcam->neg = 297 after 14 iterations, nbhd size=1, neg = 0 0073: dt=0.250000, rms=0.280 (0.582%), neg=0, invalid=1530 iter 0, gcam->neg = 377 after 10 iterations, nbhd size=1, neg = 0 0074: dt=0.250000, rms=0.279 (0.330%), neg=0, invalid=1530 iter 0, gcam->neg = 405 after 14 iterations, nbhd size=1, neg = 0 0075: dt=0.250000, rms=0.278 (0.356%), neg=0, invalid=1530 iter 0, gcam->neg = 547 after 11 iterations, nbhd size=1, neg = 0 0076: dt=0.250000, rms=0.277 (0.371%), neg=0, invalid=1530 iter 0, gcam->neg = 558 after 9 iterations, nbhd size=1, neg = 0 0077: dt=0.250000, rms=0.277 (-0.088%), neg=0, invalid=1530 **************** pass 3 of 3 ************************ setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.265, neg=0, invalid=1530 0078: dt=4.250000, rms=0.265 (-3.561%), neg=0, invalid=1530 setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.265, neg=0, invalid=1530 0079: dt=2.250000, rms=0.265 (-0.719%), neg=0, invalid=1530 setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.265, neg=0, invalid=1530 iter 0, gcam->neg = 155 after 3 iterations, nbhd size=0, neg = 0 0080: dt=1.250000, rms=0.264 (0.611%), neg=0, invalid=1530 iter 0, gcam->neg = 46 after 2 iterations, nbhd size=0, neg = 0 0081: dt=1.250000, rms=0.262 (0.550%), neg=0, invalid=1530 0082: dt=1.250000, rms=0.260 (0.746%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0083: dt=1.250000, rms=0.259 (0.525%), neg=0, invalid=1530 0084: dt=1.250000, rms=0.257 (0.774%), neg=0, invalid=1530 0085: dt=1.250000, rms=0.255 (0.596%), neg=0, invalid=1530 0086: dt=1.250000, rms=0.254 (0.393%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0087: dt=1.250000, rms=0.253 (0.442%), neg=0, invalid=1530 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0088: dt=1.250000, rms=0.253 (-3.602%), neg=0, invalid=1530 setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.253, neg=0, invalid=1530 0089: dt=0.750000, rms=0.252 (0.384%), neg=0, invalid=1530 iter 0, gcam->neg = 29 after 9 iterations, nbhd size=1, neg = 0 0090: dt=0.750000, rms=0.251 (0.545%), neg=0, invalid=1530 iter 0, gcam->neg = 78 after 3 iterations, nbhd size=0, neg = 0 0091: dt=0.750000, rms=0.248 (1.301%), neg=0, invalid=1530 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0092: dt=0.750000, rms=0.246 (0.743%), neg=0, invalid=1530 0093: dt=0.750000, rms=0.244 (0.712%), neg=0, invalid=1530 0094: dt=0.750000, rms=0.242 (0.662%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0095: dt=0.750000, rms=0.241 (0.466%), neg=0, invalid=1530 iter 0, gcam->neg = 31 after 9 iterations, nbhd size=1, neg = 0 0096: dt=0.750000, rms=0.239 (0.745%), neg=0, invalid=1530 0097: dt=0.750000, rms=0.238 (0.572%), neg=0, invalid=1530 0098: dt=0.750000, rms=0.237 (0.526%), neg=0, invalid=1530 0099: dt=0.750000, rms=0.236 (0.255%), neg=0, invalid=1530 iter 0, gcam->neg = 36 after 1 iterations, nbhd size=0, neg = 0 0100: dt=0.750000, rms=0.235 (0.654%), neg=0, invalid=1530 iter 0, gcam->neg = 18 after 8 iterations, nbhd size=1, neg = 0 0101: dt=0.750000, rms=0.233 (0.537%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0102: dt=0.750000, rms=0.232 (0.439%), neg=0, invalid=1530 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0103: dt=0.750000, rms=0.232 (0.240%), neg=0, invalid=1530 iter 0, gcam->neg = 19 after 1 iterations, nbhd size=0, neg = 0 0104: dt=0.750000, rms=0.230 (0.572%), neg=0, invalid=1530 0105: dt=0.750000, rms=0.230 (0.276%), neg=0, invalid=1530 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0106: dt=0.750000, rms=0.229 (0.385%), neg=0, invalid=1530 iter 0, gcam->neg = 40 after 0 iterations, nbhd size=0, neg = 0 0107: dt=0.750000, rms=0.228 (0.436%), neg=0, invalid=1530 0108: dt=0.750000, rms=0.227 (0.351%), neg=0, invalid=1530 0109: dt=0.750000, rms=0.227 (0.230%), neg=0, invalid=1530 0110: dt=0.750000, rms=0.226 (0.399%), neg=0, invalid=1530 0111: dt=0.750000, rms=0.226 (-0.067%), neg=0, invalid=1530 setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.226, neg=0, invalid=1530 iter 0, gcam->neg = 14 after 2 iterations, nbhd size=0, neg = 0 0112: dt=0.500000, rms=0.226 (-0.012%), neg=0, invalid=1530 setting smoothness coefficient to 0.125 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.226, neg=0, invalid=1530 iter 0, gcam->neg = 579 after 20 iterations, nbhd size=1, neg = 0 0113: dt=0.250000, rms=0.226 (-2.844%), neg=0, invalid=1530 writing transformed output volume to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/nlalign-aseg.mgz... writing warp vector field to /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/nlalign-aseg.m3z GCAMwrite registration took 379 minutes and 58 seconds. atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.000 0.000 0.000 125.254; 0.000 0.000 1.000 -134.838; 0.000 -1.000 0.000 104.897; 0.000 0.000 0.000 1.000; ras 2 vox image = -1.000 0.000 0.000 125.254; -0.000 -0.000 -1.000 104.897; -0.000 1.000 -0.000 134.838; 0.000 0.000 0.000 1.000; product = 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; transform at origin 0.000; 0.000; 0.000; 1.000; invalid voxel count = 0 extension = tm3d data size = 16 uilen = 3 loading transform id string = data size = 18396509 uilen = 24 loading transform id string = compressed_step_17 data size = 18181661 uilen = 24 loading transform id string = compressed_step_16 data size = 17944266 uilen = 24 loading transform id string = compressed_step_15 data size = 17726782 uilen = 24 loading transform id string = compressed_step_14 data size = 17490409 uilen = 24 loading transform id string = compressed_step_13 data size = 17252504 uilen = 24 loading transform id string = compressed_step_12 data size = 17064747 uilen = 24 loading transform id string = compressed_step_11 data size = 16879021 uilen = 24 loading transform id string = compressed_step_10 data size = 16688385 uilen = 23 loading transform id string = compressed_step_9 data size = 16526115 uilen = 23 loading transform id string = compressed_step_8 data size = 16332926 uilen = 23 loading transform id string = compressed_step_7 data size = 16135216 uilen = 23 loading transform id string = compressed_step_6 data size = 16001226 uilen = 23 loading transform id string = compressed_step_5 data size = 15930056 uilen = 23 loading transform id string = compressed_step_4 data size = 15833523 uilen = 23 loading transform id string = compressed_step_3 data size = 15915359 uilen = 23 loading transform id string = compressed_step_2 data size = 17077610 uilen = 23 loading transform id string = compressed_step_1 data size = 16402757 uilen = 23 loading transform id string = compressed_step_0 data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 118640881 saveTransform code writing transform size = 16 saveTransform code writing transform size = 18396513 saveTransform code writing transform size = 18181545 saveTransform code writing transform size = 17944185 saveTransform code writing transform size = 17726739 saveTransform code writing transform size = 17490374 saveTransform code writing transform size = 17252530 saveTransform code writing transform size = 17064804 saveTransform code writing transform size = 16878905 saveTransform code writing transform size = 16688405 saveTransform code writing transform size = 16526058 saveTransform code writing transform size = 16332909 saveTransform code writing transform size = 16135170 saveTransform code writing transform size = 16001238 saveTransform code writing transform size = 15930066 saveTransform code writing transform size = 15833541 saveTransform code writing transform size = 15915334 saveTransform code writing transform size = 17077632 saveTransform code writing transform size = 16402719 saveTransform code writing transform size = 71 writing morph to file /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/combined_tocvs_avg35_elreg_aseg.tm3d using bounding box no extension = tm3d data size = 118640881 uilen = 6 loading transform id string = data size = 16 uilen = 3 loading transform id string = data size = 18396513 uilen = 6 loading transform id string = data size = 18181545 uilen = 6 loading transform id string = data size = 17944185 uilen = 6 loading transform id string = data size = 17726739 uilen = 6 loading transform id string = data size = 17490374 uilen = 6 loading transform id string = data size = 17252530 uilen = 6 loading transform id string = data size = 17064804 uilen = 6 loading transform id string = data size = 16878905 uilen = 6 loading transform id string = data size = 16688405 uilen = 6 loading transform id string = data size = 16526058 uilen = 6 loading transform id string = data size = 16332909 uilen = 6 loading transform id string = data size = 16135170 uilen = 6 loading transform id string = data size = 16001238 uilen = 6 loading transform id string = data size = 15930066 uilen = 6 loading transform id string = data size = 15833541 uilen = 6 loading transform id string = data size = 15915334 uilen = 6 loading transform id string = data size = 17077632 uilen = 6 loading transform id string = data size = 16402719 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = exportGcam: padding is = 1 VolumeMorph::exportGcam -> no mriCache - this will take some time z = 0 z = 10 z = 20 z = 30 z = 40 z = 50 z = 60 z = 70 z = 80 z = 90 z = 100 z = 110 z = 120 z = 130 z = 140 z = 150 z = 160 z = 170 z = 180 z = 190 z = 200 z = 210 z = 220 z = 230 z = 240 z = 250 Invalid voxels = 12538381 Valid = 4238835 Not using bounding box box = 0 , 0 , 0 256 , 256 , 256 gcam export invalid voxels = 12538381 GCAMwrite trimming scaling estimates to be in [-2.6725 5.1914] renormalizing gcam intensities by 1.0202 skipping tmpout2.mgz - using bounding box Export performed in 3.6447 minutes Using the m3z file as it is; no assumed location. movvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri//aseg.mgz targvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/mri//aseg.mgz outvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/step1_CVSmorphed_tocvs_avg35_aseg.mgz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1368234968 Final tkRAS-to-tkRAS Matrix is: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading gcam Applying reg to gcam Applying morph to input Output registration matrix is identity mri_vol2vol done Using the m3z file as it is; no assumed location. movvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/mri//norm.mgz targvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/cvs_avg35/mri//norm.mgz outvol /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/MS_pt36_recon/dmri/xfms/cvs/step1_CVSmorphed_tocvs_avg35_norm.mgz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1368288154 Final tkRAS-to-tkRAS Matrix is: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Reading gcam Applying reg to gcam Applying morph to input Output registration matrix is identity mri_vol2vol done ======= NUMBER OF OPENMP THREADS = 1 ======= renormalizing intensities applying transform after registration not disabling zero image locations using sigma=2.000 using dt = 0.000 setting l_log_likelihood = 0.100 reading transform from /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/id.xfm... source mean = 75.0, target mean = 68.3, scaling by 0.911 converting ras xform to voxel xform initializing GCAM with vox->vox matrix: 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; det(m_affine) = 1.00 (predicted orig area = 1.0) trimming scaling estimates to be in [1.0000 1.0000] renormalizing gcam intensities by 1.0000 **************** pass 1 of 3 ************************ setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=1530 0001: dt=22.475843, rms=0.546 (5.788%), neg=0, invalid=1530 0002: dt=16.572416, rms=0.544 (0.420%), neg=0, invalid=1530 0003: dt=56.819712, rms=0.540 (0.629%), neg=0, invalid=1530 0004: dt=66.289664, rms=0.536 (0.729%), neg=0, invalid=1530 0005: dt=16.572416, rms=0.536 (0.133%), neg=0, invalid=1530 0006: dt=66.289664, rms=0.535 (0.074%), neg=0, invalid=1530 0007: dt=66.289664, rms=0.532 (0.523%), neg=0, invalid=1530 0008: dt=66.289664, rms=0.532 (-0.527%), neg=0, invalid=1530 0009: dt=0.258944, rms=0.532 (0.000%), neg=0, invalid=1530 0010: dt=0.147968, rms=0.532 (0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=1530 0011: dt=28.409856, rms=0.528 (0.865%), neg=0, invalid=1530 0012: dt=16.572416, rms=0.527 (0.158%), neg=0, invalid=1530 0013: dt=66.289664, rms=0.525 (0.371%), neg=0, invalid=1530 0014: dt=16.572416, rms=0.525 (0.055%), neg=0, invalid=1530 0015: dt=16.572416, rms=0.524 (0.046%), neg=0, invalid=1530 0016: dt=16.572416, rms=0.524 (0.078%), neg=0, invalid=1530 0017: dt=16.572416, rms=0.523 (0.102%), neg=0, invalid=1530 0018: dt=16.572416, rms=0.523 (0.115%), neg=0, invalid=1530 0019: dt=16.572416, rms=0.522 (0.122%), neg=0, invalid=1530 0020: dt=16.572416, rms=0.522 (0.125%), neg=0, invalid=1530 0021: dt=16.572416, rms=0.521 (0.122%), neg=0, invalid=1530 0022: dt=16.572416, rms=0.520 (0.116%), neg=0, invalid=1530 0023: dt=16.572416, rms=0.520 (0.107%), neg=0, invalid=1530 0024: dt=16.572416, rms=0.519 (0.097%), neg=0, invalid=1530 0025: dt=16.572416, rms=0.519 (0.089%), neg=0, invalid=1530 0026: dt=16.572416, rms=0.518 (0.083%), neg=0, invalid=1530 0027: dt=16.572416, rms=0.518 (0.079%), neg=0, invalid=1530 0028: dt=16.572416, rms=0.518 (0.076%), neg=0, invalid=1530 0029: dt=16.572416, rms=0.517 (0.072%), neg=0, invalid=1530 0030: dt=16.572416, rms=0.517 (0.067%), neg=0, invalid=1530 0031: dt=16.572416, rms=0.517 (0.062%), neg=0, invalid=1530 0032: dt=16.572416, rms=0.516 (0.055%), neg=0, invalid=1530 0033: dt=16.572416, rms=0.516 (0.050%), neg=0, invalid=1530 0034: dt=16.572416, rms=0.516 (0.045%), neg=0, invalid=1530 0035: dt=66.289664, rms=0.516 (0.012%), neg=0, invalid=1530 0036: dt=66.289664, rms=0.516 (-0.003%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=1530 0037: dt=10.000000, rms=0.514 (0.274%), neg=0, invalid=1530 0038: dt=18.579456, rms=0.509 (1.081%), neg=0, invalid=1530 0039: dt=18.579456, rms=0.508 (0.238%), neg=0, invalid=1530 0040: dt=18.579456, rms=0.503 (0.805%), neg=0, invalid=1530 0041: dt=1.990656, rms=0.503 (0.010%), neg=0, invalid=1530 0042: dt=1.990656, rms=0.503 (0.006%), neg=0, invalid=1530 0043: dt=1.990656, rms=0.503 (-0.001%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=1530 0044: dt=23.322034, rms=0.496 (1.493%), neg=0, invalid=1530 0045: dt=9.860465, rms=0.494 (0.306%), neg=0, invalid=1530 0046: dt=18.579456, rms=0.493 (0.313%), neg=0, invalid=1530 0047: dt=13.271040, rms=0.492 (0.197%), neg=0, invalid=1530 0048: dt=4.644864, rms=0.491 (0.095%), neg=0, invalid=1530 0049: dt=4.644864, rms=0.491 (0.055%), neg=0, invalid=1530 0050: dt=4.644864, rms=0.491 (0.098%), neg=0, invalid=1530 0051: dt=4.644864, rms=0.490 (0.137%), neg=0, invalid=1530 0052: dt=4.644864, rms=0.489 (0.169%), neg=0, invalid=1530 0053: dt=4.644864, rms=0.488 (0.182%), neg=0, invalid=1530 0054: dt=4.644864, rms=0.487 (0.186%), neg=0, invalid=1530 0055: dt=4.644864, rms=0.486 (0.186%), neg=0, invalid=1530 0056: dt=4.644864, rms=0.485 (0.183%), neg=0, invalid=1530 0057: dt=4.644864, rms=0.485 (0.181%), neg=0, invalid=1530 0058: dt=4.644864, rms=0.484 (0.180%), neg=0, invalid=1530 0059: dt=4.644864, rms=0.483 (0.175%), neg=0, invalid=1530 0060: dt=4.644864, rms=0.482 (0.165%), neg=0, invalid=1530 0061: dt=4.644864, rms=0.481 (0.153%), neg=0, invalid=1530 0062: dt=4.644864, rms=0.481 (0.143%), neg=0, invalid=1530 0063: dt=4.644864, rms=0.480 (0.132%), neg=0, invalid=1530 0064: dt=4.644864, rms=0.479 (0.124%), neg=0, invalid=1530 0065: dt=4.644864, rms=0.479 (0.117%), neg=0, invalid=1530 0066: dt=4.644864, rms=0.478 (0.106%), neg=0, invalid=1530 0067: dt=4.644864, rms=0.478 (0.093%), neg=0, invalid=1530 0068: dt=4.644864, rms=0.478 (0.081%), neg=0, invalid=1530 0069: dt=4.644864, rms=0.477 (0.071%), neg=0, invalid=1530 0070: dt=4.644864, rms=0.477 (0.063%), neg=0, invalid=1530 0071: dt=4.644864, rms=0.477 (0.058%), neg=0, invalid=1530 0072: dt=4.644864, rms=0.476 (0.054%), neg=0, invalid=1530 0073: dt=4.644864, rms=0.476 (0.049%), neg=0, invalid=1530 0074: dt=4.644864, rms=0.476 (0.044%), neg=0, invalid=1530 0075: dt=18.579456, rms=0.476 (0.003%), neg=0, invalid=1530 0076: dt=18.579456, rms=0.476 (0.016%), neg=0, invalid=1530 0077: dt=18.579456, rms=0.476 (0.003%), neg=0, invalid=1530 0078: dt=18.579456, rms=0.476 (0.033%), neg=0, invalid=1530 0079: dt=18.579456, rms=0.476 (0.027%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=1530 0080: dt=5.734400, rms=0.468 (1.530%), neg=0, invalid=1530 0081: dt=4.915200, rms=0.464 (0.881%), neg=0, invalid=1530 0082: dt=5.734400, rms=0.462 (0.539%), neg=0, invalid=1530 0083: dt=5.734400, rms=0.460 (0.423%), neg=0, invalid=1530 0084: dt=5.734400, rms=0.458 (0.280%), neg=0, invalid=1530 0085: dt=5.734400, rms=0.457 (0.230%), neg=0, invalid=1530 0086: dt=4.096000, rms=0.457 (0.150%), neg=0, invalid=1530 0087: dt=5.734400, rms=0.456 (0.158%), neg=0, invalid=1530 0088: dt=4.915200, rms=0.455 (0.145%), neg=0, invalid=1530 0089: dt=5.734400, rms=0.455 (0.091%), neg=0, invalid=1530 0090: dt=5.734400, rms=0.454 (0.147%), neg=0, invalid=1530 0091: dt=5.734400, rms=0.453 (0.184%), neg=0, invalid=1530 0092: dt=5.734400, rms=0.452 (0.191%), neg=0, invalid=1530 0093: dt=5.734400, rms=0.452 (0.216%), neg=0, invalid=1530 0094: dt=5.734400, rms=0.451 (0.041%), neg=0, invalid=1530 0095: dt=5.734400, rms=0.451 (0.028%), neg=0, invalid=1530 0096: dt=5.734400, rms=0.451 (0.074%), neg=0, invalid=1530 0097: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=1530 0098: dt=0.000000, rms=0.451 (-0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=1530 0099: dt=9.090909, rms=0.446 (1.126%), neg=0, invalid=1530 0100: dt=9.254902, rms=0.444 (0.485%), neg=0, invalid=1530 0101: dt=6.717949, rms=0.442 (0.382%), neg=0, invalid=1530 0102: dt=3.726027, rms=0.441 (0.122%), neg=0, invalid=1530 0103: dt=5.734400, rms=0.441 (0.152%), neg=0, invalid=1530 0104: dt=5.734400, rms=0.440 (0.118%), neg=0, invalid=1530 0105: dt=5.734400, rms=0.440 (0.115%), neg=0, invalid=1530 0106: dt=5.734400, rms=0.439 (0.092%), neg=0, invalid=1530 0107: dt=5.734400, rms=0.439 (0.090%), neg=0, invalid=1530 0108: dt=5.734400, rms=0.438 (0.152%), neg=0, invalid=1530 0109: dt=5.734400, rms=0.437 (0.186%), neg=0, invalid=1530 0110: dt=5.734400, rms=0.437 (0.202%), neg=0, invalid=1530 0111: dt=5.734400, rms=0.436 (0.204%), neg=0, invalid=1530 0112: dt=5.734400, rms=0.435 (0.194%), neg=0, invalid=1530 0113: dt=5.734400, rms=0.434 (0.180%), neg=0, invalid=1530 0114: dt=5.734400, rms=0.433 (0.170%), neg=0, invalid=1530 0115: dt=5.734400, rms=0.433 (0.156%), neg=0, invalid=1530 0116: dt=5.734400, rms=0.432 (0.135%), neg=0, invalid=1530 0117: dt=5.734400, rms=0.432 (0.112%), neg=0, invalid=1530 0118: dt=5.734400, rms=0.431 (0.093%), neg=0, invalid=1530 0119: dt=5.734400, rms=0.431 (0.080%), neg=0, invalid=1530 0120: dt=5.734400, rms=0.430 (0.071%), neg=0, invalid=1530 0121: dt=5.734400, rms=0.430 (0.064%), neg=0, invalid=1530 0122: dt=5.734400, rms=0.430 (0.061%), neg=0, invalid=1530 0123: dt=5.734400, rms=0.430 (0.056%), neg=0, invalid=1530 0124: dt=5.734400, rms=0.429 (0.050%), neg=0, invalid=1530 0125: dt=5.734400, rms=0.429 (0.043%), neg=0, invalid=1530 0126: dt=5.734400, rms=0.429 (0.040%), neg=0, invalid=1530 0127: dt=5.734400, rms=0.429 (0.007%), neg=0, invalid=1530 0128: dt=5.734400, rms=0.429 (0.003%), neg=0, invalid=1530 0129: dt=5.734400, rms=0.429 (0.006%), neg=0, invalid=1530 0130: dt=5.734400, rms=0.429 (0.006%), neg=0, invalid=1530 0131: dt=5.734400, rms=0.429 (0.005%), neg=0, invalid=1530 0132: dt=5.734400, rms=0.429 (0.003%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=1530 0133: dt=2.385714, rms=0.427 (0.376%), neg=0, invalid=1530 0134: dt=0.073728, rms=0.427 (0.000%), neg=0, invalid=1530 0135: dt=0.073728, rms=0.427 (0.000%), neg=0, invalid=1530 0136: dt=0.073728, rms=0.427 (0.001%), neg=0, invalid=1530 0137: dt=0.073728, rms=0.427 (0.000%), neg=0, invalid=1530 0138: dt=0.073728, rms=0.427 (-0.001%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=1530 0139: dt=2.064384, rms=0.424 (0.881%), neg=0, invalid=1530 0140: dt=2.064384, rms=0.421 (0.522%), neg=0, invalid=1530 0141: dt=2.064384, rms=0.420 (0.313%), neg=0, invalid=1530 0142: dt=1.769472, rms=0.419 (0.228%), neg=0, invalid=1530 0143: dt=0.516096, rms=0.419 (0.039%), neg=0, invalid=1530 0144: dt=0.516096, rms=0.419 (0.052%), neg=0, invalid=1530 0145: dt=0.516096, rms=0.418 (0.093%), neg=0, invalid=1530 0146: dt=0.516096, rms=0.418 (0.120%), neg=0, invalid=1530 0147: dt=0.516096, rms=0.417 (0.134%), neg=0, invalid=1530 0148: dt=0.516096, rms=0.417 (0.143%), neg=0, invalid=1530 0149: dt=0.516096, rms=0.416 (0.147%), neg=0, invalid=1530 0150: dt=0.516096, rms=0.415 (0.145%), neg=0, invalid=1530 0151: dt=0.516096, rms=0.415 (0.137%), neg=0, invalid=1530 0152: dt=0.516096, rms=0.414 (0.125%), neg=0, invalid=1530 0153: dt=0.516096, rms=0.414 (0.108%), neg=0, invalid=1530 0154: dt=0.516096, rms=0.414 (0.089%), neg=0, invalid=1530 0155: dt=0.516096, rms=0.413 (0.072%), neg=0, invalid=1530 0156: dt=0.516096, rms=0.413 (0.059%), neg=0, invalid=1530 0157: dt=0.516096, rms=0.413 (0.049%), neg=0, invalid=1530 0158: dt=0.516096, rms=0.413 (0.039%), neg=0, invalid=1530 0159: dt=0.000003, rms=0.413 (0.000%), neg=0, invalid=1530 0160: dt=0.000003, rms=0.413 (-0.000%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=1530 0161: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=1530 0162: dt=0.655360, rms=0.411 (0.331%), neg=0, invalid=1530 0163: dt=0.229376, rms=0.411 (0.085%), neg=0, invalid=1530 0164: dt=0.114688, rms=0.411 (0.039%), neg=0, invalid=1530 0165: dt=0.114688, rms=0.411 (0.040%), neg=0, invalid=1530 0166: dt=0.114688, rms=0.410 (0.074%), neg=0, invalid=1530 0167: dt=0.114688, rms=0.410 (0.100%), neg=0, invalid=1530 0168: dt=0.114688, rms=0.409 (0.117%), neg=0, invalid=1530 0169: dt=0.114688, rms=0.409 (0.127%), neg=0, invalid=1530 0170: dt=0.114688, rms=0.408 (0.131%), neg=0, invalid=1530 0171: dt=0.114688, rms=0.408 (0.129%), neg=0, invalid=1530 0172: dt=0.114688, rms=0.407 (0.123%), neg=0, invalid=1530 0173: dt=0.114688, rms=0.407 (0.114%), neg=0, invalid=1530 0174: dt=0.114688, rms=0.406 (0.102%), neg=0, invalid=1530 0175: dt=0.114688, rms=0.406 (0.089%), neg=0, invalid=1530 0176: dt=0.114688, rms=0.406 (0.074%), neg=0, invalid=1530 0177: dt=0.114688, rms=0.406 (0.059%), neg=0, invalid=1530 0178: dt=0.114688, rms=0.405 (0.044%), neg=0, invalid=1530 0179: dt=0.114688, rms=0.405 (0.030%), neg=0, invalid=1530 0180: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=1530 0181: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=1530 0182: dt=0.163840, rms=0.405 (0.046%), neg=0, invalid=1530 0183: dt=0.010245, rms=0.405 (0.001%), neg=0, invalid=1530 0184: dt=0.010245, rms=0.405 (0.001%), neg=0, invalid=1530 0185: dt=0.005123, rms=0.405 (0.001%), neg=0, invalid=1530 0186: dt=0.005123, rms=0.405 (0.001%), neg=0, invalid=1530 0187: dt=0.005123, rms=0.405 (0.001%), neg=0, invalid=1530 0188: dt=0.005123, rms=0.405 (0.002%), neg=0, invalid=1530 0189: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0190: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0191: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0192: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0193: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0194: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 0195: dt=0.005123, rms=0.405 (0.003%), neg=0, invalid=1530 **************** pass 2 of 3 ************************ setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=1530 0196: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=1530 0197: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=1530 0198: dt=3.272727, rms=0.390 (0.102%), neg=0, invalid=1530 0199: dt=1.161216, rms=0.390 (0.012%), neg=0, invalid=1530 0200: dt=1.161216, rms=0.390 (0.004%), neg=0, invalid=1530 0201: dt=1.161216, rms=0.390 (-0.021%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=1530 0202: dt=15.925248, rms=0.388 (0.543%), neg=0, invalid=1530 0203: dt=9.201133, rms=0.387 (0.220%), neg=0, invalid=1530 0204: dt=18.579456, rms=0.386 (0.312%), neg=0, invalid=1530 0205: dt=4.644864, rms=0.386 (0.131%), neg=0, invalid=1530 0206: dt=18.579456, rms=0.385 (0.186%), neg=0, invalid=1530 0207: dt=15.925248, rms=0.384 (0.175%), neg=0, invalid=1530 0208: dt=4.644864, rms=0.384 (0.081%), neg=0, invalid=1530 0209: dt=4.644864, rms=0.384 (0.037%), neg=0, invalid=1530 0210: dt=4.644864, rms=0.384 (0.067%), neg=0, invalid=1530 0211: dt=4.644864, rms=0.383 (0.097%), neg=0, invalid=1530 0212: dt=4.644864, rms=0.383 (0.122%), neg=0, invalid=1530 0213: dt=4.644864, rms=0.382 (0.133%), neg=0, invalid=1530 0214: dt=4.644864, rms=0.382 (0.134%), neg=0, invalid=1530 0215: dt=4.644864, rms=0.381 (0.130%), neg=0, invalid=1530 0216: dt=4.644864, rms=0.381 (0.121%), neg=0, invalid=1530 0217: dt=4.644864, rms=0.380 (0.113%), neg=0, invalid=1530 0218: dt=4.644864, rms=0.380 (0.108%), neg=0, invalid=1530 0219: dt=4.644864, rms=0.380 (0.104%), neg=0, invalid=1530 0220: dt=4.644864, rms=0.380 (0.012%), neg=0, invalid=1530 0221: dt=4.644864, rms=0.379 (0.021%), neg=0, invalid=1530 0222: dt=4.644864, rms=0.379 (0.027%), neg=0, invalid=1530 0223: dt=4.644864, rms=0.379 (0.031%), neg=0, invalid=1530 0224: dt=4.644864, rms=0.379 (0.035%), neg=0, invalid=1530 0225: dt=4.644864, rms=0.379 (0.038%), neg=0, invalid=1530 0226: dt=4.644864, rms=0.379 (0.042%), neg=0, invalid=1530 0227: dt=4.644864, rms=0.379 (0.045%), neg=0, invalid=1530 0228: dt=4.644864, rms=0.378 (0.047%), neg=0, invalid=1530 0229: dt=4.644864, rms=0.378 (0.048%), neg=0, invalid=1530 0230: dt=4.644864, rms=0.378 (0.048%), neg=0, invalid=1530 0231: dt=18.579456, rms=0.378 (0.025%), neg=0, invalid=1530 0232: dt=18.579456, rms=0.378 (0.031%), neg=0, invalid=1530 0233: dt=18.579456, rms=0.378 (0.043%), neg=0, invalid=1530 0234: dt=18.579456, rms=0.377 (0.061%), neg=0, invalid=1530 0235: dt=18.579456, rms=0.377 (0.078%), neg=0, invalid=1530 0236: dt=18.579456, rms=0.377 (0.077%), neg=0, invalid=1530 0237: dt=18.579456, rms=0.377 (0.081%), neg=0, invalid=1530 0238: dt=18.579456, rms=0.376 (0.087%), neg=0, invalid=1530 0239: dt=18.579456, rms=0.376 (0.083%), neg=0, invalid=1530 0240: dt=18.579456, rms=0.376 (0.080%), neg=0, invalid=1530 0241: dt=18.579456, rms=0.375 (0.080%), neg=0, invalid=1530 0242: dt=18.579456, rms=0.375 (0.076%), neg=0, invalid=1530 0243: dt=18.579456, rms=0.375 (0.072%), neg=0, invalid=1530 0244: dt=18.579456, rms=0.375 (0.069%), neg=0, invalid=1530 0245: dt=18.579456, rms=0.374 (0.065%), neg=0, invalid=1530 0246: dt=18.579456, rms=0.374 (0.060%), neg=0, invalid=1530 0247: dt=18.579456, rms=0.374 (0.056%), neg=0, invalid=1530 0248: dt=18.579456, rms=0.374 (0.053%), neg=0, invalid=1530 0249: dt=18.579456, rms=0.373 (0.051%), neg=0, invalid=1530 0250: dt=18.579456, rms=0.373 (0.046%), neg=0, invalid=1530 0251: dt=18.579456, rms=0.373 (0.043%), neg=0, invalid=1530 0252: dt=18.579456, rms=0.373 (0.004%), neg=0, invalid=1530 0253: dt=18.579456, rms=0.373 (0.001%), neg=0, invalid=1530 0254: dt=18.579456, rms=0.373 (0.007%), neg=0, invalid=1530 0255: dt=18.579456, rms=0.373 (0.008%), neg=0, invalid=1530 0256: dt=18.579456, rms=0.373 (0.009%), neg=0, invalid=1530 0257: dt=18.579456, rms=0.373 (0.012%), neg=0, invalid=1530 0258: dt=18.579456, rms=0.373 (0.013%), neg=0, invalid=1530 0259: dt=18.579456, rms=0.373 (0.013%), neg=0, invalid=1530 0260: dt=18.579456, rms=0.373 (0.015%), neg=0, invalid=1530 0261: dt=18.579456, rms=0.373 (0.016%), neg=0, invalid=1530 0262: dt=18.579456, rms=0.373 (0.015%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.373, neg=0, invalid=1530 0263: dt=2.133333, rms=0.372 (0.147%), neg=0, invalid=1530 0264: dt=1.024000, rms=0.372 (0.015%), neg=0, invalid=1530 0265: dt=1.024000, rms=0.372 (-0.009%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.372, neg=0, invalid=1530 0266: dt=5.734400, rms=0.369 (0.790%), neg=0, invalid=1530 0267: dt=5.734400, rms=0.367 (0.489%), neg=0, invalid=1530 0268: dt=5.734400, rms=0.366 (0.427%), neg=0, invalid=1530 0269: dt=5.734400, rms=0.365 (0.354%), neg=0, invalid=1530 0270: dt=5.734400, rms=0.363 (0.327%), neg=0, invalid=1530 0271: dt=5.734400, rms=0.362 (0.249%), neg=0, invalid=1530 0272: dt=5.734400, rms=0.362 (0.242%), neg=0, invalid=1530 0273: dt=6.545455, rms=0.361 (0.193%), neg=0, invalid=1530 0274: dt=4.347826, rms=0.360 (0.199%), neg=0, invalid=1530 0275: dt=5.818182, rms=0.360 (0.154%), neg=0, invalid=1530 0276: dt=4.915200, rms=0.359 (0.161%), neg=0, invalid=1530 0277: dt=4.615385, rms=0.359 (0.122%), neg=0, invalid=1530 0278: dt=6.608696, rms=0.358 (0.148%), neg=0, invalid=1530 0279: dt=3.490909, rms=0.358 (0.109%), neg=0, invalid=1530 0280: dt=5.734400, rms=0.357 (0.128%), neg=0, invalid=1530 0281: dt=5.734400, rms=0.357 (0.094%), neg=0, invalid=1530 0282: dt=5.734400, rms=0.356 (0.107%), neg=0, invalid=1530 0283: dt=5.734400, rms=0.356 (0.210%), neg=0, invalid=1530 0284: dt=5.734400, rms=0.355 (0.214%), neg=0, invalid=1530 0285: dt=5.734400, rms=0.354 (0.313%), neg=0, invalid=1530 0286: dt=5.734400, rms=0.353 (0.284%), neg=0, invalid=1530 0287: dt=5.734400, rms=0.353 (0.013%), neg=0, invalid=1530 0288: dt=5.734400, rms=0.352 (0.107%), neg=0, invalid=1530 0289: dt=5.734400, rms=0.352 (0.088%), neg=0, invalid=1530 0290: dt=5.734400, rms=0.352 (0.158%), neg=0, invalid=1530 0291: dt=5.734400, rms=0.351 (0.098%), neg=0, invalid=1530 0292: dt=5.734400, rms=0.351 (0.188%), neg=0, invalid=1530 0293: dt=5.734400, rms=0.350 (0.154%), neg=0, invalid=1530 0294: dt=5.734400, rms=0.349 (0.147%), neg=0, invalid=1530 0295: dt=5.734400, rms=0.349 (0.154%), neg=0, invalid=1530 0296: dt=5.734400, rms=0.348 (0.151%), neg=0, invalid=1530 0297: dt=5.734400, rms=0.348 (0.153%), neg=0, invalid=1530 0298: dt=5.734400, rms=0.348 (0.100%), neg=0, invalid=1530 0299: dt=5.734400, rms=0.347 (0.133%), neg=0, invalid=1530 0300: dt=5.734400, rms=0.347 (0.110%), neg=0, invalid=1530 0301: dt=5.734400, rms=0.346 (0.083%), neg=0, invalid=1530 0302: dt=5.734400, rms=0.346 (0.078%), neg=0, invalid=1530 0303: dt=5.734400, rms=0.346 (0.079%), neg=0, invalid=1530 0304: dt=5.734400, rms=0.346 (0.071%), neg=0, invalid=1530 0305: dt=5.734400, rms=0.345 (0.044%), neg=0, invalid=1530 0306: dt=5.734400, rms=0.345 (0.057%), neg=0, invalid=1530 0307: dt=5.734400, rms=0.345 (0.056%), neg=0, invalid=1530 0308: dt=5.734400, rms=0.345 (0.035%), neg=0, invalid=1530 0309: dt=5.734400, rms=0.345 (0.038%), neg=0, invalid=1530 0310: dt=5.734400, rms=0.345 (0.040%), neg=0, invalid=1530 0311: dt=5.734400, rms=0.345 (0.035%), neg=0, invalid=1530 0312: dt=1.433600, rms=0.345 (0.001%), neg=0, invalid=1530 0313: dt=1.433600, rms=0.345 (0.000%), neg=0, invalid=1530 0314: dt=1.433600, rms=0.345 (0.001%), neg=0, invalid=1530 0315: dt=1.433600, rms=0.345 (0.001%), neg=0, invalid=1530 0316: dt=1.433600, rms=0.345 (0.002%), neg=0, invalid=1530 0317: dt=1.433600, rms=0.345 (0.003%), neg=0, invalid=1530 0318: dt=1.433600, rms=0.345 (0.004%), neg=0, invalid=1530 0319: dt=1.433600, rms=0.345 (0.004%), neg=0, invalid=1530 0320: dt=1.433600, rms=0.344 (0.004%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.344, neg=0, invalid=1530 0321: dt=0.516096, rms=0.344 (0.027%), neg=0, invalid=1530 0322: dt=0.129024, rms=0.344 (0.002%), neg=0, invalid=1530 0323: dt=0.129024, rms=0.344 (-0.001%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.344, neg=0, invalid=1530 0324: dt=1.474560, rms=0.343 (0.371%), neg=0, invalid=1530 0325: dt=0.516096, rms=0.343 (0.126%), neg=0, invalid=1530 0326: dt=0.516096, rms=0.342 (0.115%), neg=0, invalid=1530 0327: dt=0.516096, rms=0.342 (0.111%), neg=0, invalid=1530 0328: dt=1.474560, rms=0.341 (0.293%), neg=0, invalid=1530 0329: dt=0.129024, rms=0.341 (0.023%), neg=0, invalid=1530 0330: dt=0.129024, rms=0.341 (0.023%), neg=0, invalid=1530 0331: dt=0.129024, rms=0.341 (0.044%), neg=0, invalid=1530 0332: dt=0.129024, rms=0.340 (0.061%), neg=0, invalid=1530 0333: dt=0.129024, rms=0.340 (0.076%), neg=0, invalid=1530 0334: dt=0.129024, rms=0.340 (0.088%), neg=0, invalid=1530 0335: dt=0.129024, rms=0.340 (0.098%), neg=0, invalid=1530 0336: dt=0.129024, rms=0.339 (0.107%), neg=0, invalid=1530 0337: dt=0.129024, rms=0.339 (0.113%), neg=0, invalid=1530 0338: dt=0.129024, rms=0.338 (0.118%), neg=0, invalid=1530 0339: dt=0.129024, rms=0.338 (0.121%), neg=0, invalid=1530 0340: dt=0.129024, rms=0.338 (0.123%), neg=0, invalid=1530 0341: dt=0.129024, rms=0.337 (0.123%), neg=0, invalid=1530 0342: dt=0.129024, rms=0.337 (0.122%), neg=0, invalid=1530 0343: dt=0.129024, rms=0.336 (0.120%), neg=0, invalid=1530 0344: dt=0.129024, rms=0.336 (0.117%), neg=0, invalid=1530 0345: dt=0.129024, rms=0.336 (0.114%), neg=0, invalid=1530 0346: dt=0.129024, rms=0.335 (0.110%), neg=0, invalid=1530 0347: dt=0.129024, rms=0.335 (0.106%), neg=0, invalid=1530 0348: dt=0.129024, rms=0.334 (0.102%), neg=0, invalid=1530 0349: dt=0.129024, rms=0.334 (0.098%), neg=0, invalid=1530 0350: dt=0.129024, rms=0.334 (0.093%), neg=0, invalid=1530 0351: dt=0.129024, rms=0.334 (0.089%), neg=0, invalid=1530 0352: dt=0.129024, rms=0.333 (0.084%), neg=0, invalid=1530 0353: dt=0.129024, rms=0.333 (0.079%), neg=0, invalid=1530 0354: dt=0.129024, rms=0.333 (0.075%), neg=0, invalid=1530 0355: dt=0.129024, rms=0.332 (0.071%), neg=0, invalid=1530 0356: dt=0.129024, rms=0.332 (0.067%), neg=0, invalid=1530 0357: dt=0.129024, rms=0.332 (0.063%), neg=0, invalid=1530 0358: dt=0.129024, rms=0.332 (0.060%), neg=0, invalid=1530 0359: dt=0.129024, rms=0.332 (0.056%), neg=0, invalid=1530 0360: dt=0.129024, rms=0.332 (0.053%), neg=0, invalid=1530 0361: dt=0.129024, rms=0.331 (0.050%), neg=0, invalid=1530 0362: dt=0.129024, rms=0.331 (0.047%), neg=0, invalid=1530 0363: dt=2.064384, rms=0.331 (0.036%), neg=0, invalid=1530 0364: dt=1.032192, rms=0.331 (0.023%), neg=0, invalid=1530 0365: dt=1.032192, rms=0.331 (0.022%), neg=0, invalid=1530 0366: dt=0.258048, rms=0.331 (0.007%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.331, neg=0, invalid=1530 0367: dt=0.000000, rms=0.331 (0.000%), neg=0, invalid=1530 0368: dt=0.000000, rms=0.331 (-0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.331, neg=0, invalid=1530 0369: dt=0.196608, rms=0.330 (0.162%), neg=0, invalid=1530 0370: dt=0.049152, rms=0.330 (0.040%), neg=0, invalid=1530 0371: dt=0.024576, rms=0.330 (0.020%), neg=0, invalid=1530 0372: dt=0.024576, rms=0.330 (0.039%), neg=0, invalid=1530 0373: dt=0.024576, rms=0.330 (0.055%), neg=0, invalid=1530 0374: dt=0.024576, rms=0.330 (0.069%), neg=0, invalid=1530 0375: dt=0.024576, rms=0.329 (0.081%), neg=0, invalid=1530 0376: dt=0.024576, rms=0.329 (0.092%), neg=0, invalid=1530 0377: dt=0.024576, rms=0.329 (0.101%), neg=0, invalid=1530 0378: dt=0.024576, rms=0.328 (0.108%), neg=0, invalid=1530 0379: dt=0.024576, rms=0.328 (0.114%), neg=0, invalid=1530 0380: dt=0.024576, rms=0.328 (0.119%), neg=0, invalid=1530 0381: dt=0.024576, rms=0.327 (0.122%), neg=0, invalid=1530 0382: dt=0.024576, rms=0.327 (0.125%), neg=0, invalid=1530 0383: dt=0.024576, rms=0.326 (0.126%), neg=0, invalid=1530 0384: dt=0.024576, rms=0.326 (0.127%), neg=0, invalid=1530 0385: dt=0.024576, rms=0.326 (0.126%), neg=0, invalid=1530 0386: dt=0.024576, rms=0.325 (0.126%), neg=0, invalid=1530 0387: dt=0.024576, rms=0.325 (0.124%), neg=0, invalid=1530 0388: dt=0.024576, rms=0.324 (0.122%), neg=0, invalid=1530 0389: dt=0.024576, rms=0.324 (0.119%), neg=0, invalid=1530 0390: dt=0.024576, rms=0.324 (0.116%), neg=0, invalid=1530 0391: dt=0.024576, rms=0.323 (0.113%), neg=0, invalid=1530 0392: dt=0.024576, rms=0.323 (0.109%), neg=0, invalid=1530 0393: dt=0.024576, rms=0.323 (0.105%), neg=0, invalid=1530 0394: dt=0.024576, rms=0.322 (0.101%), neg=0, invalid=1530 0395: dt=0.024576, rms=0.322 (0.097%), neg=0, invalid=1530 0396: dt=0.024576, rms=0.322 (0.093%), neg=0, invalid=1530 0397: dt=0.024576, rms=0.321 (0.088%), neg=0, invalid=1530 0398: dt=0.024576, rms=0.321 (0.084%), neg=0, invalid=1530 0399: dt=0.024576, rms=0.321 (0.080%), neg=0, invalid=1530 0400: dt=0.024576, rms=0.321 (0.076%), neg=0, invalid=1530 0401: dt=0.024576, rms=0.320 (0.072%), neg=0, invalid=1530 0402: dt=0.024576, rms=0.320 (0.068%), neg=0, invalid=1530 0403: dt=0.024576, rms=0.320 (0.064%), neg=0, invalid=1530 0404: dt=0.024576, rms=0.320 (0.060%), neg=0, invalid=1530 0405: dt=0.024576, rms=0.320 (0.057%), neg=0, invalid=1530 0406: dt=0.024576, rms=0.319 (0.054%), neg=0, invalid=1530 0407: dt=0.024576, rms=0.319 (0.051%), neg=0, invalid=1530 0408: dt=0.024576, rms=0.319 (0.048%), neg=0, invalid=1530 0409: dt=0.024576, rms=0.319 (0.045%), neg=0, invalid=1530 0410: dt=0.917504, rms=0.319 (0.078%), neg=0, invalid=1530 0411: dt=0.014336, rms=0.319 (0.001%), neg=0, invalid=1530 0412: dt=0.014336, rms=0.319 (0.001%), neg=0, invalid=1530 0413: dt=0.014336, rms=0.319 (0.002%), neg=0, invalid=1530 0414: dt=0.014336, rms=0.319 (0.003%), neg=0, invalid=1530 0415: dt=0.014336, rms=0.319 (0.004%), neg=0, invalid=1530 0416: dt=0.014336, rms=0.319 (0.005%), neg=0, invalid=1530 0417: dt=0.014336, rms=0.319 (0.006%), neg=0, invalid=1530 0418: dt=0.014336, rms=0.319 (0.007%), neg=0, invalid=1530 0419: dt=0.014336, rms=0.319 (0.007%), neg=0, invalid=1530 0420: dt=0.014336, rms=0.318 (0.008%), neg=0, invalid=1530 0421: dt=0.014336, rms=0.318 (0.008%), neg=0, invalid=1530 0422: dt=0.014336, rms=0.318 (0.009%), neg=0, invalid=1530 0423: dt=0.014336, rms=0.318 (0.009%), neg=0, invalid=1530 0424: dt=0.014336, rms=0.318 (0.009%), neg=0, invalid=1530 0425: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0426: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0427: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0428: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0429: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0430: dt=0.014336, rms=0.318 (0.010%), neg=0, invalid=1530 0431: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0432: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0433: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0434: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0435: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0436: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0437: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0438: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0439: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 0440: dt=0.014336, rms=0.318 (0.011%), neg=0, invalid=1530 setting smoothness coefficient to 0.500 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.318, neg=0, invalid=1530 0441: dt=0.000000, rms=0.318 (0.000%), neg=0, invalid=1530 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.318, neg=0, invalid=1530 New invocation of trac-all Fri May 10 17:59:10 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 16138676 16739156 0 640348 11032280 -/+ buffers/cache: 4466048 28411784 Swap: 67108848 22344 67086504 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/10-21:59:12-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/10-21:59:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/10-21:59:13-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/10-21:59:14-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/10-21:59:14-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-49 Linux compute-0-49 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 8295156 24582680 0 188492 1197568 -/+ buffers/cache: 6909096 25968740 Swap: 67108856 85780 67023076 New invocation of trac-all Sat May 11 20:52:24 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 19148744 13729088 0 641172 13875836 -/+ buffers/cache: 4631736 28246096 Swap: 67108848 22344 67086504 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-00:52:24-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-00:52:24-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-00:52:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-00:52:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-00:52:25-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-118 Linux compute-0-118 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 6035284 26842552 0 147516 451156 -/+ buffers/cache: 5436612 27441224 Swap: 67108856 136220 66972636 New invocation of trac-all Sat May 11 21:00:16 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 19169772 13708060 0 641172 13895996 -/+ buffers/cache: 4632604 28245228 Swap: 67108848 22344 67086504 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-01:00:16-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-01:00:16-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-01:00:17-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-01:00:17-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-01:00:17-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-104 Linux compute-0-104 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 1569304 31308532 0 176752 168800 -/+ buffers/cache: 1223752 31654084 Swap: 67108856 98308 67010548 New invocation of trac-all Sat May 11 23:46:26 EDT 2013 /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013/bin/trac-all -prep -c /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012/dmrirc.5.2 Subject MS_pt36_recon SUBJECTS_DIR /autofs/cluster/mscat/users/caterina/3T/recons_fsv5.2_11132012 FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Actual FREESURFER_HOME /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 celine launchpad Linux launchpad 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877832 19352464 13525368 0 641172 14067124 -/+ buffers/cache: 4644168 28233664 Swap: 67108848 22344 67086504 ######################################## Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-03:46:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-03:46:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-03:46:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-03:46:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/12-03:46:26-GMT BuildTimeStamp: Feb 26 2013 00:28:02 CVS: User: celine Machine: launchpad Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-03042013 Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_2_0-11132012 New invocation of trac-preproc celine compute-0-40 Linux compute-0-40 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 256703 total used free shared buffers cached Mem: 32877836 2945880 29931956 0 229100 853296 -/+ buffers/cache: 1863484 31014352 Swap: 67108856 62704 67046152