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30132 discussions

Interpretation of pcc.mgh for negative contrasts
by Nicola Toschi 13 Sep '18

13 Sep '18

External Email - Use Caution Hi List, a dimple question about using partial correlation (pcc.mgh) as effect size measure. I am running multivariate regression and setting positive and negative contrasts one variable at a time, e.g. a design matrix with columns like Intercept Age Gender Fact1 Fact2 .... and a bunch of contrasts like 0 0 0 1 0 0 0 0 -1 0 Now let's say the second contrast gives me a significant results after MC correction in a certain cluster, what sign should i expect in PCC in that cluster (on average)? Thank you very much in advance, Nicola

3 3

Identifying labels overlapping with overlay volume
by Mcnorgan, Christopher 13 Sep '18

13 Sep '18

External Email - Use Caution I’ve got a custom .annot file covering the entire cortical surface in fsaverage space, and I wish to see which labels overlap with an overlay statistical contrast volume generated by mri_glmfit. I extracted the vertex indices from my custom .annot file, and from the cache.*.sig.ocn.annot file produced by mri_glmfitsim and using a combination of other tools to parse and query the sets of vertices in a relational database, I found the custom .annot label names corresponding to the overlapping vertices. The process seems to have worked, but I was wondering if there already existed any FreeSurfer tools to accomplish the same task? Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

2 1

QAtools tkmedit snapshots are black
by Ehsan Adeli 13 Sep '18

13 Sep '18

External Email - Use Caution Hello, I tried to create snapshots with tkmedit, but the output snapshot files are all black. This is the command: export SUBJECTS_DIR=./ tkmedit blubber norm.mgz tkmedit shows the image correctly, but when taking a snapshot it is all black. No error messages are displayed. I was wondering if anybody else had a similar issue and if there is any solutions to that. Thank you very much, in advance. Sincerely, Ehsan Adeli, Ph.D., Stanford University

2 1

problem with trac-preproc just at the middle of Priors point
by marco.muti＠tin.it 13 Sep '18

13 Sep '18

External Email - Use Caution I'm trying to run the TRACULA software (fresurfer V 6.0) in the VM for FSL . I'm using the only elmo.2005 images but the program stops just at the middle of priors point.In the follow the log file.Can someone help me please? marco /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// Mon Sep 10 14:39:14 BST 2018/home/fsluser/usr_/local_/diffusion_recons/usr/local/freesurfer/bin/trac-all-prep -c /home/fsluser/usr_/local_/diffusion_tutorial/dmrirc.tutorialSubject elmo.2005SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_reconsFREESURFER_HOME /usr/local/freesurferActual FREESURFER_HOME /usr/local/freesurferbuild-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96cfsluserlocalhost.localdomainLinux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linuxcputime unlimitedfilesize unlimiteddatasize unlimitedstacksize 8192 kbytescoredumpsize 0 kbytesmemoryuse unlimitedvmemoryuse unlimiteddescriptors 1024 memorylocked 64 kbytesmaxproc 4096 maxlocks unlimitedmaxsignal 7172 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache availableMem: 1867264 702820 805888 12064 358556 947408Swap: 3145724 506716 2639008 ########################################Program versions:$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/09/10-13:39:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: fsluser Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.10.0-514.16.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc fsluserlocalhost.localdomainLinux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linuxcputime unlimitedfilesize unlimiteddatasize unlimitedstacksize 8192 kbytescoredumpsize 0 kbytesmemoryuse unlimitedvmemoryuse unlimiteddescriptors 1024 memorylocked 64 kbytesmaxproc 4096 maxlocks unlimitedmaxsignal 7172 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache availableMem: 1867264 703636 772376 12064 391252 946564Swap: 3145724 506712 2639012 #-------------------------------------/usr/local/freesurfer/bin/trac-preproc #-------------------------------------#@# Image corrections Mon Sep 10 14:39:15 BST 2018mri_convert --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gzmri_convert.bin --bvec-voxel /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...Getting Series No INFO: Found 78 files in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/origINFO: Scanning for Series Number 11Scanning Directory INFO: found 70 files in seriesINFO: loading series header info. RunNo = 10WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120FileName /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcmIdentification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 1048.1801 1002.6923 -265.4914 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknownINFO: sorting.INFO: (128 128 60), nframes = 70, ismosaic=1sdfi->UseSliceScaleFactor 0datatype = 4, short=4, float=3Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 10100, TR = 10100 msPE Dir COL COLAutoAlign matrix detected AutoAlign Matrix --------------------- 0.99970 0.02376 -0.00570 -0.49480;-0.02443 0.97638 -0.21466 -40.55519; 0.00047 0.21474 0.97667 12.50291; 0.00000 0.00000 0.00000 1.00000; FileName /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcmIdentification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 131.1612 149.7402 -72.6670 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.5005 40.7699 13.4796 TransferSyntaxUID unknownUseSliceScaleFactor 0 (slice 0: 1)IsDWI = 0sagrev = 1, correv =1, trarev = 0Vs = 0.0057 0.214665 0.976671INFO: no Siemens slice order reversal detected (good!). TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00i_ras = (-0.999702, 0.0244268, 0.000465598)j_ras = (-0.023757, -0.976382, 0.21474)k_ras = (0.0057, 0.214665, 0.976671)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...mri_probedicom --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dcminfo.datcp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvecs.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecscp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvals.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvalsmv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecsmv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvalsorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gzINFO: input image orientation is LPSINFO: input image determinant is 8mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gzmri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598)normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474)normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671)$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz...TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.999701, 0.0244268, 0.000465598)j_ras = (-0.023757, -0.976382, 0.21474)k_ras = (0.0057, 0.214665, 0.976671)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz...INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copyingINFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LASmv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecsmv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvalseddy_correct /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0000processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0001processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0002processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0003processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0004processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0005processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0006processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0007processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0008processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0009processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0010processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0011processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0012processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0013processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0014processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0015processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0016processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0017processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0018processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0019processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0020processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0021processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0022processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0023processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0024processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0025processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0026processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0027processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0028processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0029processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0030processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0031processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0032processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0033processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0034processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0035processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0036processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0037processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0038processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0039processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0040processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0041processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0042processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0043processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0044processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0045processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0046processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0047processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0048processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0049processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0050processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0051processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0052processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0053processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0054processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0055processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0056processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0057processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0058processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0059processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0060processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0061processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0062processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0063processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0064processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0065processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0066processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0067processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0068processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0069mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norotxfmrot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecsln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/data.nii.gzmri_convert --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gzmri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.999701, 0.0244268, 0.000465598)j_ras = (0.023757, 0.976382, -0.21474)k_ras = (0.0057, 0.214665, 0.976671)keeping frames 0 1 2 3 4 5 6 7 8 9writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz...mri_concat --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz --mean --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gzninputs = 1Checking inputsnframestot = 10Allocing outputDone allocingnframes = 10Computing mean across framesWriting to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gzbet /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain.nii.gz -m -f 0.3mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff#-------------------------------------#@# Image quality assessment Mon Sep 10 14:50:58 BST 2018/usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog --bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt cwd /home/fsluser/usr_/local_/diffusion_reconscmdline /usr/local/freesurfer/bin/dmri_motion --dwi /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz --mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog --bval /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals --T 139.399994 --out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt sysname Linuxhostname localhost.localdomainmachine x86_64user fsluserOutput motion measure file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txtInput transform file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclogInput DWI file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gzInput b-value table: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvalsLow-b image intensity threshold: 139.4Nominal diffusivity: 0.001Loading volume-to-baseline affine transformationsComputing between-volume head motion measuresINFO: Processed transforms for 70 volumesLoading DWI volume series from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gzLoading b-value table from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvalsComputing within-volume head motion measuresDone in 4.418 sec.dmri_motion done#-------------------------------------#@# Intra-subject registration Mon Sep 10 14:51:03 BST 2018mri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gzmri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brain.mgz...TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...orientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz...tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz --targ /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mat --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dattkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcltarget volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gzmovable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gzreg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $Diagnostic Level -1INFO: loading target /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gzINFO: target does not conform to COR format, so I'm going toreslice to COR. This will not affect the final registration.Ttarg: ---------------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gzTmov: ---------------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;mkheaderreg = 1, float2int = 0Computing reg from header (and possibly input matrix)---- Input registration matrix (computed) -------- 1.00000 -0.00000 -0.00000 -0.00002; 0.00000 1.00000 0.00000 0.00004;-0.00000 -0.00000 1.00000 0.99997; 0.00000 0.00000 0.00000 1.00000;------------------------------------------- Input registration matrix -------- 1.00000 -0.00000 -0.00000 -0.00002; 0.00000 1.00000 0.00000 0.00004;-0.00000 -0.00000 1.00000 0.99997; 0.00000 0.00000 0.00000 1.00000;Determinant 1subject = subject-unknownRegMat --------------------------- 1.00000 0.00000 0.00000 -0.00001; 0.00000 -0.00000 -1.00000 0.00004; 0.00000 1.00000 -0.00000 0.99997; 0.00000 0.00000 0.00000 1.00000;FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.mattmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.logMon Sep 10 14:51:06 BST 2018 setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_reconscd /home/fsluser/usr_/local_/diffusion_recons/usr/local/freesurfer/bin/bbregister --s elmo.2005 --init-fsl --dti --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --fslmat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $Linux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/LinuxFREESURFER_HOME /usr/local/freesurfermri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.niimri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.999701, 0.0244268, 0.000465598)j_ras = (0.023757, 0.976382, -0.21474)k_ras = (0.0057, 0.214665, 0.976671)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...fslregister --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fslregister.log Mon Sep 10 14:51:12 BST 2018--s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --niters 1 --maxangle 90 --tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $localhost.localdomainLinux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/LinuxnIters 1--------------------------------------/home/fsluser/usr_/local_/diffusion_reconsmri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.niimri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii...--------------------------------------/home/fsluser/usr_/local_/diffusion_reconsmri_convert /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --frame 0mri_convert.bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.999701, 0.0244268, 0.000465598)j_ras = (0.023757, 0.976382, -0.21474)k_ras = (0.0057, 0.214665, 0.976671)keeping frame 0writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii...Mov determinant is -8/home/fsluser/usr_/local_/diffusion_reconstkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat --regheader --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0 --s elmo.2005 --noedittkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tclINFO: no target volume specified, assuming FreeSurfer orig volume.target volume origmovable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.niireg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $Diagnostic Level -1INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgzTtarg: ---------------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.niiTmov: ---------------------2.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;mkheaderreg = 1, float2int = 0Computing reg from header (and possibly input matrix)---- Input registration matrix (computed) -------- 0.99970 -0.02443 -0.00047 3.11760; 0.00570 0.21466 0.97667 2.25865;-0.02376 -0.97638 0.21474 -1.16418; 0.00000 0.00000 0.00000 1.00000;------------------------------------------- Input registration matrix -------- 0.99970 -0.02443 -0.00047 3.11760; 0.00570 0.21466 0.97667 2.25865;-0.02376 -0.97638 0.21474 -1.16418; 0.00000 0.00000 0.00000 1.00000;Determinant 1subject = elmo.2005RegMat --------------------------- 0.99970 -0.02443 -0.00047 3.11760; 0.00570 0.21466 0.97667 2.25865;-0.02376 -0.97638 0.21474 -1.16418; 0.00000 0.00000 0.00000 1.00000;FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1Mon Sep 10 14:51:17 BST 2018/home/fsluser/usr_/local_/diffusion_reconsflirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat0Mon Sep 10 14:51:23 BST 2018/home/fsluser/usr_/local_/diffusion_reconsflirt.fsl -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/refvol.fslregister.nii -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.schtkregister2_cmdl --s elmo.2005 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --fslreg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat.fsl.mat --noedittkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl---- FSL registration matrix -------- 0.99918 -0.04042 0.00180 7.99378; 0.01127 0.23516 -0.97189 154.31700; 0.03886 0.97112 0.23542 -17.03460; 0.00000 0.00000 0.00000 1.00000;---------------------------------------INFO: no target volume specified, assuming FreeSurfer orig volume.target volume origmovable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.niireg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $Diagnostic Level -1INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgzTtarg: ---------------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.niiTmov: ---------------------2.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;mkheaderreg = 0, float2int = 0FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1---- Input registration matrix (computed) -------- 0.99918 -0.03886 0.01127 2.75252;-0.00180 0.23542 0.97189 -0.06236;-0.04042 -0.97112 0.23516 -1.80609; 0.00000 0.00000 0.00000 1.00000;------------------------------------------- Input registration matrix -------- 0.99918 -0.03886 0.01127 2.75252;-0.00180 0.23542 0.97189 -0.06236;-0.04042 -0.97112 0.23516 -1.80609; 0.00000 0.00000 0.00000 1.00000;Determinant 0.999999subject = elmo.2005RegMat --------------------------- 0.99918 -0.03886 0.01127 2.75252;-0.00180 0.23542 0.97189 -0.06236;-0.04042 -0.97112 0.23516 -1.80609; 0.00000 0.00000 0.00000 1.00000;(standard_in) 1: syntax error Started at Mon Sep 10 14:51:12 BST 2018 Ended at Mon Sep 10 14:51:41 BST 2018 fslregister Done To check results, run:tkregister2 --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --surf orig mri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/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 1.113 2016/05/10 03:23:20 greve Exp $setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_reconscd /home/fsluser/usr_/local_/diffusion_reconsmri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/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 Linuxhostname localhost.localdomainmachine x86_64user fslusermovvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.niiregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.datsubject elmo.2005dof 6outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.datUseMask 0UseLH 1UseRH 1nsubsamp 100PenaltySign -1PenaltySlope 0.500000PenaltyCenter 0.000000surfname whiteGMProjFrac 0.500000WMProjAbs 2.000000lhcostfile (null)rhcostfile (null)interp trilinear (1)frame 0TolPowell 0.000100nMaxItersPowell 36n1dmin 3Profile 0Gdiag_no -1AddNoise 0 (0)SynthSeed 1537118316TransRandMax 0.000000RotRandMax 0.000000Translations 0.000000 0.000000 0.000000Rotations 0.000000 0.000000 0.000000Input reg 0.99918 -0.03886 0.01127 2.75252;-0.00180 0.23542 0.97189 -0.06236;-0.04042 -0.97112 0.23516 -1.80609; 0.00000 0.00000 0.00000 1.00000; Loading movExtracting frame 0Projecting LH SurfsLoading lh.white surfLoading lh.thickness for GMGM Proj: 1 0.500000 2.000000WM Proj: 0 0.500000 2.000000Projecting RH SurfsLoading rh.white surfLoading rh.thickness for GMProjecting RH SurfsUsing lh.cortex.labelUsing rh.cortex.labelComputing relative cost 0 -25.0 -25.0 -25.0 0.985304 1 -25.0 -25.0 25.0 1.003463 2 -25.0 25.0 -25.0 0.981149 3 -25.0 25.0 25.0 1.010608 4 25.0 -25.0 -25.0 0.997072 5 25.0 -25.0 25.0 1.010833 6 25.0 25.0 -25.0 0.981523 7 25.0 25.0 25.0 1.019362REL: 8 0.481295 7.989313 0.998664 rel = 0.481938 Initial costs ----------------Number of surface hits 2679WM Intensity 208.1729 +/- 115.2740Ctx Intensity 275.5693 +/- 149.3314Pct Contrast 23.8307 +/- 42.4267Cost 0.4813RelCost 0.4819 ------------------------------------Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9886 0.9886 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9625 0.9625 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9370 0.9370 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9237 0.9237 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8538 0.8538 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.8210 0.8210 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.7789 0.7789 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7606 0.7606 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7168 0.7168 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4813 0.4813 0.0Brute Force --------------------------Min cost was 0.481295Number of iterations 729Search time 1.611000 secParameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell MinimizationInit Powel Params dof = 60 01 02 03 04 05 0fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.481295 7 0.135 0.000 0.000 0.000 0.000 0.000 0.4779112049 10 0.122 0.000 0.000 0.000 0.000 0.000 0.4778248409 12 0.123 0.000 0.000 0.000 0.000 0.000 0.4778223804 25 0.123 -0.044 0.000 0.000 0.000 0.000 0.4778011390 29 0.123 -0.036 0.000 0.000 0.000 0.000 0.4777963222 31 0.123 -0.039 0.000 0.000 0.000 0.000 0.4777931744 35 0.123 -0.039 1.000 0.000 0.000 0.000 0.4654924758 44 0.123 -0.039 1.033 0.000 0.000 0.000 0.4649766994 45 0.123 -0.039 1.037 0.000 0.000 0.000 0.4649588157 47 0.123 -0.039 1.039 0.000 0.000 0.000 0.4649545250 54 0.123 -0.039 1.039 -0.618 0.000 0.000 0.4613594586 56 0.123 -0.039 1.039 -0.356 0.000 0.000 0.4606742453 57 0.123 -0.039 1.039 -0.432 0.000 0.000 0.4592808449 58 0.123 -0.039 1.039 -0.476 0.000 0.000 0.4591395480 59 0.123 -0.039 1.039 -0.466 0.000 0.000 0.4588285780 60 0.123 -0.039 1.039 -0.455 0.000 0.000 0.4586162323 62 0.123 -0.039 1.039 -0.452 0.000 0.000 0.4586004888 63 0.123 -0.039 1.039 -0.451 0.000 0.000 0.4586003764 75 0.123 -0.039 1.039 -0.451 -0.010 0.000 0.4585257072 76 0.123 -0.039 1.039 -0.451 -0.014 0.000 0.4585225156 77 0.123 -0.039 1.039 -0.451 -0.013 0.000 0.4585219959 87 0.123 -0.039 1.039 -0.451 -0.013 0.032 0.4585072286 88 0.123 -0.039 1.039 -0.451 -0.013 0.018 0.4584264964 89 0.123 -0.039 1.039 -0.451 -0.013 0.016 0.4584253499 90 0.123 -0.039 1.039 -0.451 -0.013 0.015 0.4584251210 powell nthiter 1: fret = 0.458425 99 -0.030 -0.039 1.039 -0.451 -0.013 0.015 0.4548510808 100 -0.071 -0.039 1.039 -0.451 -0.013 0.015 0.4543073001 104 -0.062 -0.039 1.039 -0.451 -0.013 0.015 0.4542563468 106 -0.063 -0.039 1.039 -0.451 -0.013 0.015 0.4542556740 113 -0.063 -0.657 1.039 -0.451 -0.013 0.015 0.4514610163 115 -0.063 -0.401 1.039 -0.451 -0.013 0.015 0.4419651219 116 -0.063 -0.368 1.039 -0.451 -0.013 0.015 0.4417822150 118 -0.063 -0.381 1.039 -0.451 -0.013 0.015 0.4415713539 129 -0.063 -0.381 0.949 -0.451 -0.013 0.015 0.4409935232 131 -0.063 -0.381 0.983 -0.451 -0.013 0.015 0.4399692941 132 -0.063 -0.381 0.989 -0.451 -0.013 0.015 0.4399364486 133 -0.063 -0.381 0.991 -0.451 -0.013 0.015 0.4399362054 144 -0.063 -0.381 0.991 -0.435 -0.013 0.015 0.4396884912 146 -0.063 -0.381 0.991 -0.436 -0.013 0.015 0.4396863031 159 -0.063 -0.381 0.991 -0.436 -0.012 0.015 0.4396857374 168 -0.063 -0.381 0.991 -0.436 -0.012 0.002 0.4396353849 169 -0.063 -0.381 0.991 -0.436 -0.012 0.001 0.4396340069 170 -0.063 -0.381 0.991 -0.436 -0.012 -0.002 0.4396327392 172 -0.063 -0.381 0.991 -0.436 -0.012 -0.001 0.4396322829 powell nthiter 2: fret = 0.439632 184 -0.064 -0.381 0.991 -0.436 -0.012 -0.001 0.4396101542 185 -0.070 -0.381 0.991 -0.436 -0.012 -0.001 0.4395798553 208 -0.070 -0.381 0.977 -0.436 -0.012 -0.001 0.4394650593 210 -0.070 -0.381 0.979 -0.436 -0.012 -0.001 0.4394625826 222 -0.070 -0.381 0.979 -0.431 -0.012 -0.001 0.4394569675 223 -0.070 -0.381 0.979 -0.433 -0.012 -0.001 0.4394533231 234 -0.070 -0.381 0.979 -0.433 -0.004 -0.001 0.4394149746 235 -0.070 -0.381 0.979 -0.433 -0.006 -0.001 0.4394125073 powell nthiter 3: fret = 0.439413 259 -0.069 -0.381 0.979 -0.433 -0.006 -0.001 0.4394122592 269 -0.069 -0.380 0.979 -0.433 -0.006 -0.001 0.4394115605 281 -0.069 -0.380 0.975 -0.433 -0.006 -0.001 0.4393971568 305 -0.069 -0.380 0.975 -0.433 -0.004 -0.001 0.4393957905 318 -0.069 -0.380 0.975 -0.433 -0.004 -0.003 0.4393945423Powell done niters = 3Computing relative cost 0 -25.0 -25.0 -25.0 0.981197 1 -25.0 -25.0 25.0 1.000288 2 -25.0 25.0 -25.0 0.994687 3 -25.0 25.0 25.0 1.000546 4 25.0 -25.0 -25.0 1.008915 5 25.0 -25.0 25.0 1.016643 6 25.0 25.0 -25.0 0.996728 7 25.0 25.0 25.0 1.026021REL: 8 0.439395 8.025025 1.003128 rel = 0.438024 Number of iterations 3Min cost was 0.439395Number of FunctionCalls 320TolPowell 0.000100nMaxItersPowell 36OptimizationTime 0.933000 secParameters at optimum (transmm) -0.06893 -0.37986 0.97505Parameters at optimum (rotdeg) -0.43286 -0.00427 -0.00320 Final costs ----------------Number of surface hits 2680WM Intensity 204.6878 +/- 112.1423Ctx Intensity 275.3361 +/- 147.5540Pct Contrast 25.6014 +/- 41.7909Cost 0.4394RelCost 0.4819Reg at min cost was 0.99918 -0.03878 0.01130 2.68372;-0.00216 0.22808 0.97364 -0.45602;-0.04033 -0.97287 0.22781 -0.83031; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat, type = 14 Original Reg 0.99918 -0.03886 0.01127 2.75252;-0.00180 0.23542 0.97189 -0.06236;-0.04042 -0.97112 0.23516 -1.80609; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg-0.00000 -0.00009 -0.00004 0.06880; 0.00036 0.00734 -0.00175 0.39366;-0.00009 0.00175 0.00735 -0.97578; 0.00000 0.00000 0.00000 0.00000; Computing change in lh positionLH rmsDiffMean 1.025998Computing change in rh positionSurface-RMS-Diff-mm 1.020289 0.188730 1.405123mri_segreg donemri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_reconscd /home/fsluser/usr_/local_/diffusion_reconsmri_segreg --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii --init-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat --out-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linuxhostname localhost.localdomainmachine x86_64user fslusermovvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.niiregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.datsubject elmo.2005dof 6outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.datUseMask 0UseLH 1UseRH 1nsubsamp 1PenaltySign -1PenaltySlope 0.500000PenaltyCenter 0.000000surfname whiteGMProjFrac 0.500000WMProjAbs 2.000000lhcostfile (null)rhcostfile (null)interp trilinear (1)frame 0TolPowell 0.000000nMaxItersPowell 36n1dmin 3Profile 0Gdiag_no -1AddNoise 0 (0)SynthSeed 1537544095TransRandMax 0.000000RotRandMax 0.000000Translations 0.000000 0.000000 0.000000Rotations 0.000000 0.000000 0.000000Input reg 0.99918 -0.03878 0.01130 2.68372;-0.00216 0.22808 0.97364 -0.45602;-0.04033 -0.97287 0.22781 -0.83031; 0.00000 0.00000 0.00000 1.00000; Loading movExtracting frame 0Projecting LH SurfsLoading lh.white surfLoading lh.thickness for GMGM Proj: 1 0.500000 2.000000WM Proj: 0 0.500000 2.000000Projecting RH SurfsLoading rh.white surfLoading rh.thickness for GMProjecting RH SurfsUsing lh.cortex.labelUsing rh.cortex.labelComputing relative cost 0 -25.0 -25.0 -25.0 0.994360 1 -25.0 -25.0 25.0 1.009170 2 -25.0 25.0 -25.0 1.028103 3 -25.0 25.0 25.0 0.993501 4 25.0 -25.0 -25.0 1.009256 5 25.0 -25.0 25.0 1.005871 6 25.0 25.0 -25.0 0.984198 7 25.0 25.0 25.0 1.020678REL: 8 0.457378 8.045138 1.005642 rel = 0.454812 Initial costs ----------------Number of surface hits 267146WM Intensity 206.3564 +/- 113.7131Ctx Intensity 277.7282 +/- 152.7763Pct Contrast 25.3732 +/- 42.7352Cost 0.4574RelCost 0.4548 ------------------------------------Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4515 0.4515 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4497 0.4497 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.4462 0.4462 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.4461 0.4461 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.4457 0.4457 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.4444 0.4444 0.0 36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.4435 0.4435 0.0 54 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.4427 0.4427 0.0 63 -0.1000 -0.1000 0.1000 0.0000 -0.1000 -0.1000 0.4415 0.4415 0.0 258 0.0000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.4412 0.4412 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.4404 0.4404 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4394 0.4394 0.0Brute Force --------------------------Min cost was 0.439395Number of iterations 729Search time 1.510000 secParameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell MinimizationInit Powel Params dof = 60 01 02 03 04 05 0fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.457378 7 0.151 0.000 0.000 0.000 0.000 0.000 0.4567799639 9 0.149 0.000 0.000 0.000 0.000 0.000 0.4567796745 10 0.148 0.000 0.000 0.000 0.000 0.000 0.4567792997 11 0.142 0.000 0.000 0.000 0.000 0.000 0.4567788014 12 0.144 0.000 0.000 0.000 0.000 0.000 0.4567786136 20 0.144 -0.113 0.000 0.000 0.000 0.000 0.4562133870 21 0.144 -0.102 0.000 0.000 0.000 0.000 0.4562102480 36 0.144 -0.102 0.005 0.000 0.000 0.000 0.4562068973 40 0.144 -0.102 0.016 0.000 0.000 0.000 0.4562045472 41 0.144 -0.102 0.015 0.000 0.000 0.000 0.4562045116 42 0.144 -0.102 0.014 0.000 0.000 0.000 0.4562044856 51 0.144 -0.102 0.014 -0.115 0.000 0.000 0.4555371966 53 0.144 -0.102 0.014 -0.123 0.000 0.000 0.4555367143 55 0.144 -0.102 0.014 -0.127 0.000 0.000 0.4555352434 57 0.144 -0.102 0.014 -0.125 0.000 0.000 0.4555347108 58 0.144 -0.102 0.014 -0.124 0.000 0.000 0.4555344977 65 0.144 -0.102 0.014 -0.124 -0.030 0.000 0.4553394364 67 0.144 -0.102 0.014 -0.124 -0.071 0.000 0.4552874340 68 0.144 -0.102 0.014 -0.124 -0.079 0.000 0.4552792468 69 0.144 -0.102 0.014 -0.124 -0.101 0.000 0.4552413108 71 0.144 -0.102 0.014 -0.124 -0.102 0.000 0.4552404588 72 0.144 -0.102 0.014 -0.124 -0.104 0.000 0.4552395026 82 0.144 -0.102 0.014 -0.124 -0.104 -0.293 0.4522931503 83 0.144 -0.102 0.014 -0.124 -0.104 -0.291 0.4522918016 powell nthiter 1: fret = 0.452292 95 0.133 -0.102 0.014 -0.124 -0.104 -0.291 0.4522544133 96 0.090 -0.102 0.014 -0.124 -0.104 -0.291 0.4522221844 98 0.105 -0.102 0.014 -0.124 -0.104 -0.291 0.4522023296 99 0.106 -0.102 0.014 -0.124 -0.104 -0.291 0.4522022033 107 0.106 -0.174 0.014 -0.124 -0.104 -0.291 0.4516567107 109 0.106 -0.189 0.014 -0.124 -0.104 -0.291 0.4516347638 110 0.106 -0.190 0.014 -0.124 -0.104 -0.291 0.4516342016 111 0.106 -0.195 0.014 -0.124 -0.104 -0.291 0.4516309356 114 0.106 -0.194 0.014 -0.124 -0.104 -0.291 0.4516305236 122 0.106 -0.194 0.022 -0.124 -0.104 -0.291 0.4515978255 123 0.106 -0.194 0.075 -0.124 -0.104 -0.291 0.4515177696 125 0.106 -0.194 0.068 -0.124 -0.104 -0.291 0.4515073442 126 0.106 -0.194 0.060 -0.124 -0.104 -0.291 0.4515053860 127 0.106 -0.194 0.062 -0.124 -0.104 -0.291 0.4515048438 137 0.106 -0.194 0.062 -0.144 -0.104 -0.291 0.4514614868 138 0.106 -0.194 0.062 -0.149 -0.104 -0.291 0.4514588764 147 0.106 -0.194 0.062 -0.149 -0.008 -0.291 0.4511294521 148 0.106 -0.194 0.062 -0.149 -0.013 -0.291 0.4511263788 149 0.106 -0.194 0.062 -0.149 -0.018 -0.291 0.4511189418 150 0.106 -0.194 0.062 -0.149 -0.051 -0.291 0.4510869949 152 0.106 -0.194 0.062 -0.149 -0.038 -0.291 0.4510857743 153 0.106 -0.194 0.062 -0.149 -0.044 -0.291 0.4510847166 154 0.106 -0.194 0.062 -0.149 -0.043 -0.291 0.4510847161 164 0.106 -0.194 0.062 -0.149 -0.043 -0.296 0.4510831507 165 0.106 -0.194 0.062 -0.149 -0.043 -0.297 0.4510831286 powell nthiter 2: fret = 0.451083 174 0.099 -0.194 0.062 -0.149 -0.043 -0.297 0.4510503240 176 0.077 -0.194 0.062 -0.149 -0.043 -0.297 0.4510213872 178 0.080 -0.194 0.062 -0.149 -0.043 -0.297 0.4510195676 180 0.083 -0.194 0.062 -0.149 -0.043 -0.297 0.4510186920 201 0.084 -0.194 0.073 -0.149 -0.043 -0.297 0.4510115521 203 0.084 -0.194 0.072 -0.149 -0.043 -0.297 0.4510115142 215 0.084 -0.194 0.072 -0.148 -0.043 -0.297 0.4510112026 223 0.084 -0.194 0.072 -0.148 0.005 -0.297 0.4509468373 226 0.084 -0.194 0.072 -0.148 0.006 -0.297 0.4509467632 236 0.084 -0.194 0.072 -0.148 0.007 -0.307 0.4509344989 242 0.062 -0.194 0.082 -0.147 0.057 -0.314 0.4509154629 powell nthiter 3: fret = 0.450934 249 0.075 -0.194 0.072 -0.148 0.007 -0.306 0.4508891386 251 0.050 -0.194 0.072 -0.148 0.007 -0.306 0.4508574823 254 0.049 -0.194 0.072 -0.148 0.007 -0.306 0.4508574680 255 0.048 -0.194 0.072 -0.148 0.007 -0.306 0.4508572280 258 0.046 -0.194 0.072 -0.148 0.007 -0.306 0.4508570447 268 0.047 -0.189 0.072 -0.148 0.007 -0.306 0.4508534999 279 0.047 -0.189 0.063 -0.148 0.007 -0.306 0.4508490816 280 0.047 -0.189 0.061 -0.148 0.007 -0.306 0.4508484187 282 0.047 -0.189 0.057 -0.148 0.007 -0.306 0.4508481470 283 0.047 -0.189 0.058 -0.148 0.007 -0.306 0.4508481128 294 0.047 -0.189 0.058 -0.147 0.007 -0.306 0.4508480229 302 0.047 -0.189 0.058 -0.147 0.027 -0.306 0.4508401595 303 0.047 -0.189 0.058 -0.147 0.022 -0.306 0.4508368880 304 0.047 -0.189 0.058 -0.147 0.020 -0.306 0.4508368307 306 0.047 -0.189 0.058 -0.147 0.021 -0.306 0.4508366606 314 0.047 -0.189 0.058 -0.147 0.021 -0.330 0.4507887096 317 0.047 -0.189 0.058 -0.147 0.021 -0.331 0.4507886723 powell nthiter 4: fret = 0.450789 327 0.040 -0.189 0.058 -0.147 0.021 -0.331 0.4507863478 338 0.040 -0.202 0.058 -0.147 0.021 -0.331 0.4507856198 339 0.040 -0.196 0.058 -0.147 0.021 -0.331 0.4507778523 340 0.040 -0.195 0.058 -0.147 0.021 -0.331 0.4507778168 350 0.040 -0.195 0.057 -0.147 0.021 -0.331 0.4507776939 359 0.040 -0.195 0.057 -0.140 0.021 -0.331 0.4507760945 360 0.040 -0.195 0.057 -0.141 0.021 -0.331 0.4507753773 368 0.040 -0.195 0.057 -0.141 0.034 -0.331 0.4507701303 379 0.040 -0.195 0.057 -0.141 0.034 -0.342 0.4507598537 381 0.040 -0.195 0.057 -0.141 0.034 -0.341 0.4507597243 powell nthiter 5: fret = 0.450760 392 0.036 -0.195 0.057 -0.141 0.034 -0.341 0.4507576686 393 0.035 -0.195 0.057 -0.141 0.034 -0.341 0.4507573174 395 0.034 -0.195 0.057 -0.141 0.034 -0.341 0.4507572876 404 0.034 -0.194 0.057 -0.141 0.034 -0.341 0.4507572313 413 0.034 -0.194 0.052 -0.141 0.034 -0.341 0.4507558538 414 0.034 -0.194 0.050 -0.141 0.034 -0.341 0.4507554828 427 0.034 -0.194 0.050 -0.140 0.034 -0.341 0.4507551369 428 0.034 -0.194 0.050 -0.139 0.034 -0.341 0.4507551204 437 0.034 -0.194 0.050 -0.139 0.033 -0.341 0.4507549405 450 0.034 -0.194 0.050 -0.139 0.033 -0.343 0.4507547248 powell nthiter 6: fret = 0.450755 480 0.035 -0.194 0.049 -0.139 0.033 -0.343 0.4507544467 481 0.035 -0.194 0.046 -0.139 0.033 -0.343 0.4507537921 483 0.035 -0.194 0.043 -0.139 0.033 -0.343 0.4507536567 484 0.035 -0.194 0.044 -0.139 0.033 -0.343 0.4507536554 493 0.035 -0.194 0.044 -0.138 0.033 -0.343 0.4507533174 494 0.035 -0.194 0.044 -0.137 0.033 -0.343 0.4507532305 503 0.035 -0.194 0.044 -0.137 0.032 -0.343 0.4507531155 514 0.035 -0.194 0.044 -0.137 0.032 -0.342 0.4507531014 516 0.036 -0.194 0.039 -0.135 0.031 -0.341 0.4507523120 530 0.036 -0.194 0.039 -0.135 0.031 -0.341 0.4507522623 powell nthiter 7: fret = 0.450752 542 0.035 -0.194 0.039 -0.135 0.031 -0.341 0.4507520844 552 0.035 -0.195 0.039 -0.135 0.031 -0.341 0.4507516977 563 0.035 -0.195 0.039 -0.135 0.031 -0.342 0.4507516535 591 0.035 -0.195 0.037 -0.134 0.029 -0.341 0.4507515057 592 0.035 -0.195 0.036 -0.134 0.029 -0.341 0.4507514870 593 0.035 -0.195 0.035 -0.134 0.029 -0.341 0.4507513959 powell nthiter 8: fret = 0.450751 612 0.034 -0.195 0.035 -0.134 0.029 -0.341 0.4507512254 622 0.034 -0.196 0.035 -0.134 0.029 -0.341 0.4507510902 powell nthiter 9: fret = 0.450751Powell done niters = 9Computing relative cost 0 -25.0 -25.0 -25.0 0.993321 1 -25.0 -25.0 25.0 1.009943 2 -25.0 25.0 -25.0 1.031408 3 -25.0 25.0 25.0 0.987702 4 25.0 -25.0 -25.0 1.008434 5 25.0 -25.0 25.0 1.004908 6 25.0 25.0 -25.0 0.987196 7 25.0 25.0 25.0 1.021866REL: 8 0.450751 8.044778 1.005597 rel = 0.448242 Number of iterations 9Min cost was 0.450751Number of FunctionCalls 741TolPowell 0.000000nMaxItersPowell 36OptimizationTime 40.719000 secParameters at optimum (transmm) 0.03411 -0.19584 0.03511Parameters at optimum (rotdeg) -0.13370 0.02919 -0.34094 Final costs ----------------Number of surface hits 267260WM Intensity 205.3026 +/- 114.1749Ctx Intensity 276.2650 +/- 150.7064Pct Contrast 25.5313 +/- 42.4962Cost 0.4508RelCost 0.4548Reg at min cost was 0.99913 -0.03793 0.01722 2.71464;-0.00820 0.22604 0.97408 -0.66975;-0.04084 -0.97338 0.22553 -0.79550; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.99918 -0.03878 0.01130 2.68372;-0.00216 0.22808 0.97364 -0.45602;-0.04033 -0.97287 0.22781 -0.83031; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00005 -0.00085 -0.00591 -0.03092; 0.00604 0.00204 -0.00044 0.21373; 0.00050 0.00051 0.00228 -0.03481; 0.00000 0.00000 0.00000 0.00000; Computing change in lh positionLH rmsDiffMean 0.210903Computing change in rh positionSurface-RMS-Diff-mm 0.304233 0.140570 0.625049mri_segreg doneMinCost: 0.450751 205.302557 276.265001 25.531318 tkregister2_cmdl --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mattkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tclINFO: no target volume specified, assuming FreeSurfer orig volume.target volume origmovable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gzreg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $Diagnostic Level -1---- Input registration matrix -------- 0.99913 -0.03793 0.01722 2.71464;-0.00820 0.22604 0.97408 -0.66975;-0.04084 -0.97338 0.22553 -0.79550; 0.00000 0.00000 0.00000 1.00000;float2int = 0---------------------------------------INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgzTtarg: ---------------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;INFO: loading movable /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gzTmov: ---------------------2.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 2.00000 -60.00000; 0.00000 -2.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;mkheaderreg = 0, float2int = 0---- Input registration matrix -------- 0.99913 -0.03793 0.01722 2.71464;-0.00820 0.22604 0.97408 -0.66975;-0.04084 -0.97338 0.22553 -0.79550; 0.00000 0.00000 0.00000 1.00000;Determinant 0.999999subject = elmo.2005RegMat --------------------------- 0.99913 -0.03793 0.01722 2.71464;-0.00820 0.22604 0.97408 -0.66975;-0.04084 -0.97338 0.22553 -0.79550; 0.00000 0.00000 0.00000 1.00000;FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1Cleaning up Started at Mon Sep 10 14:51:06 BST 2018 Ended at Mon Sep 10 14:52:47 BST 2018BBR-Run-Time-Sec 101 bbregister DoneTo check results, run:tkregisterfv --mov /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat --surfs convert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat#-------------------------------------#@# Inter-subject registration Mon Sep 10 14:52:47 BST 2018flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_mni.nii.gz -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -cost mutualinfoconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anat.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anat.bbr.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat -concat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2anat.matconvert_xfm -omat /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2anatorig.mat -inverse /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2mni.mat#-------------------------------------#@# Masks Mon Sep 10 14:54:35 BST 2018mri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gzBinarizing based on matching valuesnMatch 5 0 2 1 7 2 41 3 46 4 77binval 1binvalnot 0fstart = 0, fend = 0, nframes = 1Found 466816 values in rangeCounting number of voxels in first frameFound 466816 voxels in final maskCount: 466816 466816.000000 16777216 2.782440mri_binarize donemri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gzBinarizing based on matching valuesnMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16binval 1binvalnot 0fstart = 0, fend = 0, nframes = 1Found 496933 values in rangeCounting number of voxels in first frameFound 496933 voxels in final maskCount: 496933 496933.000000 16777216 2.961951mri_binarize donemri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gzBinarizing based on matching valuesnMatch 2 0 4 1 43binval 0binvalnot 1fstart = 0, fend = 0, nframes = 1Found 23114 values in rangeCounting number of voxels in first frameFound 23114 voxels in final maskCount: 23114 23114.000000 16777216 0.137770mri_binarize donemri_aparc2aseg --s elmo.2005 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gzSUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_reconssubject elmo.2005outvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gzuseribbon 0baseoffset 0labeling wmlabeling hypo-intensities as wmdmaxctx 2.000000RipUnknown 0 Reading lh white surface /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.white Reading lh pial surface /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/lh.pial Loading lh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/label/lh.aparc.annotreading colortable from annotation file...colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.white Reading rh pial surface /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/surf/rh.pial Loading rh annotations from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/label/rh.aparc.annotreading colortable from annotation file...colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)Have color table for lh white annotationHave color table for rh white annotationLoading ribbon segmentation from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgzLoading filled from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aseg.mgzASeg Vox2RAS: ------------1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1019533Used brute-force search on 0 voxelsFixing Parahip LH WM Found 1 clusters 0 k 889.000000Fixing Parahip RH WM Found 1 clusters 0 k 714.000000Writing output aseg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gzmri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gzBinarizing based on thresholdmin 1000max 2999binval 1binvalnot 0fstart = 0, fend = 0, nframes = 1Found 577605 values in rangeCounting number of voxels in first frameFound 577605 voxels in final maskCount: 577605 577605.000000 16777216 3.442794mri_binarize donemri_binarize --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gzBinarizing based on thresholdmin 1000max 4999binval 1binvalnot 0fstart = 0, fend = 0, nframes = 1Found 848289 values in rangeCounting number of voxels in first frameFound 848289 voxels in final maskCount: 848289 848289.000000 16777216 5.056196mri_binarize donemri_binarize --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $cwd /home/fsluser/usr_/local_/diffusion_reconscmdline mri_binarize.bin --i /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz --match 16 --o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz sysname Linuxhostname localhost.localdomainmachine x86_64user fsluser input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgzframe 0nErode3d 0nErode2d 0output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gzBinarizing based on matching valuesnMatch 1 0 16binval 1binvalnot 0fstart = 0, fend = 0, nframes = 1Found 21835 values in rangeCounting number of voxels in first frameFound 21835 voxels in final maskCount: 21835 21835.000000 16777216 0.130147mri_binarize donefslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz -add /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gzmri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gzmri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/brainmask.mgz...TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz -mul /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gzmri_convert /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gzmri_convert.bin /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz...TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...fslmaths /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gzorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/White-Matter++.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/notventricles.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/notventricles.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm+bs.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg_mask.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourorientLAS /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gzINFO: input image orientation is LIAINFO: input image determinant is -1mri_convert -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gzmri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 6.33299e-08 -2.04891e-08 -ojd 7.07805e-08 1 1.74623e-09 -okd 9.31323e-09 -2.32831e-10 1 -oc 3.70524 44.2681 16.0046 -rt nearest /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/anat_brain_mask-vent.nii.gz...TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 6.33299e-08, -2.04891e-08)j_ras = (-9.31323e-09, 2.32831e-10, -1)k_ras = (7.07805e-08, 1, 1.74623e-09)Reslicing using nearest writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz...flirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2mni.mat -interp nearestneighbourfslstats -t /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_snr.txtflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbourflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/lowb_brain_mask.nii.gz -ref /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbourln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/nodif_brain_mask.nii.gz#-------------------------------------#@# Tensor fit Mon Sep 10 15:00:40 BST 2018dtifit -k /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz -m /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs -b /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals -o /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit0 128 0 128 0 600 slices processed1 slices processed2 slices processed3 slices processed4 slices processed5 slices processed6 slices processed7 slices processed8 slices processed9 slices processed10 slices processed11 slices processed12 slices processed13 slices processed14 slices processed15 slices processed16 slices processed17 slices processed18 slices processed19 slices processed20 slices processed21 slices processed22 slices processed23 slices processed24 slices processed25 slices processed26 slices processed27 slices processed28 slices processed29 slices processed30 slices processed31 slices processed32 slices processed33 slices processed34 slices processed35 slices processed36 slices processed37 slices processed38 slices processed39 slices processed40 slices processed41 slices processed42 slices processed43 slices processed44 slices processed45 slices processed46 slices processed47 slices processed48 slices processed49 slices processed50 slices processed51 slices processed52 slices processed53 slices processed54 slices processed55 slices processed56 slices processed57 slices processed58 slices processed59 slices processedflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L1.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L2.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_L3.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MD.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_MO.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.matflirt -in /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_S0.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/diff2mni.bbr.mat#-------------------------------------#@# Priors Mon Sep 10 15:00:50 BST 2018/usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc cwd /home/fsluser/usr_/local_/diffusion_reconscmdline /usr/local/freesurfer/bin/dmri_train --outdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.26311.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff --reg /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linuxhostname localhost.localdomainmachine x86_64user fsluserOutput directory: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mniOutput directory in test subject's space: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diffOutput base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbrTraining subject directory list: /tmp/subj33.elmo.2005.26311.txtLocation of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trkLocation of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gzLocation of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gzLocation of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gzLabel ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gzBrain mask for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gzFA map for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gzAffine registration from atlas to base for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.matNumber of control points for initial spline: 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5Exclude previously chosen center streamlines: 0Use truncated streamlines: 1Loading brain mask of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gzLoading FA map of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gzLoading affine registration from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.matLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.bbr.trkLoading streamline start ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gzLoading streamline end ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gzLoading streamlines from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.bbr.trkINFO: Rejected 1094 streamlines for straying off maskINFO: Rejected 73 streamlines for reversing directionINFO: Rejected 17 streamlines as length outliersINFO: Have 7248 total streamlines (min/mean/max length: 59/99/139)Loading segmentation from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/cortex+2mm.nii.gzLoading segmentation from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/aparc+aseg.nii.gzLoading cortex mask from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/cortex+2mm.nii.gzLinux localhost.localdomain 3.10.0-514.16.1.el7.x86_64 #1 SMP Wed Apr 12 15:04:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Sep 10 15:07:07 BST 2018

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回复： questions about trac-all -stat
by 薛倩雯 13 Sep '18

13 Sep '18

External Email - Use Caution Hi Yendiki, Anastasia, I am very sorry that I did not make myself clear. I mean I want to know how trac-all –stat does it. (1)how to determine the first position and last position of all subjects' pathways when converting all pathstats.byvoxel.txt files to a table for group analyses? In the tabel , The first position and last position of all subjects' pathways are determined by the longest pathway. (2)how to complete correspondence of points between subjects? In the course slides, it said"Correspondence of points between subjects based on Euclidean distance in MNI space".This sentence is so vague that I can't understand it. (3)what is values in table for group analyses,diffusion measure of center or something else? I am very sorry that my question is a bit more, but I still hope that you can answer my doubts. Thanks! Qianwen ------------------ 原始邮件 ------------------ 发件人: "Yendiki, Anastasia"<AYENDIKI(a)mgh.harvard.edu>; 发送时间: 2018年9月12日(星期三) 晚上10:40 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] questions about trac-all -stat Hi Qianwen – You don’t have to do (1) and (2), trac-all –stat does that for you. For a description of the measures, see the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics and the course slides: http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of 薛倩雯 <627611631(a)qq.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 12, 2018 at 1:13 AM To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about trac-all -stat External Email - Use Caution Dear experts, I have some questions about along-path analysis: (1)how to determine the first position and last position of all subjects' pathway when converting all pathstats.byvoxel.txt files to a table for group analyses? (2)how to complete correspondence of points between subjects? (3)what is values in table for group analyses,diffusion measure of center or something else? Thanks! Qianwen

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/mri/orig/001.mgz vs T1.mgz
by Alexopoulos, Dimitrios 13 Sep '18

13 Sep '18

External Email - Use Caution I have a quick question as it relates to image outputs from freesurfer 6.0 (i.e. /mri/orig/001.mgz vs. nu/T1.mgz). Images below: Left - /mri/orig/001.mgz Right - T1.mgz The outputs (segmentations/surfaces) look good, but I noticed the output volumes (nu.mgz, T1.mgz, brainmask.mgz) looked tilted compared to the input image (/mri/orig/001.mgz) . Is this expected/possible? Jim [cid:image003.png@01D44A8B.E2E44FB0][cid:image004.png@01D44A8B.E2E44FB0] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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6.0.1 automatic download
by Chris Gorgolewski 13 Sep '18

13 Sep '18

External Email - Use Caution Hi, I noticed that https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Lin… is no longer available, but instead there is https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Lin… Is it the same thing or an updated version (if so why not 6.0.2)? Is this the right way to grab the same 6.0.1 version in a programmatic way? Best, Chris

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Job posting: 2-year postdoctoral position
by Scott Love 13 Sep '18

13 Sep '18

External Email - Use Caution Enquires and applications to Dr. Martine Migaud (Martine.Migaud(a)inra.fr) Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-year postdoctoral position is available in the group of Dr. Martine Migaud, at the laboratory of Reproductive and Behavioral Physiology (https://www6.val-de-loire.inra.fr/physiologie_reproduction_comportements) which brings together over 50 researchers from INRA, CNRS, the University of Tours and the French horse and riding institute (IFCE). Context and mission: The Project is part of a recently awarded grant from the French National Agency for Research and involves magnetic resonance imaging (MRI) analysis in a large animal model (sheep). This project aims to explore through MRI approaches, the mechanisms of brain plasticity in the hypothalamus, a structure involved in the control of reproduction. In this project, we aim to develop MR acquisition and post-processing methods to monitor brain changes and to obtain imaging biomarkers, based on the use of multi-modal neuro-imaging tools to investigate anatomical, connectivity and hypothalamic microstructure variations in function of the environment. Our lab makes use of sheep as an in vivo model system and for in vitro immunohistochemical and molecular approaches. The recruited post-doc will have access to the CIRE platform within the laboratory, dedicated to applied surgery and imaging of large animal models. The platform is equipped with state of the art imaging facilities including a clinical MRI scanner (3T Verio, Siemens) and a CT-Scanner (https://www6.val-de-loire.inra.fr/cire/Imagerie) He/she will also benefit from a strong collaborative local environment formed by the members of the CIRE platform and other scientists from our unit. In addition, the project is carried out in collaboration with the Team Development & Plasticity of the Neuroendocrine Brain, INSERM U1172, directed by Dr. V. Prévot. The position is available for two years and would ideally start in October 2018. Place: The laboratory is located in Nouzilly, in close proximity to Tours, in the heart of the Loire Valley, France. Tours is a pleasant city from which one can also reach Paris or Bordeaux very easily within 1h00 and 2h00 respectively by high-speed train. Candidate profile: The successful candidate will have a PhD in neuroscience, Electrical or Biomedical Engineering, or related fields with strong experience in MRI neuroimaging and in statistical analysis. Knowledge and previous experience in computer programming and analysis software (eg. Python, Matlab, C++, FSL, Freesurfer, Linux, Perl…) is mandatory. We are looking for a highly enthusiastic and autonomous candidate who can develop his/her line of research with an interest in interdisciplinary research and excellent interaction and communication skills in the context of a collaborative teamwork. To apply, please send by e-mail, your C.V., a motivation letter and the names and contact information of two referees to Dr. Martine Migaud (Martine.Migaud(a)inra.fr) We will consider applications until October 31, 2018.

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Optseq PSDWindow
by Leavitt, Mackenzie 12 Sep '18

12 Sep '18

External Email - Use Caution Hi, We are attempting to use optseq2 for a study design where the events last 5 seconds. ? I've found previous answers that indicate that PSDWIN max should be set between 21 to 24 seconds if your event is 3 seconds in length. For 5 seconds in length, I assume this would be between 25 and 30? My actual question is this: how does one determine the length of the hemodynamic response function and set their PSD max? Is there a heuristic you can use? Best, MacKenzie =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Problem to download dev version
by stdp82＠virgilio.it 12 Sep '18

12 Sep '18

External Email - Use Caution I'm tryining to download the Development Version (OSX) at: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall When I click on "here", I push the "guess" botton but the operation is failing. What do I do? Thanks Stefano

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