Hi Marco – This is strange and it’s not something that we can replicate locally. Because it looks like it dies when loading 31/33 of the training data, my first guess would be that it runs out of memory.

Best, a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "marco.muti@tin.itmailto:marco.muti@tin.it" <marco.muti@tin.itmailto:marco.muti@tin.it> Reply-To: "marco.muti@outlook.commailto:marco.muti@outlook.com" <marco.muti@outlook.commailto:marco.muti@outlook.com>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 13, 2018 at 7:35 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] problem with trac-preproc just at the middle of Priors point

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

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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.tutorial Subject elmo.2005 SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c fsluser localhost.localdomain 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/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 7172 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited

total used free shared buff/cache available Mem: 1867264 702820 805888 12064 358556 947408 Swap: 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

fsluser localhost.localdomain 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/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 7172 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited

total used free shared buff/cache available Mem: 1867264 703636 772376 12064 391252 946564 Swap: 3145724 506712 2639012

#------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Sep 10 14:39:15 BST 2018 mri_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.gz mri_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/orig INFO: Scanning for Series Number 11 Scanning Directory INFO: found 70 files in series INFO: loading series header info.

RunNo = 10 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification 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 256 Image 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 unknown INFO: sorting. INFO: (128 128 60), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 10100, TR = 10100 ms PE Dir COL COL AutoAlign 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.dcm Identification 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 256 Image 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 unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 sagrev = 1, correv =1, trarev = 0 Vs = 0.0057 0.214665 0.976671 INFO: no Siemens slice order reversal detected (good!). TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00 i_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.dat cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvecs.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs cp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/orig/bvals.txt /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals orientLAS /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 INFO: input image orientation is LPS INFO: input image determinant is 8 mri_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.gz mri_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=0.00 i_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, copying INFO: found /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals eddy_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 0 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0000 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0001 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0002 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0003 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0004 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0005 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0006 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0007 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0008 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0009 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0010 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0011 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0012 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0013 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0014 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0015 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0016 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0017 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0018 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0019 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0020 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0021 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0022 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0023 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0024 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0025 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0026 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0027 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0028 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0029 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0030 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0031 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0032 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0033 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0034 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0035 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0036 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0037 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0038 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0039 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0040 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0041 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0042 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0043 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0044 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0045 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0046 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0047 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0048 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0049 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0050 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0051 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0052 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0053 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0054 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0055 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0056 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0057 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0058 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0059 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0060 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0061 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0062 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0063 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0064 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0065 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0066 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0067 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0068 processing /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_tmp0069 mv -f /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvecs.norot xfmrot /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/bvecs ln -sf /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/data.nii.gz mri_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.gz mri_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=0.00 i_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 9 writing 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.gz ninputs = 1 Checking inputs nframestot = 10 Allocing output Done allocing nframes = 10 Computing mean across frames Writing to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/lowb.nii.gz bet /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 0.3 mv -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_recons cmdline /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 Linux hostname localhost.localdomain machine x86_64 user fsluser Output motion measure file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_motion.txt Input transform file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog Input DWI file: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz Input b-value table: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals Low-b image intensity threshold: 139.4 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 70 volumes Loading DWI volume series from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz Loading b-value table from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/bvals Computing within-volume head motion measures Done in 4.418 sec. dmri_motion done #------------------------------------- #@# Intra-subject registration Mon Sep 10 14:51:03 BST 2018 mri_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.gz mri_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=7.00 i_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.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat_orig.nii.gz reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.00000 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.gz Tmov: -------------------- -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 = 0 Computing 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 1 subject = subject-unknown RegMat --------------------------- 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 = -1 convert_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.mat tmp /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041 Log file is /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat.log Mon Sep 10 14:51:06 BST 2018

setenv SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons cd /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/Linux FREESURFER_HOME /usr/local/freesurfer mri_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.nii mri_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=0.00 i_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.localdomain 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/Linux nIters 1 -------------------------------------- /home/fsluser/usr_/local_/diffusion_recons mri_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.nii mri_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=7.00 i_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_recons mri_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 0 mri_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=0.00 i_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 0 writing 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_recons tkregister2_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 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/fslregister/reg0.28082.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz 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/xfms/tmp.bbregister.28041/fslregister/movvol.fslregister.nii Tmov: -------------------- -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 = 0 Computing 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 1 subject = elmo.2005 RegMat --------------------------- 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 = -1 Mon Sep 10 14:51:17 BST 2018 /home/fsluser/usr_/local_/diffusion_recons flirt.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.mat0 Mon Sep 10 14:51:23 BST 2018 /home/fsluser/usr_/local_/diffusion_recons flirt.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.sch tkregister2_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 --noedit tkregister_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 orig movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/orig.mgz 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/xfms/tmp.bbregister.28041/template.nii Tmov: -------------------- -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 FSLOUTPUTTYPE 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 0.999999 subject = elmo.2005 RegMat --------------------------- 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_recons cd /home/fsluser/usr_/local_/diffusion_recons 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 sysname Linux hostname localhost.localdomain machine x86_64 user fsluser movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/reg.init.dat subject elmo.2005 dof 6 outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1537118316 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input 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 mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing 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 1.019362 REL: 8 0.481295 7.989313 0.998664 rel = 0.481938 Initial costs ---------------- Number of surface hits 2679 WM Intensity 208.1729 +/- 115.2740 Ctx Intensity 275.5693 +/- 149.3314 Pct Contrast 23.8307 +/- 42.4267 Cost 0.4813 RelCost 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 0.0 Brute Force -------------------------- Min cost was 0.481295 Number of iterations 729 Search time 1.611000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 --------------------------------------------

Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_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 0.4393945423 Powell done niters = 3 Computing 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 1.026021 REL: 8 0.439395 8.025025 1.003128 rel = 0.438024 Number of iterations 3 Min cost was 0.439395 Number of FunctionCalls 320 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.933000 sec Parameters at optimum (transmm) -0.06893 -0.37986 0.97505 Parameters at optimum (rotdeg) -0.43286 -0.00427 -0.00320 Final costs ---------------- Number of surface hits 2680 WM Intensity 204.6878 +/- 112.1423 Ctx Intensity 275.3361 +/- 147.5540 Pct Contrast 25.6014 +/- 41.7909 Cost 0.4394 RelCost 0.4819 Reg 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 position LH rmsDiffMean 1.025998 Computing change in rh position Surface-RMS-Diff-mm 1.020289 0.188730 1.405123 mri_segreg done 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/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_recons cd /home/fsluser/usr_/local_/diffusion_recons 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/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 Linux hostname localhost.localdomain machine x86_64 user fsluser movvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/template.nii regfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/tmp.bbregister.28041/bbr.pass1.dat subject elmo.2005 dof 6 outregfile /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1537544095 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input 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 mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing 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 1.020678 REL: 8 0.457378 8.045138 1.005642 rel = 0.454812 Initial costs ---------------- Number of surface hits 267146 WM Intensity 206.3564 +/- 113.7131 Ctx Intensity 277.7282 +/- 152.7763 Pct Contrast 25.3732 +/- 42.7352 Cost 0.4574 RelCost 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 0.0 Brute Force -------------------------- Min cost was 0.439395 Number of iterations 729 Search time 1.510000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 --------------------------------------------

Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_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 = 0.450751 Powell done niters = 9 Computing 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 1.021866 REL: 8 0.450751 8.044778 1.005597 rel = 0.448242 Number of iterations 9 Min cost was 0.450751 Number of FunctionCalls 741 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 40.719000 sec Parameters at optimum (transmm) 0.03411 -0.19584 0.03511 Parameters at optimum (rotdeg) -0.13370 0.02919 -0.34094 Final costs ---------------- Number of surface hits 267260 WM Intensity 205.3026 +/- 114.1749 Ctx Intensity 276.2650 +/- 150.7064 Pct Contrast 25.5313 +/- 42.4962 Cost 0.4508 RelCost 0.4548 Reg 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 position LH rmsDiffMean 0.210903 Computing change in rh position Surface-RMS-Diff-mm 0.304233 0.140570 0.625049 mri_segreg done MinCost: 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.mat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz reg file /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 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.mgz 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/dwi.nii.gz Tmov: -------------------- -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 0.999999 subject = elmo.2005 RegMat --------------------------- 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 = -1 Cleaning up

Started at Mon Sep 10 14:51:06 BST 2018 Ended at Mon Sep 10 14:52:47 BST 2018 BBR-Run-Time-Sec 101

bbregister Done To 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.mat convert_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.mat convert_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 2018 flirt -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 mutualinfo convert_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.mat convert_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.mat convert_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.mat convert_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.mat convert_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 2018 mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 466816 values in range Counting number of voxels in first frame Found 466816 voxels in final mask Count: 466816 466816.000000 16777216 2.782440 mri_binarize done mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 496933 values in range Counting number of voxels in first frame Found 496933 voxels in final mask Count: 496933 496933.000000 16777216 2.961951 mri_binarize done mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 23114 values in range Counting number of voxels in first frame Found 23114 voxels in final mask Count: 23114 23114.000000 16777216 0.137770 mri_binarize done mri_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.gz SUBJECTS_DIR /home/fsluser/usr_/local_/diffusion_recons subject elmo.2005 outvol /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 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.annot reading 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.annot reading 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 annotation Have color table for rh white annotation Loading ribbon segmentation from /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/ribbon.mgz Loading 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.mgz ASeg 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 = 1019533 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 1 clusters 0 k 889.000000 Fixing Parahip RH WM Found 1 clusters 0 k 714.000000 Writing output aseg to /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 577605 values in range Counting number of voxels in first frame Found 577605 voxels in final mask Count: 577605 577605.000000 16777216 3.442794 mri_binarize done mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 848289 values in range Counting number of voxels in first frame Found 848289 voxels in final mask Count: 848289 848289.000000 16777216 5.056196 mri_binarize done mri_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_recons cmdline 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 Linux hostname localhost.localdomain machine x86_64 user fsluser

input /home/fsluser/usr_/local_/diffusion_recons/elmo.2005/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 21835 values in range Counting number of voxels in first frame Found 21835 voxels in final mask Count: 21835 21835.000000 16777216 0.130147 mri_binarize done fslmaths /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.gz mri_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.gz mri_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=7.00 i_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.gz mri_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.gz mri_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=7.00 i_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.gz orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour orientLAS /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 INFO: input image orientation is LIA INFO: input image determinant is -1 mri_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.gz mri_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=0.00 i_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 nearestneighbour flirt -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 nearestneighbour fslstats -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.txt flirt -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 nearestneighbour flirt -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 nearestneighbour ln -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 2018 dtifit -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/dtifit 0 128 0 128 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed flirt -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.mat flirt -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.mat flirt -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.mat flirt -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.mat flirt -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.mat flirt -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.mat flirt -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_recons cmdline /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 Linux hostname localhost.localdomain machine x86_64 user fsluser Output directory: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni Output directory in test subject's space: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/diff Output 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_bbr Training subject directory list: /tmp/subj33.elmo.2005.26311.txt Location 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.trk Location 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.gz Location 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.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label 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 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat Number of control points for initial spline: 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 1 Loading brain mask of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/dtifit_FA.nii.gz Loading affine registration from /home/fsluser/usr_/local_/diffusion_tutorial/elmo.2005/dmri/xfms/mni2diff.bbr.mat Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.bbr.trk Loading streamline start ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Loading streamline end ROI from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz Loading streamlines from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.bbr.trk INFO: Rejected 1094 streamlines for straying off mask INFO: Rejected 73 streamlines for reversing direction INFO: Rejected 17 streamlines as length outliers INFO: Have 7248 total streamlines (min/mean/max length: 59/99/139) Loading segmentation from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc005/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc006/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc007/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc008/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc009/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc011/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc012/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc013/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc014/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc015/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc016/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc017/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc018/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc019/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc020/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc021/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc022/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc023/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc024/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc025/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc026/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc027/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc028/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc030/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer/trctrain/trc031/dlabel/mni/cortex+2mm.nii.gz 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/Linux

trac-preproc exited with ERRORS at Mon Sep 10 15:07:07 BST 2018