INFO: SUBJECTS_DIR is /fastfs/igis/MRI_fs_rec_t1 INFO: Diffusion root is /fastfs/igis/MRI_fs_rec_dti Actual FREESURFER_HOME /sw/global/applications/freesurfer/5.2.0/x86_64 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /sw/global/applications/freesurfer/5.2.0/x86_64 Previous: /sw/global/applications/freesurfer/5.1.0/x86_64 trac-preproc -c /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/scripts/dmrirc.local -log /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/scripts/trac-all.log -cmd /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/scripts/trac-all.cmd #------------------------------------- /sw/global/applications/freesurfer/5.2.0/x86_64/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Apr 9 13:50:18 CEST 2013 mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/orig/20120522_072644aaDTIimagen60364-10-069-1T1.nii /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/orig/20120522_072644aaDTIimagen60364-10-069-1T1.nii /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/orig/20120522_072644aaDTIimagen60364-10-069-1T1.nii... TR=15000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.990385, -0.115328, 0.0763987) j_ras = (-0.103749, 0.984522, 0.141251) k_ras = (0.0915064, -0.131967, 0.987021) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.nii.gz... cp /fastfs/igis/MRI_fs_rec_dti/bvalvec/bvecs.txt /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.mghdti.bvecs cp /fastfs/igis/MRI_fs_rec_dti/bvalvec/bvals.txt /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.mghdti.bvals flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -13.806 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.nii.gz x y z /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.nii.gz INFO: found /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.mghdti.bvecs /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs mv -f /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.mghdti.bvals /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvals eddy_correct /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_orig_flip.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz 0 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0000 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0001 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0002 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0003 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0004 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0005 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0006 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0007 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0008 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0009 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0010 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0011 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0012 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0013 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0014 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0015 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0016 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0017 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0018 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0019 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0020 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0021 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0022 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0023 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0024 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0025 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0026 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0027 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0028 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0029 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0030 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0031 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0032 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0033 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0034 processing /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_tmp0035 mv -f /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs.norot xfmrot /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.ecclog /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs.norot /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs ln -sf /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/data.nii.gz fslroi /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz 0 4 fslmaths /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -Tmean /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz bet /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb_brain_mask.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff #------------------------------------- #@# Intra-subject registration Tue Apr 9 13:58:27 CEST 2013 mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brain.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brain.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brain.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.9407e-08, 0) j_ras = (0, 0, -1) k_ras = (5.96046e-08, 1, 0) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz... flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz tkregister2 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz --targ /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2anat.mat --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2anatorig.dat tkregister_tcl /sw/global/applications/freesurfer/5.2.0/x86_64/tktools/tkregister2.tcl target volume /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz movable volume /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz reg file /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2anatorig.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2anat.mat Log file is /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat.log Tue Apr 9 13:58:32 CEST 2013 setenv SUBJECTS_DIR /fastfs/igis/MRI_fs_rec_t1 cd /fastfs/igis/MRI_fs_rec_dti/scripts /sw/global/applications/freesurfer/5.2.0/x86_64/bin/bbregister --s 64-10-069-1_T1 --init-fsl --dti --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat --fslmat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux n063 2.6.32.49-0.3-default #1 SMP 2011-12-02 11:28:04 +0100 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /sw/global/applications/freesurfer/5.2.0/x86_64 mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.990385, -0.115328, 0.0763987) j_ras = (-0.103749, 0.984522, 0.141251) k_ras = (0.0915064, -0.131967, 0.987021) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii... fslregister --s 64-10-069-1_T1 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister --dof 6 --fsvol brainmask Log file is /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat.fslregister.log Tue Apr 9 13:58:40 CEST 2013 --s 64-10-069-1_T1 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ n063 Linux n063 2.6.32.49-0.3-default #1 SMP 2011-12-02 11:28:04 +0100 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /fastfs/igis/MRI_fs_rec_dti/scripts mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/refvol.fslregister.nii mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.9407e-08, 0) j_ras = (0, 0, -1) k_ras = (5.96046e-08, 1, 0) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/refvol.fslregister.nii... -------------------------------------- /fastfs/igis/MRI_fs_rec_dti/scripts mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii --frame 0 mri_convert /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.990385, -0.115328, 0.0763987) j_ras = (-0.103749, 0.984522, 0.141251) k_ras = (0.0915064, -0.131967, 0.987021) keeping frame 0 writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii... Mov determinant is -13.806 /fastfs/igis/MRI_fs_rec_dti/scripts tkregister2_cmdl --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/reg0.7479.dat --regheader --fslregout /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat.fsl.mat0 --s 64-10-069-1_T1 --noedit tkregister_tcl /sw/global/applications/freesurfer/5.2.0/x86_64/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii reg file /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/reg0.7479.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.398 0.000 0.000 153.500; 0.000 0.000 2.400 -72.000; 0.000 -2.398 0.000 153.500; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.990 0.115 -0.076 3.190; 0.092 -0.132 0.987 -46.818; 0.104 -0.985 -0.141 -8.432; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.990 0.115 -0.076 3.190; 0.092 -0.132 0.987 -46.818; 0.104 -0.985 -0.141 -8.432; 0.000 0.000 0.000 1.000; Determinant 1 subject = 64-10-069-1_T1 RegMat --------------------------- 0.990 0.115 -0.076 3.190; 0.092 -0.132 0.987 -46.818; 0.104 -0.985 -0.141 -8.432; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -13.806, ref det = -1 Tue Apr 9 13:58:52 CEST 2013 /fastfs/igis/MRI_fs_rec_dti/scripts flirt.fsl -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/refvol.fslregister.nii -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/fslmat0.trans.mat -schedule /sw/global/libraries/fsl/5.0.1/x86_64/etc/flirtsch/xyztrans.sch -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat.fsl.mat0 Tue Apr 9 13:59:10 CEST 2013 /fastfs/igis/MRI_fs_rec_dti/scripts flirt.fsl -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/refvol.fslregister.nii -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat.fsl.mat -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/fslregister/fslmat0.trans.mat -schedule /sw/global/applications/freesurfer/5.2.0/x86_64/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s 64-10-069-1_T1 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --fslreg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat.fsl.mat --noedit tkregister_tcl /sw/global/applications/freesurfer/5.2.0/x86_64/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.990 0.103 -0.093 -37.039; -0.078 -0.142 -0.987 190.670; -0.115 0.985 -0.132 -8.629; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii reg file /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii Tmov: -------------------- -2.398 0.000 0.000 153.500; 0.000 0.000 2.400 -72.000; 0.000 -2.398 0.000 153.500; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -13.806, ref det = -1 ---- Input registration matrix (computed) -------- 0.990 0.115 -0.078 0.930; 0.093 -0.132 0.987 -43.593; 0.103 -0.985 -0.142 -6.963; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.990 0.115 -0.078 0.930; 0.093 -0.132 0.987 -43.593; 0.103 -0.985 -0.142 -6.963; 0.000 0.000 0.000 1.000; Determinant 1 subject = 64-10-069-1_T1 RegMat --------------------------- 0.990 0.115 -0.078 0.930; 0.093 -0.132 0.987 -43.593; 0.103 -0.985 -0.142 -6.963; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: T (standard_in) 1: syntax error Started at Tue Apr 9 13:58:40 CEST 2013 Ended at Tue Apr 9 13:59:39 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --surf orig mri_segreg --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --init-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --out-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /fastfs/igis/MRI_fs_rec_t1 cd /fastfs/igis/MRI_fs_rec_dti/scripts mri_segreg --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --init-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat --out-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/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 n063 machine x86_64 user pfuhl movvol /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii regfile /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.init.dat subject 64-10-069-1_T1 dof 6 outregfile /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/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 1366391307 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.990 0.115 -0.078 0.930; 0.093 -0.132 0.987 -43.593; 0.103 -0.985 -0.142 -6.963; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.987213 1 -25.0 -25.0 25.0 1.008305 2 -25.0 25.0 -25.0 0.989295 3 -25.0 25.0 25.0 0.987369 4 25.0 -25.0 -25.0 1.025131 5 25.0 -25.0 25.0 1.040959 6 25.0 25.0 -25.0 1.086545 7 25.0 25.0 25.0 1.043273 REL: 8 0.687695 8.168090 1.021011 rel = 0.673543 Initial costs ---------------- Number of surface hits 2496 WM Intensity 406.4563 +/- 183.3851 Ctx Intensity 484.3636 +/- 220.5539 Pct Contrast 15.6550 +/- 40.8450 Cost 0.6877 RelCost 0.6735 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9632 0.9632 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9475 0.9475 0.0 11 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.9436 0.9436 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9283 0.9283 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.9210 0.9210 0.0 42 -4.0000 -4.0000 0.0000 0.0000 4.0000 -4.0000 0.9083 0.9083 0.0 48 -4.0000 -4.0000 0.0000 4.0000 0.0000 -4.0000 0.8741 0.8741 0.0 126 -4.0000 0.0000 0.0000 4.0000 -4.0000 -4.0000 0.8694 0.8694 0.0 127 -4.0000 0.0000 0.0000 4.0000 -4.0000 0.0000 0.8274 0.8274 0.0 160 -4.0000 0.0000 4.0000 4.0000 4.0000 0.0000 0.8151 0.8151 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8054 0.8054 0.0 292 0.0000 -4.0000 0.0000 4.0000 0.0000 0.0000 0.7364 0.7364 0.0 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.7012 0.7012 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6877 0.6877 0.0 370 0.0000 0.0000 0.0000 4.0000 -4.0000 0.0000 0.6798 0.6798 0.0 373 0.0000 0.0000 0.0000 4.0000 0.0000 0.0000 0.5284 0.5284 0.0 Brute Force -------------------------- Min cost was 0.528406 Number of iterations 729 Search time 2.955000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 4.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 4 4 0 5 0 7 0.046 0.000 0.000 4.000 0.000 0.000 0.5277822098 8 0.095 0.000 0.000 4.000 0.000 0.000 0.5273623343 10 0.115 0.000 0.000 4.000 0.000 0.000 0.5267423328 12 0.129 0.000 0.000 4.000 0.000 0.000 0.5266664660 13 0.128 0.000 0.000 4.000 0.000 0.000 0.5266638101 14 0.127 0.000 0.000 4.000 0.000 0.000 0.5266621248 26 0.127 -0.029 0.000 4.000 0.000 0.000 0.5265141473 30 0.127 -0.029 1.000 4.000 0.000 0.000 0.5055094215 33 0.127 -0.029 1.618 4.000 0.000 0.000 0.4971329721 36 0.127 -0.029 1.759 4.000 0.000 0.000 0.4969911229 37 0.127 -0.029 1.851 4.000 0.000 0.000 0.4969496292 39 0.127 -0.029 1.816 4.000 0.000 0.000 0.4967521335 41 0.127 -0.029 1.823 4.000 0.000 0.000 0.4967470336 42 0.127 -0.029 1.821 4.000 0.000 0.000 0.4967445070 47 0.127 -0.029 1.821 2.382 0.000 0.000 0.4478756382 56 0.127 -0.029 1.821 2.381 0.000 0.000 0.4478747773 67 0.127 -0.029 1.821 2.381 -0.044 0.000 0.4477336483 68 0.127 -0.029 1.821 2.381 -0.034 0.000 0.4476387653 69 0.127 -0.029 1.821 2.381 -0.026 0.000 0.4476134679 73 0.127 -0.029 1.821 2.381 -0.026 1.000 0.4195008540 79 0.127 -0.029 1.821 2.381 -0.026 0.888 0.4185598050 80 0.127 -0.029 1.821 2.381 -0.026 0.785 0.4182922965 81 0.127 -0.029 1.821 2.381 -0.026 0.788 0.4182297666 82 0.127 -0.029 1.821 2.381 -0.026 0.831 0.4180833756 84 0.127 -0.029 1.821 2.381 -0.026 0.814 0.4179988573 86 0.127 -0.029 1.821 2.381 -0.026 0.812 0.4179976289 96 0.157 -0.029 1.821 2.381 -0.026 0.812 0.4175099177 97 0.201 -0.029 1.821 2.381 -0.026 0.812 0.4164584144 100 0.210 -0.029 1.821 2.381 -0.026 0.812 0.4162508443 101 0.218 -0.029 1.821 2.381 -0.026 0.812 0.4161877328 102 0.217 -0.029 1.821 2.381 -0.026 0.812 0.4161857428 112 0.217 -0.112 1.821 2.381 -0.026 0.812 0.4153865998 113 0.217 -0.105 1.821 2.381 -0.026 0.812 0.4153456153 114 0.217 -0.094 1.821 2.381 -0.026 0.812 0.4153142380 116 0.217 -0.088 1.821 2.381 -0.026 0.812 0.4153107107 117 0.217 -0.089 1.821 2.381 -0.026 0.812 0.4153105528 124 0.217 -0.089 2.202 2.381 -0.026 0.812 0.4094508504 128 0.217 -0.089 2.206 2.381 -0.026 0.812 0.4094498801 129 0.217 -0.089 2.205 2.381 -0.026 0.812 0.4094493655 137 0.217 -0.089 2.205 2.224 -0.026 0.812 0.4066098251 139 0.217 -0.089 2.205 2.237 -0.026 0.812 0.4065089691 141 0.217 -0.089 2.205 2.249 -0.026 0.812 0.4064672215 142 0.217 -0.089 2.205 2.254 -0.026 0.812 0.4064655462 143 0.217 -0.089 2.205 2.252 -0.026 0.812 0.4064643173 152 0.217 -0.089 2.205 2.252 -0.054 0.812 0.4063145046 153 0.217 -0.089 2.205 2.252 -0.055 0.812 0.4063127635 155 0.217 -0.089 2.205 2.252 -0.058 0.812 0.4063080449 156 0.217 -0.089 2.205 2.252 -0.059 0.812 0.4063055808 157 0.217 -0.089 2.205 2.252 -0.060 0.812 0.4063047337 164 0.217 -0.089 2.205 2.252 -0.060 0.918 0.4046512337 165 0.217 -0.089 2.205 2.252 -0.060 0.946 0.4043751604 168 0.217 -0.089 2.205 2.252 -0.060 0.947 0.4043750850 181 0.220 -0.089 2.205 2.252 -0.060 0.947 0.4043636820 183 0.223 -0.089 2.205 2.252 -0.060 0.947 0.4043619261 185 0.222 -0.089 2.205 2.252 -0.060 0.947 0.4043617024 192 0.222 -0.221 2.205 2.252 -0.060 0.947 0.4039679653 195 0.222 -0.292 2.205 2.252 -0.060 0.947 0.4031216820 198 0.222 -0.286 2.205 2.252 -0.060 0.947 0.4030985020 199 0.222 -0.283 2.205 2.252 -0.060 0.947 0.4030953519 200 0.222 -0.282 2.205 2.252 -0.060 0.947 0.4030952781 208 0.222 -0.282 2.224 2.252 -0.060 0.947 0.4029291986 209 0.222 -0.282 2.275 2.252 -0.060 0.947 0.4028848838 211 0.222 -0.282 2.254 2.252 -0.060 0.947 0.4028030378 213 0.222 -0.282 2.257 2.252 -0.060 0.947 0.4027989959 215 0.222 -0.282 2.259 2.252 -0.060 0.947 0.4027985319 223 0.222 -0.282 2.259 2.082 -0.060 0.947 0.4021641843 227 0.222 -0.282 2.259 2.060 -0.060 0.947 0.4018172321 229 0.222 -0.282 2.259 2.061 -0.060 0.947 0.4018142379 232 0.222 -0.282 2.259 2.063 -0.060 0.947 0.4018101514 243 0.222 -0.282 2.259 2.063 -0.056 0.947 0.4017841350 254 0.222 -0.282 2.259 2.063 -0.056 0.980 0.4015784608 256 0.222 -0.282 2.259 2.063 -0.056 0.977 0.4015756806 266 0.249 -0.282 2.259 2.063 -0.056 0.977 0.4010695451 269 0.250 -0.282 2.259 2.063 -0.056 0.977 0.4010688931 278 0.250 -0.287 2.259 2.063 -0.056 0.977 0.4010444448 287 0.250 -0.287 2.290 2.063 -0.056 0.977 0.4007350232 288 0.250 -0.287 2.345 2.063 -0.056 0.977 0.4006016144 289 0.250 -0.287 2.332 2.063 -0.056 0.977 0.4005127780 290 0.250 -0.287 2.323 2.063 -0.056 0.977 0.4004994174 291 0.250 -0.287 2.324 2.063 -0.056 0.977 0.4004989147 302 0.250 -0.287 2.324 2.054 -0.056 0.977 0.4004876972 313 0.250 -0.287 2.324 2.054 -0.046 0.977 0.4004077557 314 0.250 -0.287 2.324 2.054 -0.041 0.977 0.4003946724 317 0.250 -0.287 2.324 2.054 -0.040 0.977 0.4003938154 318 0.250 -0.287 2.324 2.054 -0.039 0.977 0.4003932304 336 0.249 -0.287 2.324 2.054 -0.039 0.977 0.4003832033 339 0.244 -0.287 2.324 2.054 -0.039 0.977 0.4003686296 350 0.244 -0.297 2.324 2.054 -0.039 0.977 0.4002549525 351 0.244 -0.301 2.324 2.054 -0.039 0.977 0.4002345104 352 0.244 -0.303 2.324 2.054 -0.039 0.977 0.4002339699 363 0.244 -0.303 2.333 2.054 -0.039 0.977 0.4001990996 372 0.244 -0.303 2.333 2.041 -0.039 0.977 0.4001841267 374 0.244 -0.303 2.333 2.045 -0.039 0.977 0.4001794150 385 0.244 -0.303 2.333 2.045 -0.038 0.977 0.4001684695 386 0.244 -0.303 2.333 2.045 -0.032 0.977 0.4001552879 388 0.244 -0.303 2.333 2.045 -0.033 0.977 0.4001547627 398 0.244 -0.303 2.333 2.045 -0.033 0.988 0.4001320358 399 0.244 -0.303 2.333 2.045 -0.033 0.987 0.4001316691 400 0.244 -0.303 2.333 2.045 -0.033 0.986 0.4001316188 410 0.241 -0.303 2.333 2.045 -0.033 0.986 0.4001152997 413 0.237 -0.303 2.333 2.045 -0.033 0.986 0.4001051588 425 0.237 -0.304 2.333 2.045 -0.033 0.986 0.4001046700 437 0.237 -0.304 2.340 2.045 -0.033 0.986 0.4000945726 438 0.237 -0.304 2.338 2.045 -0.033 0.986 0.4000938523 446 0.237 -0.304 2.338 2.037 -0.033 0.986 0.4000841572 448 0.237 -0.304 2.338 2.039 -0.033 0.986 0.4000833165 450 0.237 -0.304 2.338 2.038 -0.033 0.986 0.4000832640 460 0.237 -0.304 2.338 2.038 -0.029 0.986 0.4000788066 471 0.237 -0.304 2.338 2.038 -0.029 0.996 0.4000672083 472 0.237 -0.304 2.338 2.038 -0.029 0.994 0.4000650132 475 0.231 -0.305 2.344 2.031 -0.026 1.002 0.4000227433 478 0.221 -0.307 2.352 2.020 -0.020 1.014 0.4000101473 479 0.224 -0.306 2.349 2.024 -0.022 1.010 0.4000036518 483 0.225 -0.306 2.349 2.025 -0.022 1.009 0.4000032627 486 0.225 -0.306 2.349 2.025 -0.022 1.009 0.4000028976 488 0.225 -0.306 2.349 2.025 -0.022 1.009 0.4000028118 500 0.225 -0.306 2.349 2.025 -0.022 1.007 0.4000024578 502 0.225 -0.306 2.349 2.025 -0.022 1.008 0.4000020510 512 0.225 -0.304 2.349 2.025 -0.022 1.008 0.3999947024 523 0.225 -0.304 2.376 2.025 -0.022 1.008 0.3999301546 524 0.225 -0.304 2.379 2.025 -0.022 1.008 0.3999267227 526 0.225 -0.304 2.384 2.025 -0.022 1.008 0.3999251237 536 0.225 -0.304 2.384 2.010 -0.022 1.008 0.3999093938 538 0.225 -0.304 2.384 2.015 -0.022 1.008 0.3999040070 550 0.225 -0.304 2.384 2.015 -0.025 1.008 0.3999010700 551 0.225 -0.304 2.384 2.015 -0.026 1.008 0.3999005871 554 0.218 -0.305 2.389 2.008 -0.023 1.015 0.3998119460 555 0.208 -0.306 2.398 1.997 -0.017 1.028 0.3997548315 562 0.208 -0.306 2.397 1.997 -0.017 1.028 0.3997545997 567 0.179 -0.309 2.456 1.955 -0.005 1.061 0.3991345747 572 0.161 -0.310 2.493 1.930 0.002 1.082 0.3985771982 575 0.160 -0.310 2.495 1.928 0.003 1.084 0.3985723808 577 0.160 -0.310 2.495 1.928 0.003 1.084 0.3985723041 590 0.160 -0.310 2.495 1.928 0.003 1.041 0.3983781552 591 0.160 -0.310 2.495 1.928 0.003 1.047 0.3983680078 592 0.160 -0.310 2.495 1.928 0.003 1.049 0.3983677184 593 0.160 -0.310 2.495 1.928 0.003 1.050 0.3983673448 606 0.160 -0.300 2.495 1.928 0.003 1.050 0.3982929495 607 0.160 -0.301 2.495 1.928 0.003 1.050 0.3982916934 617 0.160 -0.301 2.501 1.928 0.003 1.050 0.3981073419 618 0.160 -0.301 2.530 1.928 0.003 1.050 0.3979040261 620 0.160 -0.301 2.521 1.928 0.003 1.050 0.3978537872 621 0.160 -0.301 2.520 1.928 0.003 1.050 0.3978537299 631 0.160 -0.301 2.520 1.923 0.003 1.050 0.3978442859 642 0.160 -0.301 2.520 1.923 -0.020 1.050 0.3977966671 644 0.160 -0.301 2.520 1.923 -0.011 1.050 0.3977465041 646 0.160 -0.301 2.520 1.923 -0.012 1.050 0.3977463370 655 0.166 -0.301 2.507 1.932 -0.015 1.042 0.3976402012 656 0.166 -0.301 2.507 1.932 -0.015 1.042 0.3976396994 658 0.166 -0.301 2.508 1.932 -0.014 1.043 0.3976390378 659 0.166 -0.301 2.508 1.932 -0.015 1.043 0.3976388146 660 0.166 -0.301 2.508 1.932 -0.015 1.043 0.3976383411 671 0.166 -0.301 2.508 1.932 -0.015 1.034 0.3976265367 683 0.166 -0.299 2.508 1.932 -0.015 1.034 0.3976241535 695 0.166 -0.299 2.534 1.932 -0.015 1.034 0.3976131482 696 0.166 -0.299 2.521 1.932 -0.015 1.034 0.3975074184 705 0.166 -0.299 2.521 1.914 -0.015 1.034 0.3975010137 706 0.166 -0.299 2.521 1.921 -0.015 1.034 0.3974770742 707 0.166 -0.299 2.521 1.923 -0.015 1.034 0.3974753187 719 0.166 -0.299 2.521 1.923 -0.016 1.034 0.3974751546 728 0.171 -0.299 2.512 1.929 -0.018 1.028 0.3974179977 729 0.171 -0.299 2.512 1.929 -0.018 1.028 0.3974178907 730 0.171 -0.299 2.512 1.929 -0.017 1.029 0.3974178417 731 0.171 -0.299 2.512 1.929 -0.017 1.029 0.3974173205 734 0.170 -0.299 2.513 1.929 -0.017 1.029 0.3974172044 737 0.170 -0.299 2.513 1.929 -0.017 1.029 0.3974169367 739 0.175 -0.296 2.518 1.926 -0.020 1.015 0.3972930028 744 0.177 -0.295 2.521 1.924 -0.022 1.007 0.3972687618 746 0.177 -0.295 2.521 1.923 -0.022 1.006 0.3972685344 747 0.178 -0.295 2.521 1.923 -0.022 1.006 0.3972683813 749 0.178 -0.295 2.521 1.923 -0.022 1.005 0.3972682538 763 0.178 -0.295 2.521 1.923 -0.022 1.040 0.3972004732 764 0.178 -0.295 2.521 1.923 -0.022 1.028 0.3971696966 776 0.178 -0.301 2.521 1.923 -0.022 1.027 0.3971395264 785 0.180 -0.301 2.516 1.927 -0.023 1.024 0.3971289941 786 0.180 -0.301 2.517 1.926 -0.023 1.025 0.3971282771 787 0.180 -0.301 2.517 1.926 -0.023 1.025 0.3971281228 789 0.180 -0.301 2.517 1.926 -0.023 1.025 0.3971277992 799 0.180 -0.301 2.517 1.925 -0.023 1.025 0.3971275980 810 0.180 -0.301 2.517 1.925 -0.019 1.025 0.3971189051 811 0.180 -0.301 2.517 1.925 -0.018 1.025 0.3971188004 814 0.184 -0.299 2.522 1.922 -0.021 1.011 0.3970425564 819 0.185 -0.298 2.523 1.921 -0.022 1.008 0.3970407717 820 0.185 -0.298 2.522 1.921 -0.021 1.009 0.3970405321 825 0.185 -0.298 2.522 1.921 -0.022 1.008 0.3970402761 828 0.200 -0.298 2.532 1.914 -0.026 0.988 0.3970120316 837 0.185 -0.298 2.522 1.921 -0.021 1.027 0.3969694984 839 0.185 -0.298 2.522 1.921 -0.021 1.026 0.3969693609 851 0.185 -0.302 2.522 1.921 -0.021 1.026 0.3969595609 852 0.185 -0.301 2.522 1.921 -0.021 1.026 0.3969592682 860 0.187 -0.301 2.518 1.924 -0.022 1.024 0.3969507406 861 0.187 -0.301 2.519 1.924 -0.022 1.024 0.3969507259 862 0.187 -0.301 2.519 1.924 -0.022 1.024 0.3969502953 864 0.187 -0.301 2.519 1.924 -0.022 1.024 0.3969499405 888 0.191 -0.299 2.524 1.921 -0.025 1.010 0.3968918281 893 0.191 -0.299 2.524 1.921 -0.025 1.010 0.3968918061 894 0.191 -0.299 2.524 1.921 -0.025 1.010 0.3968916947 895 0.191 -0.299 2.524 1.921 -0.025 1.010 0.3968915499 897 0.191 -0.299 2.524 1.921 -0.025 1.010 0.3968915267 900 0.197 -0.300 2.525 1.920 -0.029 1.011 0.3967680711 903 0.207 -0.301 2.527 1.920 -0.034 1.013 0.3966105936 904 0.233 -0.304 2.531 1.918 -0.049 1.019 0.3963937554 905 0.241 -0.305 2.533 1.917 -0.054 1.021 0.3963622275 906 0.249 -0.306 2.534 1.916 -0.058 1.022 0.3963574484 907 0.247 -0.305 2.534 1.917 -0.057 1.022 0.3963566932 910 0.248 -0.305 2.534 1.917 -0.058 1.022 0.3963565878 915 0.248 -0.305 2.534 1.917 -0.058 1.022 0.3963563407 920 0.248 -0.305 2.534 1.917 -0.058 1.022 0.3963562222 926 0.250 -0.305 2.536 1.915 -0.059 1.017 0.3963477498 927 0.249 -0.305 2.536 1.915 -0.059 1.017 0.3963476562 928 0.249 -0.305 2.536 1.915 -0.059 1.017 0.3963476173 931 0.249 -0.305 2.536 1.916 -0.059 1.018 0.3963472157 947 0.249 -0.308 2.536 1.916 -0.059 1.018 0.3963453790 956 0.245 -0.308 2.545 1.909 -0.057 1.023 0.3962910004 957 0.245 -0.308 2.545 1.909 -0.057 1.023 0.3962904833 970 0.245 -0.308 2.545 1.917 -0.057 1.023 0.3962516920 974 0.245 -0.308 2.545 1.924 -0.057 1.023 0.3962374454 975 0.245 -0.308 2.545 1.925 -0.057 1.023 0.3962362850 977 0.245 -0.308 2.545 1.926 -0.057 1.023 0.3962360070 978 0.245 -0.308 2.545 1.927 -0.057 1.023 0.3962354915 988 0.245 -0.308 2.545 1.927 -0.071 1.023 0.3962326615 990 0.245 -0.308 2.545 1.927 -0.064 1.023 0.3962145733 997 0.241 -0.308 2.544 1.927 -0.062 1.022 0.3962100832 999 0.241 -0.308 2.544 1.927 -0.062 1.022 0.3962099454 1003 0.241 -0.308 2.544 1.927 -0.062 1.022 0.3962098676 1006 0.241 -0.308 2.544 1.927 -0.062 1.022 0.3962098019 1017 0.242 -0.307 2.545 1.927 -0.063 1.020 0.3962089348 1021 0.242 -0.307 2.545 1.927 -0.063 1.020 0.3962088300 1024 0.242 -0.307 2.545 1.927 -0.063 1.020 0.3962088250 1034 0.242 -0.302 2.545 1.927 -0.063 1.020 0.3961870659 1036 0.242 -0.301 2.545 1.927 -0.063 1.020 0.3961855246 1045 0.242 -0.300 2.544 1.927 -0.063 1.020 0.3961845719 1050 0.242 -0.300 2.544 1.928 -0.063 1.020 0.3961845702 1061 0.242 -0.300 2.544 1.930 -0.063 1.020 0.3961820098 1063 0.242 -0.300 2.544 1.931 -0.063 1.020 0.3961813528 1082 0.242 -0.300 2.544 1.931 -0.063 1.020 0.3961811592 1084 0.242 -0.300 2.544 1.931 -0.062 1.020 0.3961810244 1087 0.242 -0.300 2.544 1.931 -0.062 1.020 0.3961810004 Powell done niters = 12 Computing relative cost 0 -25.0 -25.0 -25.0 1.006256 1 -25.0 -25.0 25.0 1.018389 2 -25.0 25.0 -25.0 1.024572 3 -25.0 25.0 25.0 0.977660 4 25.0 -25.0 -25.0 1.010355 5 25.0 -25.0 25.0 0.991156 6 25.0 25.0 -25.0 1.040227 7 25.0 25.0 25.0 1.030206 REL: 8 0.396181 8.098821 1.012353 rel = 0.391347 Number of iterations 12 Min cost was 0.396181 Number of FunctionCalls 1090 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 4.295000 sec Parameters at optimum (transmm) 0.24159 -0.30042 2.54366 Parameters at optimum (rotdeg) 1.93063 -0.06245 1.01987 Final costs ---------------- Number of surface hits 2496 WM Intensity 359.6837 +/- 157.4919 Ctx Intensity 482.0620 +/- 186.8773 Pct Contrast 27.6355 +/- 37.2536 Cost 0.3962 RelCost 0.6735 Reg at min cost was 0.988 0.118 -0.096 1.952; 0.107 -0.097 0.990 -43.610; 0.108 -0.988 -0.108 -5.883; 0.000 0.000 0.000 1.000; Writing optimal reg to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/bbr.pass1.dat, type = 14 Original Reg 0.990 0.115 -0.078 0.930; 0.093 -0.132 0.987 -43.593; 0.103 -0.985 -0.142 -6.963; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.002 -0.003 0.018 -1.022; -0.014 -0.035 -0.003 0.018; -0.004 0.004 -0.033 -1.080; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 3.127166 Computing change in rh position Surface RMS Diff (mm) 3.064252 4.646139 mri_segreg done mri_segreg --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --init-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/bbr.pass1.dat --out-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /fastfs/igis/MRI_fs_rec_t1 cd /fastfs/igis/MRI_fs_rec_dti/scripts mri_segreg --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii --init-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/bbr.pass1.dat --out-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname n063 machine x86_64 user pfuhl movvol /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/template.nii regfile /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/tmp.bbregister.7438/bbr.pass1.dat subject 64-10-069-1_T1 dof 6 outregfile /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 1366063481 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.988 0.118 -0.096 1.952; 0.107 -0.097 0.990 -43.610; 0.108 -0.988 -0.108 -5.883; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.002256 1 -25.0 -25.0 25.0 1.009947 2 -25.0 25.0 -25.0 1.036532 3 -25.0 25.0 25.0 1.003930 4 25.0 -25.0 -25.0 1.043452 5 25.0 -25.0 25.0 1.027480 6 25.0 25.0 -25.0 1.019728 7 25.0 25.0 25.0 1.039364 REL: 8 0.412475 8.182688 1.022836 rel = 0.403266 Initial costs ---------------- Number of surface hits 249202 WM Intensity 358.8065 +/- 151.9189 Ctx Intensity 484.3279 +/- 185.0265 Pct Contrast 28.1255 +/- 36.9911 Cost 0.4125 RelCost 0.4033 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4036 0.4036 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4035 0.4035 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.4033 0.4033 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.4032 0.4032 0.0 27 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.4019 0.4019 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.4000 0.4000 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.4000 0.4000 0.0 111 -0.1000 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.3995 0.3995 0.0 124 -0.1000 0.0000 0.0000 0.0000 0.1000 0.0000 0.3992 0.3992 0.0 247 0.0000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.3991 0.3991 0.0 270 0.0000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.3991 0.3991 0.0 273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.3982 0.3982 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.3970 0.3970 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3962 0.3962 0.0 Brute Force -------------------------- Min cost was 0.396181 Number of iterations 729 Search time 2.879000 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 8 0.020 0.000 0.000 0.000 0.000 0.000 0.4124593830 10 0.014 0.000 0.000 0.000 0.000 0.000 0.4124560470 11 0.015 0.000 0.000 0.000 0.000 0.000 0.4124560415 19 0.015 -0.241 0.000 0.000 0.000 0.000 0.4086039287 20 0.015 -0.253 0.000 0.000 0.000 0.000 0.4085934679 29 0.015 -0.254 -0.305 0.000 0.000 0.000 0.4044903598 31 0.015 -0.254 -0.283 0.000 0.000 0.000 0.4044708354 33 0.015 -0.254 -0.287 0.000 0.000 0.000 0.4044701647 44 0.015 -0.254 -0.287 0.002 0.000 0.000 0.4044698304 53 0.015 -0.254 -0.287 0.002 -0.168 0.000 0.4035237751 54 0.015 -0.254 -0.287 0.002 -0.157 0.000 0.4035144107 55 0.015 -0.254 -0.287 0.002 -0.152 0.000 0.4035126897 57 0.015 -0.254 -0.287 0.002 -0.151 0.000 0.4035126382 58 0.015 -0.254 -0.287 0.002 -0.150 0.000 0.4035123716 65 0.015 -0.254 -0.287 0.002 -0.150 -0.110 0.4029622711 67 0.015 -0.254 -0.287 0.002 -0.150 -0.114 0.4029609469 68 0.015 -0.254 -0.287 0.002 -0.150 -0.115 0.4029607316 78 0.057 -0.254 -0.287 0.002 -0.150 -0.115 0.4026840312 79 0.080 -0.254 -0.287 0.002 -0.150 -0.115 0.4026350017 80 0.085 -0.254 -0.287 0.002 -0.150 -0.115 0.4026299337 81 0.092 -0.254 -0.287 0.002 -0.150 -0.115 0.4026254556 84 0.100 -0.254 -0.287 0.002 -0.150 -0.115 0.4026246939 85 0.097 -0.254 -0.287 0.002 -0.150 -0.115 0.4026239890 94 0.097 -0.297 -0.287 0.002 -0.150 -0.115 0.4025573937 95 0.097 -0.289 -0.287 0.002 -0.150 -0.115 0.4025504594 96 0.097 -0.287 -0.287 0.002 -0.150 -0.115 0.4025499073 106 0.097 -0.287 -0.325 0.002 -0.150 -0.115 0.4024268566 117 0.097 -0.287 -0.325 -0.009 -0.150 -0.115 0.4024153495 120 0.097 -0.287 -0.325 -0.010 -0.150 -0.115 0.4024151662 130 0.097 -0.287 -0.325 -0.010 -0.248 -0.115 0.4022656099 131 0.097 -0.287 -0.325 -0.010 -0.215 -0.115 0.4022605176 134 0.097 -0.287 -0.325 -0.010 -0.206 -0.115 0.4022602468 135 0.097 -0.287 -0.325 -0.010 -0.208 -0.115 0.4022598342 136 0.097 -0.287 -0.325 -0.010 -0.210 -0.115 0.4022596599 145 0.097 -0.287 -0.325 -0.010 -0.210 -0.068 0.4021620805 146 0.097 -0.287 -0.325 -0.010 -0.210 -0.064 0.4021580128 148 0.097 -0.287 -0.325 -0.010 -0.210 -0.037 0.4021560843 149 0.097 -0.287 -0.325 -0.010 -0.210 -0.049 0.4021484425 151 0.097 -0.287 -0.325 -0.010 -0.210 -0.048 0.4021483710 161 0.110 -0.287 -0.325 -0.010 -0.210 -0.048 0.4020705689 162 0.142 -0.287 -0.325 -0.010 -0.210 -0.048 0.4020480905 164 0.129 -0.287 -0.325 -0.010 -0.210 -0.048 0.4020316447 166 0.128 -0.287 -0.325 -0.010 -0.210 -0.048 0.4020316231 176 0.128 -0.299 -0.325 -0.010 -0.210 -0.048 0.4020206404 178 0.128 -0.298 -0.325 -0.010 -0.210 -0.048 0.4020205052 188 0.128 -0.298 -0.330 -0.010 -0.210 -0.048 0.4020108605 189 0.128 -0.298 -0.338 -0.010 -0.210 -0.048 0.4020043477 200 0.128 -0.298 -0.338 -0.015 -0.210 -0.048 0.4020024986 201 0.128 -0.298 -0.338 -0.016 -0.210 -0.048 0.4020024597 202 0.128 -0.298 -0.338 -0.017 -0.210 -0.048 0.4020022474 214 0.128 -0.298 -0.338 -0.017 -0.235 -0.048 0.4019737797 216 0.128 -0.298 -0.338 -0.017 -0.233 -0.048 0.4019735036 226 0.128 -0.298 -0.338 -0.017 -0.233 -0.047 0.4019723365 227 0.128 -0.298 -0.338 -0.017 -0.233 -0.037 0.4019697926 229 0.128 -0.298 -0.338 -0.017 -0.233 -0.039 0.4019696207 230 0.128 -0.298 -0.338 -0.017 -0.233 -0.038 0.4019695713 237 0.139 -0.303 -0.343 -0.019 -0.241 -0.034 0.4019553703 239 0.139 -0.303 -0.343 -0.019 -0.241 -0.035 0.4019552790 240 0.139 -0.303 -0.343 -0.019 -0.241 -0.035 0.4019552108 249 0.139 -0.303 -0.343 -0.019 -0.241 -0.040 0.4019530545 250 0.139 -0.303 -0.343 -0.019 -0.241 -0.043 0.4019523275 251 0.139 -0.303 -0.343 -0.019 -0.241 -0.045 0.4019520111 254 0.139 -0.303 -0.343 -0.019 -0.241 -0.051 0.4019515662 264 0.139 -0.301 -0.343 -0.019 -0.241 -0.051 0.4019500213 266 0.139 -0.297 -0.343 -0.019 -0.241 -0.051 0.4019491027 267 0.139 -0.298 -0.343 -0.019 -0.241 -0.051 0.4019490916 277 0.139 -0.298 -0.342 -0.019 -0.241 -0.051 0.4019489570 287 0.139 -0.298 -0.342 -0.013 -0.241 -0.051 0.4019469132 306 0.145 -0.300 -0.344 -0.014 -0.245 -0.049 0.4019430588 307 0.145 -0.300 -0.344 -0.014 -0.245 -0.049 0.4019429974 309 0.144 -0.300 -0.344 -0.014 -0.245 -0.049 0.4019428728 310 0.144 -0.300 -0.344 -0.014 -0.245 -0.049 0.4019427374 323 0.144 -0.300 -0.344 -0.014 -0.245 -0.057 0.4019424803 324 0.144 -0.300 -0.344 -0.014 -0.245 -0.054 0.4019422624 325 0.144 -0.300 -0.344 -0.014 -0.245 -0.055 0.4019420702 334 0.144 -0.296 -0.344 -0.014 -0.245 -0.055 0.4019382623 336 0.144 -0.292 -0.344 -0.014 -0.245 -0.055 0.4019374877 337 0.144 -0.293 -0.344 -0.014 -0.245 -0.055 0.4019374774 347 0.144 -0.293 -0.347 -0.014 -0.245 -0.055 0.4019368710 348 0.144 -0.293 -0.348 -0.014 -0.245 -0.055 0.4019368088 358 0.144 -0.293 -0.348 -0.009 -0.245 -0.055 0.4019343908 376 0.146 -0.294 -0.348 -0.010 -0.246 -0.054 0.4019340641 383 0.147 -0.287 -0.352 -0.005 -0.247 -0.060 0.4019329783 389 0.146 -0.290 -0.351 -0.007 -0.246 -0.058 0.4019324678 390 0.146 -0.289 -0.351 -0.006 -0.246 -0.058 0.4019322724 392 0.146 -0.289 -0.351 -0.006 -0.246 -0.058 0.4019322392 396 0.146 -0.289 -0.351 -0.006 -0.246 -0.058 0.4019320654 398 0.146 -0.289 -0.351 -0.006 -0.246 -0.058 0.4019320567 408 0.146 -0.289 -0.351 -0.006 -0.246 -0.060 0.4019319460 431 0.146 -0.289 -0.352 -0.006 -0.246 -0.060 0.4019319163 452 0.146 -0.289 -0.352 -0.006 -0.248 -0.060 0.4019316642 466 0.146 -0.289 -0.352 -0.006 -0.248 -0.060 0.4019316593 478 0.146 -0.289 -0.352 -0.006 -0.248 -0.061 0.4019314675 493 0.146 -0.289 -0.352 -0.006 -0.248 -0.061 0.4019314352 503 0.146 -0.289 -0.353 -0.006 -0.248 -0.061 0.4019314289 533 0.146 -0.290 -0.353 -0.007 -0.248 -0.061 0.4019313951 559 0.146 -0.290 -0.353 -0.007 -0.248 -0.061 0.4019313790 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.999997 1 -25.0 -25.0 25.0 1.011296 2 -25.0 25.0 -25.0 1.036320 3 -25.0 25.0 25.0 1.006262 4 25.0 -25.0 -25.0 1.043766 5 25.0 -25.0 25.0 1.027277 6 25.0 25.0 -25.0 1.018895 7 25.0 25.0 25.0 1.035563 REL: 8 0.401931 8.179374 1.022422 rel = 0.393117 Number of iterations 7 Min cost was 0.401931 Number of FunctionCalls 639 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 94.641000 sec Parameters at optimum (transmm) 0.14617 -0.28983 -0.35263 Parameters at optimum (rotdeg) -0.00678 -0.24804 -0.06055 Final costs ---------------- Number of surface hits 249202 WM Intensity 356.2217 +/- 150.1759 Ctx Intensity 482.5856 +/- 181.1256 Pct Contrast 28.5465 +/- 36.6572 Cost 0.4019 RelCost 0.4033 Reg at min cost was 0.988 0.122 -0.094 2.078; 0.106 -0.097 0.990 -43.903; 0.112 -0.988 -0.109 -6.222; 0.000 0.000 0.000 1.000; Writing optimal reg to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.988 0.118 -0.096 1.952; 0.107 -0.097 0.990 -43.610; 0.108 -0.988 -0.108 -5.883; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.004 -0.002 -0.126; 0.001 0.000 -0.000 0.293; -0.004 -0.001 0.001 0.339; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.580689 Computing change in rh position Surface RMS Diff (mm) 0.514780 0.706305 mri_segreg done tkregister2_cmdl --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /sw/global/applications/freesurfer/5.2.0/x86_64/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz reg file /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.988 0.122 -0.094 2.078; 0.106 -0.097 0.990 -43.903; 0.112 -0.988 -0.109 -6.222; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz Tmov: -------------------- -2.398 0.000 0.000 153.500; 0.000 0.000 2.400 -72.000; 0.000 -2.398 0.000 153.500; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.988 0.122 -0.094 2.078; 0.106 -0.097 0.990 -43.903; 0.112 -0.988 -0.109 -6.222; 0.000 0.000 0.000 1.000; Determinant 1 subject = 64-10-069-1_T1 RegMat --------------------------- 0.988 0.122 -0.094 2.078; 0.106 -0.097 0.990 -43.903; 0.112 -0.988 -0.109 -6.222; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -13.806, ref det = -1 Cleaning up Started at Tue Apr 9 13:58:32 CEST 2013 Ended at Tue Apr 9 14:02:05 CEST 2013 BBR-Run-Time-Sec 213 bbregister Done To check results, run: tkregister2 --mov /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.dat --surf convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anatorig.bbr.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -concat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2diff.bbr.mat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2anatorig.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anat.bbr.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat #------------------------------------- #@# Inter-subject registration Tue Apr 9 14:02:05 CEST 2013 flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_mni.nii.gz -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/mni2anat.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat -concat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/mni2diff.flt.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat -concat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/mni2diff.bbr.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2mni.mat -concat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2anat.mat convert_xfm -omat /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/mni2anatorig.mat -inverse /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Tue Apr 9 14:05:49 CEST 2013 mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 Found 443695 values in range Counting number of voxels Found 443695 voxels in final mask mri_binarize done mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 Found 468887 values in range Counting number of voxels Found 468887 voxels in final mask mri_binarize done mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 22935 values in range Counting number of voxels Found 22935 voxels in final mask mri_binarize done mri_aparc2aseg --s 64-10-069-1_T1 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /fastfs/igis/MRI_fs_rec_t1 subject 64-10-069-1_T1 outvol /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/surf/lh.white Reading lh pial surface /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/surf/lh.pial Loading lh annotations from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/surf/rh.white Reading rh pial surface /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/surf/rh.pial Loading rh annotations from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/ribbon.mgz Loading filled from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 832955 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 1 clusters 0 k 961.000000 Fixing Parahip RH WM Found 2 clusters 0 k 1.000000 1 k 737.000000 Writing output aseg to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 421042 values in range Counting number of voxels Found 421042 voxels in final mask mri_binarize done mri_binarize --i /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 683313 values in range Counting number of voxels Found 683313 voxels in final mask mri_binarize done mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 16 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fastfs/igis/MRI_fs_rec_dti/scripts cmdline mri_binarize --i /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz --match 16 --o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname n063 machine x86_64 user pfuhl input /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 17940 values in range Counting number of voxels Found 17940 voxels in final mask mri_binarize done fslmaths /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz -add /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/Brain-Stem.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/brainmask.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.9407e-08, 0) j_ras = (0, 0, -1) k_ras = (5.96046e-08, 1, 0) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz -mul /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fastfs/igis/MRI_fs_rec_t1/64-10-069-1_T1/mri/aparc+aseg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.9407e-08, 0) j_ras = (0, 0, -1) k_ras = (5.96046e-08, 1, 0) writing to /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/White-Matter.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/White-Matter.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter++.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/White-Matter++.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/White-Matter++.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/White-Matter++.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/notventricles.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/notventricles.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/notventricles.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/notventricles.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/cortex.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex+2mm.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm+bs.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex+2mm+bs.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/cortex+2mm+bs.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg+2mm.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg_mask.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg_mask.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/aparc+aseg_mask.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/anat_brain_mask.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask-vent.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/anat_brain_mask-vent.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/lowb.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz -k /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi_snr.txt flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/lowb_brain_mask.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/lowb_brain_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/lowb_brain_mask.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/lowb_brain_mask.nii.gz -ref /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/brain_anat_orig.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Tue Apr 9 14:14:05 CEST 2013 dtifit -k /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dwi.nii.gz -m /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvecs -b /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/bvals -o /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_FA.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L1.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L1.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L2.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L2.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L3.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L3.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_MD.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_MD.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_MO.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_MO.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_S0.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_S0.flt.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.flt.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L1.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L2.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_L3.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_MD.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_MO.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat flirt -in /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_S0.nii.gz -ref /sw/global/libraries/fsl/5.0.1/x86_64/data/standard/MNI152_T1_1mm_brain.nii.gz -out /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/diff2mni.bbr.mat #------------------------------------- #@# Priors Tue Apr 9 14:14:56 CEST 2013 /sw/global/applications/freesurfer/5.2.0/x86_64/bin/dmri_train --outdir /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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/subj33.64-10-069-1_T1.5004.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 dlabe l/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 /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg_mask.nii.gz --fa /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz --cptdir /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_dti/scripts cmdline /sw/global/applications/freesurfer/5.2.0/x86_64/bin/dmri_train --outdir /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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/subj33.64-10-069-1_T1.5004.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.cc g_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 /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg_mask.nii.gz --fa /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz --cptdir /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/diff --reg /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 n063 machine x86_64 user pfuhl Output directory: /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni Output directory in test subject's space: /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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/subj33.64-10-069-1_T1.5004.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: /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/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 /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/dtifit_FA.nii.gz Loading affine registration from /fastfs/igis/MRI_fs_rec_dti/64-10-069-1_T1/dmri/xfms/mni2diff.bbr.mat Loading streamline start ROI from /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz niiRead(): error opening file /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz ERROR: Could not read /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz Linux n063 2.6.32.49-0.3-default #1 SMP 2011-12-02 11:28:04 +0100 x86_64 x86_64 x86_64 GNU/Linux