mri_motion_correct.fsl log file $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ /usr/local/freesurfer/stable4/bin/mri_motion_correct.fsl /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 Linux node0313 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux Wed Dec 31 15:00:57 EST 2008 /usr/local/freesurfer/stable4/bin/mri_convert /usr/local/freesurfer/stable4/bin/flirt ----------------------------------------- Converting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/004.mgz Wed Dec 31 15:01:04 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -odt float mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/004.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -odt float $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/004.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from 0 to 3 (noscale = 0)... writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/005.mgz Wed Dec 31 15:01:08 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img -odt float mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/005.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img -odt float $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/005.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from 0 to 3 (noscale = 0)... writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/006.mgz Wed Dec 31 15:01:12 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/006.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img -odt float mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/006.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img -odt float $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/006.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from 0 to 3 (noscale = 0)... writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/007.mgz Wed Dec 31 15:01:15 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/007.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img -odt float mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/007.mgz /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img -odt float $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/orig/007.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from 0 to 3 (noscale = 0)... writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img Wed Dec 31 15:01:19 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 fsl_rigid_register -maxangle 90 -r /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -i /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img -o /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -tmpdir /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Wed Dec 31 15:01:19 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 tkregister2_cmdl --targ /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img --mov /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img --reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat --fslregout /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img movable volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img reg file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.4 2008/10/09 17:01:44 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img 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 0.000; 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 0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; register: file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 Init FSL Mat based on geometry ------------------- 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 calling eval flirt -in /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.hdr -out /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.hdr -init /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat -omat /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.fslmat -schedule /usr/local/freesurfer/stable4/bin/flirt.newdefault.20080811.sch -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Wed Dec 31 15:01:19 EST 2008 Ended at Wed Dec 31 15:05:34 EST 2008 fsl_rigid_register Done To check results, run: tkmedit -f /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -aux /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mv /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img ----------------------------------------- Motion Correcting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img Wed Dec 31 15:05:34 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 fsl_rigid_register -maxangle 90 -r /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -i /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img -o /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -tmpdir /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Wed Dec 31 15:05:34 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 tkregister2_cmdl --targ /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img --mov /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img --reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat --fslregout /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img movable volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img reg file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.4 2008/10/09 17:01:44 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img 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 0.000; 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 0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; register: file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 Init FSL Mat based on geometry ------------------- 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 calling eval flirt -in /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.hdr -out /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.hdr -init /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat -omat /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.fslmat -schedule /usr/local/freesurfer/stable4/bin/flirt.newdefault.20080811.sch -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Wed Dec 31 15:05:34 EST 2008 Ended at Wed Dec 31 15:09:33 EST 2008 fsl_rigid_register Done To check results, run: tkmedit -f /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -aux /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mv /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img ----------------------------------------- Motion Correcting /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img Wed Dec 31 15:09:34 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 fsl_rigid_register -maxangle 90 -r /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -i /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img -o /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -tmpdir /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Wed Dec 31 15:09:34 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.nii... -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 tkregister2_cmdl --targ /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img --mov /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img --reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat --fslregout /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img movable volume /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img reg file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.4 2008/10/09 17:01:44 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img 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 0.000; 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 0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; register: file /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 Init FSL Mat based on geometry ------------------- 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 -0.00000000 -0.00000000 -0.00000000 1.00000000 -0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 calling eval flirt -in /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/invol.fsl_rigid_register.hdr -out /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/refvol.fsl_rigid_register.hdr -init /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/initxfm.fslmat -omat /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.fslmat -schedule /usr/local/freesurfer/stable4/bin/flirt.newdefault.20080811.sch -------------------------------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Wed Dec 31 15:09:34 EST 2008 Ended at Wed Dec 31 15:13:27 EST 2008 fsl_rigid_register Done To check results, run: tkmedit -f /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img -aux /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img mv /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/resampled.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img ----------------------------------------- Averaging Wed Dec 31 15:13:27 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_average -noconform /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/avgvol.img inhibiting isotropic volume interpolation 1 of 4: reading /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-1.img... 2 of 4: reading /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-2.img... 3 of 4: reading /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-3.img... 4 of 4: reading /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/cor-4.img... writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/avgvol.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; alignment and averaging took 0 minutes and 27 seconds. -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting Average to output Wed Dec 31 15:13:54 EST 2008 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/avgvol.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0 mri_convert /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/avgvol.img /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0 $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/tmp-mri_motion_correct.fsl-9284/avgvol.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/test_subject_099/mri/rawavg.mgz... ----------------------------------------- Started at: Wed Dec 31 15:00:57 EST 2008 Ended at: Wed Dec 31 15:14:00 EST 2008 mri_motion_correct.fsl: done