BOTANICA:/usr/local/freesurfer/subjects/retinotopy> preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj12 -fsd bold -force -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.sj12.log -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ michelle setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj12 -fsd bold -force Mon Oct 3 15:34:45 EDT 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sj12 Template ----------------------------- mktemplate-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:34:46 EDT 2011 Detected input format at nii /usr/local/freesurfer/subjects/retinotopy mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/template.nii.gz --frame 0 mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/template.nii.gz --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) keeping frame 0 writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/template.nii.gz... Run: 001 ---------------- Mon Oct 3 15:34:48 EDT 2011 /usr/local/freesurfer/subjects/retinotopy mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/template.nii.gz --mid-frame mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) keeping frame 74 writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/template.nii.gz... Run: 002 ---------------- Mon Oct 3 15:34:50 EDT 2011 /usr/local/freesurfer/subjects/retinotopy mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/template.nii.gz --mid-frame mri_convert /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/f.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) keeping frame 74 writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/template.nii.gz... Mon Oct 3 15:34:52 EDT 2011 mktemplate-sess completed sj12 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sj12 -d /usr/local/freesurfer/subjects/retinotopy ------------------------------------------------ /usr/local/freesurfer/subjects/retinotopy/sj12 Mon Oct 3 15:34:52 EDT 2011 mkbrainmask -i template.nii -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_1638 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert template.nii /tmp/mkbrainmask_1638/in.nii mri_convert template.nii /tmp/mkbrainmask_1638/in.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to /tmp/mkbrainmask_1638/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/retinotopy/sj12/bold bet.fsl /tmp/mkbrainmask_1638/in.nii /tmp/mkbrainmask_1638/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_1638/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1638/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1638/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1638/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1638/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1638/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 47438 values in range Counting number of voxels Found 47438 voxels in final mask mri_binarize done Diliating 1 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_binarize --i /tmp/mkbrainmask_1638/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1638/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1638/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1638/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1638/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1638/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 47438 values in range Dilating 1 voxels in 3d Counting number of voxels Found 54416 voxels in final mask mri_binarize done /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert /tmp/mkbrainmask_1638/brain_mask.nii masks/brain.nii.gz mri_convert /tmp/mkbrainmask_1638/brain_mask.nii masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /tmp/mkbrainmask_1638/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mkbrainmask -i 001/template.nii -o 001/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_1797 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 001/template.nii /tmp/mkbrainmask_1797/in.nii mri_convert 001/template.nii /tmp/mkbrainmask_1797/in.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 001/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to /tmp/mkbrainmask_1797/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/retinotopy/sj12/bold bet.fsl /tmp/mkbrainmask_1797/in.nii /tmp/mkbrainmask_1797/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_1797/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1797/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1797/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1797/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1797/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1797/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 46787 values in range Counting number of voxels Found 46787 voxels in final mask mri_binarize done Diliating 1 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_binarize --i /tmp/mkbrainmask_1797/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1797/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1797/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1797/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1797/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1797/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 46787 values in range Dilating 1 voxels in 3d Counting number of voxels Found 53604 voxels in final mask mri_binarize done /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert /tmp/mkbrainmask_1797/brain_mask.nii 001/masks/brain.nii.gz mri_convert /tmp/mkbrainmask_1797/brain_mask.nii 001/masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /tmp/mkbrainmask_1797/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 001/masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input 001/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 001/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 49780 values in range Eroding 3 voxels in 3d Counting number of voxels Found 24897 voxels in final mask mri_binarize done meanval --i 001/f.nii --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat Mon Oct 3 15:35:05 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12/bold /usr/local/freesurfer/bin/meanval --i 001/f.nii --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.meanval.1917/blah.1917 --in 001/f.nii --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.meanval.1917/blah.1917 --in 001/f.nii --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat sysname Linux hostname BOTANICA machine x86_64 user michelle Loading 001/masks/brain.e3.nii.gz Loading 001/f.nii Voxel Volume is 26.9997 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 24897 672210 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to 001/global.meanval.dat 0 690.262 Writing to 001/global.waveform.dat mkbrainmask -i 002/template.nii -o 002/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_1968 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 002/template.nii /tmp/mkbrainmask_1968/in.nii mri_convert 002/template.nii /tmp/mkbrainmask_1968/in.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 002/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to /tmp/mkbrainmask_1968/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/retinotopy/sj12/bold bet.fsl /tmp/mkbrainmask_1968/in.nii /tmp/mkbrainmask_1968/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_1968/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1968/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1968/brain_mask.nii --min .01 --o /tmp/mkbrainmask_1968/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1968/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1968/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 46879 values in range Counting number of voxels Found 46879 voxels in final mask mri_binarize done Diliating 1 /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_binarize --i /tmp/mkbrainmask_1968/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1968/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i /tmp/mkbrainmask_1968/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_1968/brain_mask.nii sysname Linux hostname BOTANICA machine x86_64 user michelle input /tmp/mkbrainmask_1968/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_1968/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 46879 values in range Dilating 1 voxels in 3d Counting number of voxels Found 53752 voxels in final mask mri_binarize done /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert /tmp/mkbrainmask_1968/brain_mask.nii 002/masks/brain.nii.gz mri_convert /tmp/mkbrainmask_1968/brain_mask.nii 002/masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /tmp/mkbrainmask_1968/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 002/masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input 002/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 002/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 49952 values in range Eroding 3 voxels in 3d Counting number of voxels Found 25030 voxels in final mask mri_binarize done meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat Mon Oct 3 15:35:13 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12/bold /usr/local/freesurfer/bin/meanval --i 002/f.nii --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.meanval.2075/blah.2075 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.meanval.2075/blah.2075 --in 002/f.nii --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Linux hostname BOTANICA machine x86_64 user michelle Loading 002/masks/brain.e3.nii.gz Loading 002/f.nii Voxel Volume is 26.9997 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 25030 675801 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to 002/global.meanval.dat 0 688.813 Writing to 002/global.waveform.dat Mon Oct 3 15:35:16 EDT 2011 mkbrainmask-sess done sj12 Registration ----------------------------- register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run -------------------------------------------------------------- register-sess logfile is /usr/local/freesurfer/subjects/retinotopy/log/register-sess.sj12.log -------------------------------------------------------------- Mon Oct 3 15:35:16 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:35:16 EDT 2011 Run: 001 ---------------- Mon Oct 3 15:35:16 EDT 2011 -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 bbregister --s ld12 --init-fsl --6 --bold --mov bold/001/template.nii --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat Log file is bold/001/register.dof6.dat.log Mon Oct 3 15:35:16 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 /usr/local/freesurfer/bin/bbregister --s ld12 --init-fsl --6 --bold --mov bold/001/template.nii --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert bold/001/template.nii bold/001/tmp.bbregister.2203/template.nii mri_convert bold/001/template.nii bold/001/tmp.bbregister.2203/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/001/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to bold/001/tmp.bbregister.2203/template.nii... fslregister --s ld12 --mov bold/001/tmp.bbregister.2203/template.nii --reg bold/001/tmp.bbregister.2203/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.2203/fslregister --dof 6 Log file is bold/001/tmp.bbregister.2203/reg.init.dat.fslregister.log Mon Oct 3 15:35:16 EDT 2011 --s ld12 --mov bold/001/tmp.bbregister.2203/template.nii --reg bold/001/tmp.bbregister.2203/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.2203/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ BOTANICA Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 mri_convert /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz bold/001/tmp.bbregister.2203/fslregister/refvol.fslregister.nii mri_convert /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz bold/001/tmp.bbregister.2203/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz... TR=19.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.01863e-09, 0) j_ras = (3.72529e-09, -3.79471e-18, -1) k_ras = (-4.59841e-09, 1, 3.72529e-09) writing to bold/001/tmp.bbregister.2203/fslregister/refvol.fslregister.nii... -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 mri_convert bold/001/tmp.bbregister.2203/template.nii bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/001/tmp.bbregister.2203/template.nii bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/001/tmp.bbregister.2203/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) keeping frame 0 writing to bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii... Mov determinant is -26.9997 /usr/local/freesurfer/subjects/retinotopy/sj12 tkregister2_cmdl --mov bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii --reg bold/001/tmp.bbregister.2203/fslregister/reg0.2244.dat --regheader --fslregout bold/001/tmp.bbregister.2203/reg.init.dat.fsl.mat0 --s ld12 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii reg file bold/001/tmp.bbregister.2203/fslregister/reg0.2244.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 /usr/local/freesurfer/subjects/ld12/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 bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.000 0.000 0.000 96.000; 0.000 0.000 3.000 -34.500; 0.000 -3.000 0.000 96.000; 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 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; Determinant 1 subject = ld12 RegMat --------------------------- 1.000 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -26.9997, ref det = -1 Mon Oct 3 15:35:23 EDT 2011 /usr/local/freesurfer/subjects/retinotopy/sj12 flirt.fsl -ref bold/001/tmp.bbregister.2203/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.2203/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/etc/flirtsch/xyztrans.sch -init bold/001/tmp.bbregister.2203/reg.init.dat.fsl.mat0 Mon Oct 3 15:35:32 EDT 2011 /usr/local/freesurfer/subjects/retinotopy/sj12 flirt.fsl -ref bold/001/tmp.bbregister.2203/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.2203/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.2203/reg.init.dat.fsl.mat -init bold/001/tmp.bbregister.2203/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s ld12 --mov bold/001/tmp.bbregister.2203/template.nii --reg bold/001/tmp.bbregister.2203/reg.init.dat --fslreg bold/001/tmp.bbregister.2203/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 0.002 0.007 34.348; 0.007 -0.140 -0.990 193.490; -0.001 0.990 -0.140 36.359; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.2203/template.nii reg file bold/001/tmp.bbregister.2203/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 /usr/local/freesurfer/subjects/ld12/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 bold/001/tmp.bbregister.2203/template.nii Tmov: -------------------- -3.000 0.000 0.000 96.000; 0.000 0.000 3.000 -34.500; 0.000 -3.000 0.000 96.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -26.9997, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 0.001 0.007 2.950; -0.007 -0.140 0.990 18.187; 0.002 -0.990 -0.140 -4.117; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.001 0.007 2.950; -0.007 -0.140 0.990 18.187; 0.002 -0.990 -0.140 -4.117; 0.000 0.000 0.000 1.000; Determinant 1 subject = ld12 RegMat --------------------------- 1.000 0.001 0.007 2.950; -0.007 -0.140 0.990 18.187; 0.002 -0.990 -0.140 -4.117; 0.000 0.000 0.000 1.000; Started at Mon Oct 3 15:35:16 EDT 2011 Ended at Mon Oct 3 15:35:48 EDT 2011 fslregister Done To check results, run: tkregister2 --mov bold/001/tmp.bbregister.2203/template.nii --reg bold/001/tmp.bbregister.2203/reg.init.dat --surf orig mri_segreg --mov bold/001/tmp.bbregister.2203/template.nii --init-reg bold/001/tmp.bbregister.2203/reg.init.dat --out-reg bold/001/tmp.bbregister.2203/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 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 mri_segreg --mov bold/001/tmp.bbregister.2203/template.nii --init-reg bold/001/tmp.bbregister.2203/reg.init.dat --out-reg bold/001/tmp.bbregister.2203/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 BOTANICA machine x86_64 user michelle movvol bold/001/tmp.bbregister.2203/template.nii regfile bold/001/tmp.bbregister.2203/reg.init.dat subject ld12 dof 6 outregfile bold/001/tmp.bbregister.2203/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 1318599727 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 0.001 0.007 2.950; -0.007 -0.140 0.990 18.187; 0.002 -0.990 -0.140 -4.117; 0.000 0.000 0.000 1.000; Loading mov 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 1.071662 1 -25.0 -25.0 25.0 1.115086 2 -25.0 25.0 -25.0 1.087294 3 -25.0 25.0 25.0 1.064325 4 25.0 -25.0 -25.0 1.001309 5 25.0 -25.0 25.0 1.008142 6 25.0 25.0 -25.0 1.024039 7 25.0 25.0 25.0 1.073412 REL: 8 1.119908 8.445269 1.055659 rel = 1.06086 Initial costs ---------------- Number of surface hits 1958 WM Intensity 681.3599 +/- 116.5689 Ctx Intensity 667.1597 +/- 137.1526 Pct Contrast -3.1228 +/- 16.7112 Cost 1.1199 RelCost 1.0609 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9899 0.9899 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9279 0.9279 0.0 Brute Force -------------------------- Min cost was 0.927944 Number of iterations 729 Search time 4.722000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 -4.000 0.000 -4.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 -4 3 0 4 -4 5 -4 5 -4.618 -4.000 -4.000 0.000 -4.000 -4.000 0.9278140336 7 -4.335 -4.000 -4.000 0.000 -4.000 -4.000 0.9266452634 8 -4.317 -4.000 -4.000 0.000 -4.000 -4.000 0.9265053929 10 -4.271 -4.000 -4.000 0.000 -4.000 -4.000 0.9264909633 11 -4.293 -4.000 -4.000 0.000 -4.000 -4.000 0.9263761665 13 -4.290 -4.000 -4.000 0.000 -4.000 -4.000 0.9263724168 15 -4.287 -4.000 -4.000 0.000 -4.000 -4.000 0.9263703890 20 -4.287 -5.618 -4.000 0.000 -4.000 -4.000 0.9077254347 26 -4.287 -5.581 -4.000 0.000 -4.000 -4.000 0.9073732820 29 -4.287 -5.583 -4.000 0.000 -4.000 -4.000 0.9073585368 33 -4.287 -5.583 -3.000 0.000 -4.000 -4.000 0.8933383441 36 -4.287 -5.583 -2.382 0.000 -4.000 -4.000 0.8880676751 38 -4.287 -5.583 -2.551 0.000 -4.000 -4.000 0.8861508696 40 -4.287 -5.583 -2.526 0.000 -4.000 -4.000 0.8860642287 43 -4.287 -5.583 -2.528 0.000 -4.000 -4.000 0.8860637427 57 -4.287 -5.583 -2.528 -0.044 -4.000 -4.000 0.8857963165 60 -4.287 -5.583 -2.528 -0.055 -4.000 -4.000 0.8857392301 63 -4.287 -5.583 -2.528 -0.057 -4.000 -4.000 0.8857280764 67 -4.287 -5.583 -2.528 -0.057 -3.000 -4.000 0.8844357493 71 -4.287 -5.583 -2.528 -0.057 -3.382 -4.000 0.8820500897 72 -4.287 -5.583 -2.528 -0.057 -3.373 -4.000 0.8819169842 73 -4.287 -5.583 -2.528 -0.057 -3.247 -4.000 0.8816201199 75 -4.287 -5.583 -2.528 -0.057 -3.297 -4.000 0.8815666249 78 -4.287 -5.583 -2.528 -0.057 -3.308 -4.000 0.8815615615 80 -4.287 -5.583 -2.528 -0.057 -3.303 -4.000 0.8815543824 89 -4.287 -5.583 -2.528 -0.057 -3.303 -3.926 0.8815021623 90 -4.287 -5.583 -2.528 -0.057 -3.303 -3.947 0.8814779502 91 -4.287 -5.583 -2.528 -0.057 -3.303 -3.953 0.8814754590 92 -4.287 -5.583 -2.528 -0.057 -3.303 -3.958 0.8814752375 95 -4.287 -5.583 -2.528 -0.057 -3.303 -3.959 0.8814751202 104 -4.294 -5.583 -2.528 -0.057 -3.303 -3.959 0.8814130232 106 -4.305 -5.583 -2.528 -0.057 -3.303 -3.959 0.8813727765 115 -4.305 -5.700 -2.528 -0.057 -3.303 -3.959 0.8803968272 120 -4.305 -5.695 -2.528 -0.057 -3.303 -3.959 0.8803684945 130 -4.305 -5.695 -2.566 -0.057 -3.303 -3.959 0.8803130627 131 -4.305 -5.695 -2.644 -0.057 -3.303 -3.959 0.8802520645 135 -4.305 -5.695 -2.650 -0.057 -3.303 -3.959 0.8802494548 138 -4.305 -5.695 -2.649 -0.057 -3.303 -3.959 0.8802492640 139 -4.305 -5.695 -2.647 -0.057 -3.303 -3.959 0.8802492385 141 -4.305 -5.695 -2.648 -0.057 -3.303 -3.959 0.8802491124 148 -4.305 -5.695 -2.648 -0.222 -3.303 -3.959 0.8796407039 150 -4.305 -5.695 -2.648 -0.148 -3.303 -3.959 0.8794073738 152 -4.305 -5.695 -2.648 -0.165 -3.303 -3.959 0.8793896965 153 -4.305 -5.695 -2.648 -0.163 -3.303 -3.959 0.8793891575 165 -4.305 -5.695 -2.648 -0.163 -3.306 -3.959 0.8793834644 167 -4.305 -5.695 -2.648 -0.163 -3.313 -3.959 0.8793801477 168 -4.305 -5.695 -2.648 -0.163 -3.310 -3.959 0.8793793109 169 -4.305 -5.695 -2.648 -0.163 -3.311 -3.959 0.8793793109 176 -4.305 -5.695 -2.648 -0.163 -3.311 -3.952 0.8793687354 187 -4.370 -5.695 -2.648 -0.163 -3.311 -3.952 0.8784850555 192 -4.369 -5.695 -2.648 -0.163 -3.311 -3.952 0.8784843422 202 -4.369 -5.704 -2.648 -0.163 -3.311 -3.952 0.8784635586 204 -4.369 -5.706 -2.648 -0.163 -3.311 -3.952 0.8784629844 217 -4.369 -5.706 -2.629 -0.163 -3.311 -3.952 0.8784382398 218 -4.369 -5.706 -2.626 -0.163 -3.311 -3.952 0.8784370522 219 -4.369 -5.706 -2.622 -0.163 -3.311 -3.952 0.8784365859 220 -4.369 -5.706 -2.623 -0.163 -3.311 -3.952 0.8784364046 230 -4.369 -5.706 -2.623 -0.186 -3.311 -3.952 0.8783400458 231 -4.369 -5.706 -2.623 -0.196 -3.311 -3.952 0.8783211812 232 -4.369 -5.706 -2.623 -0.203 -3.311 -3.952 0.8783157117 245 -4.369 -5.706 -2.623 -0.203 -3.289 -3.952 0.8781821783 246 -4.369 -5.706 -2.623 -0.203 -3.276 -3.952 0.8781784245 247 -4.369 -5.706 -2.623 -0.203 -3.281 -3.952 0.8781704683 248 -4.369 -5.706 -2.623 -0.203 -3.282 -3.952 0.8781701103 256 -4.369 -5.706 -2.623 -0.203 -3.282 -3.979 0.8781668177 257 -4.369 -5.706 -2.623 -0.203 -3.282 -3.967 0.8781438210 258 -4.369 -5.706 -2.623 -0.203 -3.282 -3.966 0.8781430436 259 -4.369 -5.706 -2.623 -0.203 -3.282 -3.963 0.8781421038 262 -4.369 -5.706 -2.623 -0.203 -3.282 -3.964 0.8781420546 272 -4.382 -5.706 -2.623 -0.203 -3.282 -3.964 0.8780841130 274 -4.379 -5.706 -2.623 -0.203 -3.282 -3.964 0.8780777358 276 -4.378 -5.706 -2.623 -0.203 -3.282 -3.964 0.8780773506 291 -4.378 -5.707 -2.623 -0.203 -3.282 -3.964 0.8780683891 298 -4.378 -5.707 -2.460 -0.203 -3.282 -3.964 0.8773408093 299 -4.378 -5.707 -2.445 -0.203 -3.282 -3.964 0.8773125544 300 -4.378 -5.707 -2.380 -0.203 -3.282 -3.964 0.8772613468 302 -4.378 -5.707 -2.387 -0.203 -3.282 -3.964 0.8772559071 303 -4.378 -5.707 -2.397 -0.203 -3.282 -3.964 0.8772545371 304 -4.378 -5.707 -2.394 -0.203 -3.282 -3.964 0.8772542964 305 -4.378 -5.707 -2.395 -0.203 -3.282 -3.964 0.8772542597 313 -4.378 -5.707 -2.395 -0.283 -3.282 -3.964 0.8767000029 314 -4.378 -5.707 -2.395 -0.305 -3.282 -3.964 0.8763671182 315 -4.378 -5.707 -2.395 -0.347 -3.282 -3.964 0.8760520004 316 -4.378 -5.707 -2.395 -0.357 -3.282 -3.964 0.8760319147 317 -4.378 -5.707 -2.395 -0.363 -3.282 -3.964 0.8760258623 318 -4.378 -5.707 -2.395 -0.366 -3.282 -3.964 0.8760241076 320 -4.378 -5.707 -2.395 -0.370 -3.282 -3.964 0.8760238165 323 -4.378 -5.707 -2.395 -0.372 -3.282 -3.964 0.8760235369 334 -4.378 -5.707 -2.395 -0.372 -3.280 -3.964 0.8760061508 335 -4.378 -5.707 -2.395 -0.372 -3.256 -3.964 0.8758798823 338 -4.378 -5.707 -2.395 -0.372 -3.255 -3.964 0.8758797483 352 -4.378 -5.707 -2.395 -0.372 -3.255 -3.966 0.8758782310 354 -4.378 -5.707 -2.395 -0.372 -3.255 -3.967 0.8758779419 365 -4.387 -5.707 -2.395 -0.372 -3.255 -3.967 0.8758054482 369 -4.388 -5.707 -2.395 -0.372 -3.255 -3.967 0.8758045296 393 -4.388 -5.707 -2.383 -0.372 -3.255 -3.967 0.8758010202 396 -4.388 -5.707 -2.384 -0.372 -3.255 -3.967 0.8758009638 407 -4.388 -5.707 -2.384 -0.367 -3.255 -3.967 0.8757990422 419 -4.388 -5.707 -2.384 -0.368 -3.243 -3.967 0.8757897793 420 -4.388 -5.707 -2.384 -0.368 -3.244 -3.967 0.8757894746 433 -4.388 -5.707 -2.384 -0.368 -3.244 -3.970 0.8757829182 436 -4.398 -5.707 -2.373 -0.363 -3.233 -3.973 0.8757774376 442 -4.394 -5.707 -2.377 -0.365 -3.237 -3.972 0.8757715791 444 -4.392 -5.707 -2.380 -0.366 -3.240 -3.971 0.8757706415 449 -4.392 -5.707 -2.380 -0.366 -3.240 -3.971 0.8757706268 488 -4.392 -5.707 -2.385 -0.366 -3.240 -3.971 0.8757647711 489 -4.392 -5.707 -2.389 -0.366 -3.240 -3.971 0.8757642390 490 -4.392 -5.707 -2.388 -0.366 -3.240 -3.971 0.8757641223 501 -4.392 -5.707 -2.388 -0.361 -3.240 -3.971 0.8757631742 502 -4.392 -5.707 -2.388 -0.362 -3.240 -3.971 0.8757631175 503 -4.392 -5.707 -2.388 -0.363 -3.240 -3.971 0.8757631143 515 -4.392 -5.707 -2.388 -0.363 -3.231 -3.971 0.8757540958 523 -4.396 -5.707 -2.384 -0.361 -3.227 -3.972 0.8757455693 526 -4.395 -5.707 -2.384 -0.361 -3.227 -3.972 0.8757455570 527 -4.395 -5.707 -2.384 -0.361 -3.227 -3.972 0.8757454417 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.007833 1 -25.0 -25.0 25.0 1.038531 2 -25.0 25.0 -25.0 1.014251 3 -25.0 25.0 25.0 0.995954 4 25.0 -25.0 -25.0 1.048261 5 25.0 -25.0 25.0 1.032191 6 25.0 25.0 -25.0 0.996664 7 25.0 25.0 25.0 1.056951 REL: 8 0.875745 8.190637 1.023830 rel = 0.855363 Number of iterations 5 Min cost was 0.875745 Number of FunctionCalls 531 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.957000 sec Parameters at optimum (transmm) -4.39534 -5.70678 -2.38379 Parameters at optimum (rotdeg) -0.36127 -3.22696 -3.97205 Final costs ---------------- Number of surface hits 2130 WM Intensity 646.2827 +/- 157.2973 Ctx Intensity 643.7324 +/- 178.5164 Pct Contrast -2.1110 +/- 24.4764 Cost 0.8757 RelCost 1.0609 Reg at min cost was 0.995 0.047 0.084 0.038; -0.076 -0.150 0.986 12.189; 0.059 -0.988 -0.146 -6.443; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/tmp.bbregister.2203/bbr.pass1.dat, type = 14 Original Reg 1.000 0.001 0.007 2.950; -0.007 -0.140 0.990 18.187; 0.002 -0.990 -0.140 -4.117; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.005 -0.045 -0.077 2.911; 0.069 0.010 0.004 5.997; -0.056 -0.003 0.006 2.326; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 7.275973 Computing change in rh position Surface RMS Diff (mm) 8.313471 12.645205 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/001/tmp.bbregister.2203/template.nii --init-reg bold/001/tmp.bbregister.2203/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.2203/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 mri_segreg --mov bold/001/tmp.bbregister.2203/template.nii --init-reg bold/001/tmp.bbregister.2203/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.2203/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname BOTANICA machine x86_64 user michelle movvol bold/001/tmp.bbregister.2203/template.nii regfile bold/001/tmp.bbregister.2203/bbr.pass1.dat subject ld12 dof 6 outregfile bold/001/register.dof6.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 1318074154 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.995 0.047 0.084 0.038; -0.076 -0.150 0.986 12.189; 0.059 -0.988 -0.146 -6.443; 0.000 0.000 0.000 1.000; Loading mov 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 1.038394 1 -25.0 -25.0 25.0 1.046368 2 -25.0 25.0 -25.0 1.057134 3 -25.0 25.0 25.0 1.022420 4 25.0 -25.0 -25.0 1.050717 5 25.0 -25.0 25.0 1.022613 6 25.0 25.0 -25.0 1.017661 7 25.0 25.0 25.0 1.046234 REL: 8 0.931348 8.301541 1.037693 rel = 0.897518 Initial costs ---------------- Number of surface hits 211887 WM Intensity 651.4462 +/- 152.3470 Ctx Intensity 647.7569 +/- 173.5675 Pct Contrast -2.3827 +/- 22.9014 Cost 0.9313 RelCost 0.8975 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8815 0.8815 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8806 0.8806 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8801 0.8801 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.8796 0.8796 0.0 20 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.8792 0.8792 0.0 22 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.8791 0.8791 0.0 23 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.8786 0.8786 0.0 49 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.8785 0.8785 0.0 50 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.8780 0.8780 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8776 0.8776 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.8774 0.8774 0.0 151 -0.1000 0.0000 0.1000 0.0000 0.1000 0.0000 0.8773 0.8773 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.8769 0.8769 0.0 307 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.0000 0.8769 0.8769 0.0 310 0.0000 -0.1000 0.1000 0.0000 0.0000 0.0000 0.8768 0.8768 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.8765 0.8765 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8757 0.8757 0.0 Brute Force -------------------------- Min cost was 0.875745 Number of iterations 729 Search time 4.846000 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 2 1.000 0.000 0.000 0.000 0.000 0.000 0.9256006829 5 1.618 0.000 0.000 0.000 0.000 0.000 0.9250178235 7 1.423 0.000 0.000 0.000 0.000 0.000 0.9249090988 8 1.442 0.000 0.000 0.000 0.000 0.000 0.9248844165 11 1.449 0.000 0.000 0.000 0.000 0.000 0.9248809521 12 1.450 0.000 0.000 0.000 0.000 0.000 0.9248808893 18 1.450 -0.618 0.000 0.000 0.000 0.000 0.9245617482 20 1.450 -0.545 0.000 0.000 0.000 0.000 0.9244392927 21 1.450 -0.337 0.000 0.000 0.000 0.000 0.9242398170 24 1.450 -0.341 0.000 0.000 0.000 0.000 0.9242291690 27 1.450 -0.342 0.000 0.000 0.000 0.000 0.9242229297 33 1.450 -0.342 -0.618 0.000 0.000 0.000 0.9212647791 35 1.450 -0.342 -0.700 0.000 0.000 0.000 0.9212382471 45 1.450 -0.342 -0.704 1.000 0.000 0.000 0.9141262984 50 1.450 -0.342 -0.704 1.103 0.000 0.000 0.9140254342 55 1.450 -0.342 -0.704 1.099 0.000 0.000 0.9140226973 60 1.450 -0.342 -0.704 1.099 1.000 0.000 0.9127442850 64 1.450 -0.342 -0.704 1.099 0.618 0.000 0.9117955975 66 1.450 -0.342 -0.704 1.099 0.587 0.000 0.9117652587 68 1.450 -0.342 -0.704 1.099 0.501 0.000 0.9116984953 70 1.450 -0.342 -0.704 1.099 0.512 0.000 0.9116954056 71 1.450 -0.342 -0.704 1.099 0.522 0.000 0.9116951747 72 1.450 -0.342 -0.704 1.099 0.518 0.000 0.9116946037 76 1.450 -0.342 -0.704 1.099 0.518 1.000 0.9110228233 80 1.450 -0.342 -0.704 1.099 0.518 0.618 0.9103606702 81 1.450 -0.342 -0.704 1.099 0.518 0.673 0.9102940185 83 1.450 -0.342 -0.704 1.099 0.518 0.682 0.9102808449 85 1.450 -0.342 -0.704 1.099 0.518 0.681 0.9102794382 89 2.450 -0.342 -0.704 1.099 0.518 0.681 0.9069234832 93 2.068 -0.342 -0.704 1.099 0.518 0.681 0.9064133196 94 2.154 -0.342 -0.704 1.099 0.518 0.681 0.9063104801 101 2.155 -0.342 -0.704 1.099 0.518 0.681 0.9063104627 104 2.155 -1.961 -0.704 1.099 0.518 0.681 0.9051536999 105 2.155 -1.193 -0.704 1.099 0.518 0.681 0.9021607317 109 2.155 -1.122 -0.704 1.099 0.518 0.681 0.9020563082 110 2.155 -1.071 -0.704 1.099 0.518 0.681 0.9020393460 111 2.155 -1.079 -0.704 1.099 0.518 0.681 0.9020230605 112 2.155 -1.093 -0.704 1.099 0.518 0.681 0.9020168875 114 2.155 -1.090 -0.704 1.099 0.518 0.681 0.9020038741 115 2.155 -1.087 -0.704 1.099 0.518 0.681 0.9019982234 116 2.155 -1.086 -0.704 1.099 0.518 0.681 0.9019946608 124 2.155 -1.086 -0.322 1.099 0.518 0.681 0.9018115957 125 2.155 -1.086 -0.477 1.099 0.518 0.681 0.9016550201 126 2.155 -1.086 -0.476 1.099 0.518 0.681 0.9016549053 128 2.155 -1.086 -0.473 1.099 0.518 0.681 0.9016546899 129 2.155 -1.086 -0.472 1.099 0.518 0.681 0.9016546748 136 2.155 -1.086 -0.472 1.481 0.518 0.681 0.9010589720 137 2.155 -1.086 -0.472 1.490 0.518 0.681 0.9010551529 138 2.155 -1.086 -0.472 1.559 0.518 0.681 0.9009932222 140 2.155 -1.086 -0.472 1.638 0.518 0.681 0.9009803780 144 2.155 -1.086 -0.472 1.656 0.518 0.681 0.9009691416 147 2.155 -1.086 -0.472 1.658 0.518 0.681 0.9009641403 151 2.155 -1.086 -0.472 1.658 1.518 0.681 0.9000889899 155 2.155 -1.086 -0.472 1.658 1.136 0.681 0.8988607163 156 2.155 -1.086 -0.472 1.658 1.108 0.681 0.8988317685 157 2.155 -1.086 -0.472 1.658 1.024 0.681 0.8987905650 160 2.155 -1.086 -0.472 1.658 1.023 0.681 0.8987905568 163 2.155 -1.086 -0.472 1.658 1.023 1.681 0.8965014517 167 2.155 -1.086 -0.472 1.658 1.023 1.299 0.8958042939 168 2.155 -1.086 -0.472 1.658 1.023 1.304 0.8957837507 170 2.155 -1.086 -0.472 1.658 1.023 1.354 0.8957481296 179 2.860 -1.829 -0.241 2.216 1.528 2.027 0.8805555637 182 4.001 -3.031 0.134 3.120 2.345 3.116 0.8404183881 183 5.846 -4.977 0.741 4.583 3.666 4.878 0.8066187699 186 5.141 -4.234 0.510 4.024 3.161 4.205 0.8005076576 188 5.327 -4.429 0.570 4.171 3.294 4.382 0.7985322551 190 5.334 -4.437 0.573 4.177 3.300 4.389 0.7985118043 191 5.343 -4.447 0.576 4.184 3.306 4.397 0.7984987296 194 5.341 -4.444 0.575 4.182 3.304 4.395 0.7984974139 197 5.340 -4.443 0.575 4.181 3.303 4.394 0.7984940320 201 3.722 -4.443 0.575 4.181 3.303 4.394 0.7895419067 202 4.253 -4.443 0.575 4.181 3.303 4.394 0.7857733168 206 4.306 -4.443 0.575 4.181 3.303 4.394 0.7857263319 208 4.313 -4.443 0.575 4.181 3.303 4.394 0.7857256669 209 4.312 -4.443 0.575 4.181 3.303 4.394 0.7857256613 212 4.312 -4.443 0.575 4.181 3.303 5.394 0.7793826534 217 4.312 -4.443 0.575 4.181 3.303 5.223 0.7791169209 218 4.312 -4.443 0.575 4.181 3.303 5.229 0.7791045810 223 4.312 -4.443 0.575 4.181 3.303 5.230 0.7791017936 225 4.312 -4.443 1.575 4.181 3.303 5.230 0.7647761816 230 4.312 -4.443 1.644 4.181 3.303 5.230 0.7646489286 232 4.312 -4.443 1.671 4.181 3.303 5.230 0.7646372529 234 4.312 -4.443 1.668 4.181 3.303 5.230 0.7646371854 236 4.312 -4.443 1.669 4.181 3.303 5.230 0.7646371511 240 4.312 -4.443 1.670 2.563 3.303 5.230 0.7522779307 241 4.312 -4.443 1.670 3.054 3.303 5.230 0.7484020951 245 4.312 -4.443 1.670 3.141 3.303 5.230 0.7482699965 247 4.312 -4.443 1.670 3.131 3.303 5.230 0.7482593041 258 4.312 -4.443 1.670 3.131 3.685 5.230 0.7469803921 259 4.312 -4.443 1.670 3.131 3.602 5.230 0.7468871724 260 4.312 -4.443 1.670 3.131 3.606 5.230 0.7468811729 270 3.877 -3.984 1.527 2.786 3.294 4.814 0.7453170761 272 4.065 -4.182 1.589 2.935 3.429 4.994 0.7429686988 286 4.447 -4.182 1.589 2.935 3.429 4.994 0.7403619379 287 4.482 -4.182 1.589 2.935 3.429 4.994 0.7403465182 289 4.486 -4.182 1.589 2.935 3.429 4.994 0.7403463268 298 4.487 -4.182 1.589 2.935 3.429 4.894 0.7401666827 299 4.487 -4.182 1.589 2.935 3.429 4.876 0.7401287782 303 4.487 -4.182 1.589 2.935 3.429 4.868 0.7401161229 305 4.487 -4.182 1.589 2.935 3.429 4.870 0.7401087146 310 4.487 -4.182 2.589 2.935 3.429 4.870 0.7244983450 315 4.487 -4.182 2.770 2.935 3.429 4.870 0.7239976490 316 4.487 -4.182 2.779 2.935 3.429 4.870 0.7239880812 317 4.487 -4.182 2.833 2.935 3.429 4.870 0.7239778306 319 4.487 -4.182 2.813 2.935 3.429 4.870 0.7239663354 329 4.487 -4.182 2.815 2.317 3.429 4.870 0.7234135715 331 4.487 -4.182 2.815 2.599 3.429 4.870 0.7218364563 340 4.487 -4.182 2.815 2.599 4.429 4.870 0.7189346214 344 4.487 -4.182 2.815 2.599 4.047 4.870 0.7161004777 354 4.487 -4.182 2.815 2.599 4.046 4.870 0.7161001436 359 4.051 -3.723 2.672 2.254 3.734 4.454 0.7075824964 361 4.148 -3.825 2.703 2.330 3.803 4.547 0.7066159704 362 4.156 -3.834 2.706 2.338 3.810 4.555 0.7065763993 364 4.171 -3.849 2.711 2.349 3.820 4.569 0.7065225528 365 4.174 -3.853 2.712 2.351 3.822 4.572 0.7065153626 367 4.175 -3.853 2.712 2.352 3.823 4.572 0.7065145789 369 4.284 -3.525 3.836 1.768 4.216 4.151 0.6936612392 376 4.268 -3.572 3.672 1.853 4.159 4.212 0.6932790172 377 4.269 -3.570 3.681 1.849 4.162 4.209 0.6932719002 378 4.271 -3.565 3.696 1.841 4.167 4.203 0.6932440133 380 4.273 -3.559 3.716 1.830 4.174 4.196 0.6932351047 381 4.272 -3.561 3.712 1.833 4.173 4.197 0.6932290762 383 4.272 -3.561 3.710 1.833 4.172 4.198 0.6932267779 384 4.272 -3.562 3.709 1.834 4.172 4.198 0.6932190550 390 4.654 -3.562 3.709 1.834 4.172 4.198 0.6917555703 391 4.574 -3.562 3.709 1.834 4.172 4.198 0.6916703947 392 4.581 -3.562 3.709 1.834 4.172 4.198 0.6916687951 422 4.582 -3.562 3.709 2.834 4.172 4.198 0.6900819143 426 4.582 -3.562 3.709 2.452 4.172 4.198 0.6862040901 427 4.582 -3.562 3.709 2.402 4.172 4.198 0.6861642312 428 4.582 -3.562 3.709 2.409 4.172 4.198 0.6861633913 431 4.582 -3.562 3.709 2.408 4.172 4.198 0.6861583045 438 4.582 -3.562 3.709 2.408 4.337 4.198 0.6856194300 440 4.582 -3.562 3.709 2.408 4.299 4.198 0.6856095808 442 4.582 -3.562 3.709 2.408 4.316 4.198 0.6856044216 445 4.582 -3.562 3.709 2.408 4.317 4.198 0.6856040912 447 4.582 -3.562 3.709 2.408 4.318 4.198 0.6856036532 448 4.582 -3.562 3.709 2.408 4.319 4.198 0.6856035639 458 4.581 -3.565 3.696 2.414 4.315 4.203 0.6856035141 460 4.581 -3.563 3.703 2.411 4.317 4.201 0.6855911686 461 4.581 -3.563 3.704 2.410 4.317 4.200 0.6855885490 470 4.560 -3.563 3.704 2.410 4.317 4.200 0.6855721985 472 4.557 -3.563 3.704 2.410 4.317 4.200 0.6855719744 474 4.558 -3.563 3.704 2.410 4.317 4.200 0.6855719700 496 4.427 -3.425 3.661 2.307 4.224 4.076 0.6836796938 497 4.429 -3.427 3.661 2.308 4.225 4.077 0.6836720556 500 4.430 -3.428 3.662 2.309 4.226 4.078 0.6836628695 509 4.430 -3.428 3.662 2.415 4.226 4.078 0.6834750941 510 4.430 -3.428 3.662 2.410 4.226 4.078 0.6834633368 511 4.430 -3.428 3.662 2.384 4.226 4.078 0.6834415270 513 4.430 -3.428 3.662 2.388 4.226 4.078 0.6834290390 516 4.430 -3.428 3.662 2.387 4.226 4.078 0.6834286610 524 4.430 -3.428 3.662 2.387 4.386 4.078 0.6829203588 525 4.430 -3.428 3.662 2.387 4.388 4.078 0.6829193035 526 4.430 -3.428 3.662 2.387 4.402 4.078 0.6829112744 530 4.430 -3.428 3.662 2.387 4.408 4.078 0.6829074054 539 4.433 -3.420 3.690 2.372 4.418 4.068 0.6828206734 552 4.376 -3.365 3.685 2.357 4.456 4.017 0.6826307575 553 4.386 -3.375 3.686 2.360 4.449 4.026 0.6825961493 565 4.526 -3.375 3.686 2.360 4.449 4.026 0.6823962920 566 4.506 -3.375 3.686 2.360 4.449 4.026 0.6823798736 567 4.494 -3.375 3.686 2.360 4.449 4.026 0.6823741191 569 4.488 -3.375 3.686 2.360 4.449 4.026 0.6823732430 578 4.488 -3.375 3.686 2.360 4.449 4.160 0.6819291075 579 4.488 -3.375 3.686 2.360 4.449 4.165 0.6819172333 582 4.488 -3.375 3.686 2.360 4.449 4.171 0.6819150354 583 4.488 -3.375 3.686 2.360 4.449 4.169 0.6819044987 595 4.487 -3.375 3.684 2.361 4.449 4.170 0.6819042344 603 4.487 -3.375 3.684 2.368 4.449 4.170 0.6819021625 604 4.487 -3.375 3.684 2.372 4.449 4.170 0.6818904900 607 4.487 -3.375 3.684 2.374 4.449 4.170 0.6818835179 615 4.487 -3.375 3.684 2.374 4.355 4.170 0.6817392387 617 4.487 -3.375 3.684 2.374 4.358 4.170 0.6817387868 625 4.431 -3.320 3.679 2.359 4.396 4.119 0.6815268339 626 4.437 -3.327 3.680 2.361 4.391 4.125 0.6814821205 629 4.438 -3.327 3.680 2.361 4.391 4.125 0.6814780096 632 4.438 -3.327 3.680 2.361 4.391 4.125 0.6814763256 633 4.443 -3.235 3.670 2.350 4.364 4.183 0.6808843976 640 4.444 -3.220 3.668 2.348 4.360 4.193 0.6808492423 646 4.444 -3.220 3.668 2.348 4.360 4.193 0.6808487237 654 4.583 -3.220 3.668 2.348 4.360 4.193 0.6806082716 655 4.571 -3.220 3.668 2.348 4.360 4.193 0.6806023798 657 4.568 -3.220 3.668 2.348 4.360 4.193 0.6806023229 670 4.568 -3.218 3.668 2.348 4.361 4.192 0.6806013306 679 4.563 -3.235 3.610 2.378 4.340 4.214 0.6805211722 682 4.562 -3.236 3.608 2.379 4.340 4.214 0.6805185412 690 4.562 -3.236 3.608 2.497 4.340 4.214 0.6802073736 691 4.562 -3.236 3.608 2.501 4.340 4.214 0.6801888968 693 4.562 -3.236 3.608 2.534 4.340 4.214 0.6801674720 695 4.562 -3.236 3.608 2.527 4.340 4.214 0.6801571587 696 4.562 -3.236 3.608 2.526 4.340 4.214 0.6801484726 698 4.562 -3.236 3.608 2.525 4.340 4.214 0.6801444291 705 4.562 -3.236 3.608 2.525 4.308 4.214 0.6801138726 706 4.562 -3.236 3.608 2.525 4.297 4.214 0.6800990889 716 4.568 -3.143 3.598 2.515 4.270 4.272 0.6800630801 720 4.566 -3.179 3.602 2.519 4.280 4.250 0.6799850541 723 4.565 -3.180 3.602 2.519 4.281 4.249 0.6799776514 727 4.565 -3.180 3.602 2.519 4.281 4.249 0.6799735398 728 4.565 -3.180 3.602 2.519 4.280 4.249 0.6799730761 737 4.605 -3.180 3.602 2.519 4.280 4.249 0.6799610690 738 4.594 -3.180 3.602 2.519 4.280 4.249 0.6799599063 739 4.596 -3.180 3.602 2.519 4.280 4.249 0.6799598967 750 4.595 -3.180 3.602 2.519 4.281 4.249 0.6799586436 775 4.595 -3.180 3.602 2.546 4.281 4.249 0.6799341635 776 4.595 -3.180 3.602 2.536 4.281 4.249 0.6799248771 777 4.595 -3.180 3.602 2.537 4.281 4.249 0.6799238238 785 4.595 -3.180 3.602 2.537 4.294 4.249 0.6799191025 788 4.595 -3.180 3.602 2.537 4.292 4.249 0.6799188966 801 4.596 -3.178 3.602 2.537 4.290 4.250 0.6799183365 807 4.596 -3.178 3.602 2.537 4.290 4.250 0.6799160502 818 4.598 -3.178 3.602 2.537 4.290 4.250 0.6799160159 833 4.597 -3.178 3.602 2.536 4.290 4.250 0.6799140861 834 4.597 -3.178 3.602 2.536 4.291 4.250 0.6799130993 873 4.597 -3.178 3.602 2.536 4.292 4.250 0.6799129396 Powell done niters = 10 Computing relative cost 0 -25.0 -25.0 -25.0 1.053665 1 -25.0 -25.0 25.0 1.059629 2 -25.0 25.0 -25.0 1.033384 3 -25.0 25.0 25.0 1.050912 4 25.0 -25.0 -25.0 1.026924 5 25.0 -25.0 25.0 1.026526 6 25.0 25.0 -25.0 1.027053 7 25.0 25.0 25.0 1.063437 REL: 8 0.679913 8.341530 1.042691 rel = 0.652075 Number of iterations 10 Min cost was 0.679913 Number of FunctionCalls 966 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 176.321000 sec Parameters at optimum (transmm) 4.59813 -3.17797 3.60165 Parameters at optimum (rotdeg) 2.53643 4.29159 4.24983 Final costs ---------------- Number of surface hits 222111 WM Intensity 655.9067 +/- 147.0230 Ctx Intensity 666.6987 +/- 166.7677 Pct Contrast 0.0622 +/- 19.7942 Cost 0.6799 RelCost 0.8975 Reg at min cost was 1.000 -0.020 0.003 3.272; -0.005 -0.108 0.994 9.220; -0.020 -0.994 -0.108 -2.282; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 0.995 0.047 0.084 0.038; -0.076 -0.150 0.986 12.189; 0.059 -0.988 -0.146 -6.443; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.004 0.067 0.082 -3.234; -0.072 -0.042 -0.008 2.969; 0.078 0.006 -0.038 -4.161; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 10.302097 Computing change in rh position Surface RMS Diff (mm) 8.222576 15.710553 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done Cleaning up Started at Mon Oct 3 15:35:16 EDT 2011 Ended at Mon Oct 3 15:39:31 EDT 2011 BBR-Run-Time-Sec 255 bbregister Done To check results, run: tkregister2 --mov bold/001/template.nii --reg bold/001/register.dof6.dat --surf Run: 002 ---------------- Mon Oct 3 15:39:31 EDT 2011 -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 bbregister --s ld12 --init-fsl --6 --bold --mov bold/001/template.nii --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat --mov bold/002/template.nii --reg bold/002/register.dof6.dat --init-reg-out bold/002/init.register.dof6.dat Log file is bold/002/register.dof6.dat.log Mon Oct 3 15:39:31 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 /usr/local/freesurfer/bin/bbregister --s ld12 --init-fsl --6 --bold --mov bold/001/template.nii --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat --mov bold/002/template.nii --reg bold/002/register.dof6.dat --init-reg-out bold/002/init.register.dof6.dat $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert bold/002/template.nii bold/002/tmp.bbregister.2424/template.nii mri_convert bold/002/template.nii bold/002/tmp.bbregister.2424/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/002/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to bold/002/tmp.bbregister.2424/template.nii... fslregister --s ld12 --mov bold/002/tmp.bbregister.2424/template.nii --reg bold/002/tmp.bbregister.2424/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/002/tmp.bbregister.2424/fslregister --dof 6 Log file is bold/002/tmp.bbregister.2424/reg.init.dat.fslregister.log Mon Oct 3 15:39:31 EDT 2011 --s ld12 --mov bold/002/tmp.bbregister.2424/template.nii --reg bold/002/tmp.bbregister.2424/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/002/tmp.bbregister.2424/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ BOTANICA Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 mri_convert /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz bold/002/tmp.bbregister.2424/fslregister/refvol.fslregister.nii mri_convert /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz bold/002/tmp.bbregister.2424/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/ld12/mri/brainmask.mgz... TR=19.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.01863e-09, 0) j_ras = (3.72529e-09, -3.79471e-18, -1) k_ras = (-4.59841e-09, 1, 3.72529e-09) writing to bold/002/tmp.bbregister.2424/fslregister/refvol.fslregister.nii... -------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 mri_convert bold/002/tmp.bbregister.2424/template.nii bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/002/tmp.bbregister.2424/template.nii bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/002/tmp.bbregister.2424/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) keeping frame 0 writing to bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii... Mov determinant is -26.9997 /usr/local/freesurfer/subjects/retinotopy/sj12 tkregister2_cmdl --mov bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii --reg bold/002/tmp.bbregister.2424/fslregister/reg0.2466.dat --regheader --fslregout bold/002/tmp.bbregister.2424/reg.init.dat.fsl.mat0 --s ld12 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii reg file bold/002/tmp.bbregister.2424/fslregister/reg0.2466.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 /usr/local/freesurfer/subjects/ld12/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 bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.000 0.000 0.000 96.000; 0.000 0.000 3.000 -34.500; 0.000 -3.000 0.000 96.000; 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 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; Determinant 1 subject = ld12 RegMat --------------------------- 1.000 0.005 0.014 3.703; -0.013 -0.142 0.990 15.620; 0.006 -0.990 -0.142 -2.416; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -26.9997, ref det = -1 Mon Oct 3 15:39:37 EDT 2011 /usr/local/freesurfer/subjects/retinotopy/sj12 flirt.fsl -ref bold/002/tmp.bbregister.2424/fslregister/refvol.fslregister.nii -in bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/002/tmp.bbregister.2424/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/etc/flirtsch/xyztrans.sch -init bold/002/tmp.bbregister.2424/reg.init.dat.fsl.mat0 Mon Oct 3 15:39:46 EDT 2011 /usr/local/freesurfer/subjects/retinotopy/sj12 flirt.fsl -ref bold/002/tmp.bbregister.2424/fslregister/refvol.fslregister.nii -in bold/002/tmp.bbregister.2424/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/002/tmp.bbregister.2424/reg.init.dat.fsl.mat -init bold/002/tmp.bbregister.2424/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s ld12 --mov bold/002/tmp.bbregister.2424/template.nii --reg bold/002/tmp.bbregister.2424/reg.init.dat --fslreg bold/002/tmp.bbregister.2424/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.000 0.003 0.009 34.191; 0.009 -0.140 -0.990 193.214; -0.001 0.990 -0.140 36.067; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/tmp.bbregister.2424/template.nii reg file bold/002/tmp.bbregister.2424/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 /usr/local/freesurfer/subjects/ld12/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 bold/002/tmp.bbregister.2424/template.nii Tmov: -------------------- -3.000 0.000 0.000 96.000; 0.000 0.000 3.000 -34.500; 0.000 -3.000 0.000 96.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -26.9997, ref det = -1 ---- Input registration matrix (computed) -------- 1.000 0.001 0.009 2.908; -0.009 -0.140 0.990 18.024; 0.003 -0.990 -0.140 -4.398; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.001 0.009 2.908; -0.009 -0.140 0.990 18.024; 0.003 -0.990 -0.140 -4.398; 0.000 0.000 0.000 1.000; Determinant 1 subject = ld12 RegMat --------------------------- 1.000 0.001 0.009 2.908; -0.009 -0.140 0.990 18.024; 0.003 -0.990 -0.140 -4.398; 0.000 0.000 0.000 1.000; Started at Mon Oct 3 15:39:31 EDT 2011 Ended at Mon Oct 3 15:40:01 EDT 2011 fslregister Done To check results, run: tkregister2 --mov bold/002/tmp.bbregister.2424/template.nii --reg bold/002/tmp.bbregister.2424/reg.init.dat --surf orig mri_segreg --mov bold/002/tmp.bbregister.2424/template.nii --init-reg bold/002/tmp.bbregister.2424/reg.init.dat --out-reg bold/002/tmp.bbregister.2424/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 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 mri_segreg --mov bold/002/tmp.bbregister.2424/template.nii --init-reg bold/002/tmp.bbregister.2424/reg.init.dat --out-reg bold/002/tmp.bbregister.2424/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 BOTANICA machine x86_64 user michelle movvol bold/002/tmp.bbregister.2424/template.nii regfile bold/002/tmp.bbregister.2424/reg.init.dat subject ld12 dof 6 outregfile bold/002/tmp.bbregister.2424/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 1318143652 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 0.001 0.009 2.908; -0.009 -0.140 0.990 18.024; 0.003 -0.990 -0.140 -4.398; 0.000 0.000 0.000 1.000; Loading mov 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 1.051159 1 -25.0 -25.0 25.0 1.122937 2 -25.0 25.0 -25.0 1.106324 3 -25.0 25.0 25.0 1.066839 4 25.0 -25.0 -25.0 1.021747 5 25.0 -25.0 25.0 1.010139 6 25.0 25.0 -25.0 1.032059 7 25.0 25.0 25.0 1.082736 REL: 8 1.118928 8.493942 1.061743 rel = 1.05386 Initial costs ---------------- Number of surface hits 1964 WM Intensity 682.3943 +/- 115.7855 Ctx Intensity 667.6349 +/- 138.0855 Pct Contrast -3.3228 +/- 16.8129 Cost 1.1189 RelCost 1.0539 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9875 0.9875 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9659 0.9659 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9435 0.9435 0.0 Brute Force -------------------------- Min cost was 0.943479 Number of iterations 729 Search time 5.090000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 -4.000 0.000 -4.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 -4 3 0 4 -4 5 -4 2 -3.000 -4.000 -4.000 0.000 -4.000 -4.000 0.9433693576 6 -3.382 -4.000 -4.000 0.000 -4.000 -4.000 0.9405092905 8 -3.285 -4.000 -4.000 0.000 -4.000 -4.000 0.9398200991 9 -3.264 -4.000 -4.000 0.000 -4.000 -4.000 0.9397704920 10 -3.245 -4.000 -4.000 0.000 -4.000 -4.000 0.9397271601 12 -3.209 -4.000 -4.000 0.000 -4.000 -4.000 0.9397134179 13 -3.222 -4.000 -4.000 0.000 -4.000 -4.000 0.9397023876 14 -3.224 -4.000 -4.000 0.000 -4.000 -4.000 0.9397014682 16 -3.226 -4.000 -4.000 0.000 -4.000 -4.000 0.9397006666 21 -3.227 -5.618 -4.000 0.000 -4.000 -4.000 0.9195336263 22 -3.227 -5.446 -4.000 0.000 -4.000 -4.000 0.9145744366 25 -3.227 -5.235 -4.000 0.000 -4.000 -4.000 0.9134060048 32 -3.227 -5.239 -4.000 0.000 -4.000 -4.000 0.9133791223 33 -3.227 -5.241 -4.000 0.000 -4.000 -4.000 0.9133631991 37 -3.227 -5.241 -3.000 0.000 -4.000 -4.000 0.9126901804 41 -3.227 -5.241 -3.382 0.000 -4.000 -4.000 0.9116309073 43 -3.227 -5.241 -3.458 0.000 -4.000 -4.000 0.9114217285 46 -3.227 -5.241 -3.464 0.000 -4.000 -4.000 0.9114193299 48 -3.227 -5.241 -3.462 0.000 -4.000 -4.000 0.9114183940 64 -3.227 -5.241 -3.462 0.000 -3.000 -4.000 0.9108007931 68 -3.227 -5.241 -3.462 0.000 -3.382 -4.000 0.9091834569 69 -3.227 -5.241 -3.462 0.000 -3.364 -4.000 0.9090150912 70 -3.227 -5.241 -3.462 0.000 -3.247 -4.000 0.9082195759 72 -3.227 -5.241 -3.462 0.000 -3.292 -4.000 0.9080903510 74 -3.227 -5.241 -3.462 0.000 -3.290 -4.000 0.9080895231 106 -3.225 -5.244 -3.461 0.000 -3.288 -4.000 0.9080521494 107 -3.224 -5.246 -3.460 0.000 -3.287 -4.000 0.9080366611 111 -4.842 -5.246 -3.460 0.000 -3.287 -4.000 0.9079215225 117 -3.352 -5.246 -3.460 0.000 -3.287 -4.000 0.9078081277 120 -3.354 -5.246 -3.460 0.000 -3.287 -4.000 0.9078080580 136 -3.354 -5.246 -3.460 0.000 -3.287 -3.999 0.9077966947 137 -3.354 -5.246 -3.460 0.000 -3.287 -3.998 0.9077854902 139 -3.354 -5.246 -2.460 0.000 -3.287 -3.998 0.9046552640 144 -3.354 -5.246 -2.394 0.000 -3.287 -3.998 0.9045661968 148 -3.354 -5.246 -2.404 0.000 -3.287 -3.998 0.9045656010 150 -3.354 -5.246 -2.410 0.000 -3.287 -3.998 0.9045652133 151 -3.354 -5.246 -2.413 0.000 -3.287 -3.998 0.9045650876 154 -3.354 -5.246 -2.412 0.000 -3.287 -3.998 0.9045647353 178 -3.354 -5.246 -2.412 0.000 -2.905 -3.998 0.9036160805 179 -3.354 -5.246 -2.412 0.000 -3.001 -3.998 0.9035058981 181 -3.354 -5.246 -2.412 0.000 -3.110 -3.998 0.9032104799 186 -3.354 -5.246 -2.412 0.000 -3.120 -3.998 0.9031667145 210 -4.972 -5.246 -2.412 0.000 -3.120 -3.998 0.9011791806 216 -4.794 -5.246 -2.412 0.000 -3.120 -3.998 0.8999388420 217 -4.722 -5.246 -2.412 0.000 -3.120 -3.998 0.8996470722 222 -4.721 -5.246 -2.412 0.000 -3.120 -3.998 0.8996469302 232 -4.721 -5.246 -2.412 0.000 -3.120 -4.052 0.8995770626 233 -4.721 -5.246 -2.412 0.000 -3.120 -4.040 0.8995668247 234 -4.721 -5.246 -2.412 0.000 -3.120 -4.037 0.8995646281 235 -4.721 -5.246 -2.412 0.000 -3.120 -4.022 0.8995527090 238 -4.721 -5.246 -2.412 0.000 -3.120 -4.019 0.8995512182 239 -4.721 -5.246 -2.412 0.000 -3.120 -4.018 0.8995510534 240 -4.721 -5.246 -2.412 0.000 -3.120 -4.017 0.8995507208 241 -4.721 -5.246 -2.412 0.000 -3.120 -4.015 0.8995505742 248 -4.721 -5.246 -2.030 0.000 -3.120 -4.015 0.8984463914 252 -4.721 -5.246 -1.983 0.000 -3.120 -4.015 0.8984247188 253 -4.721 -5.246 -2.003 0.000 -3.120 -4.015 0.8984043446 255 -4.721 -5.246 -2.005 0.000 -3.120 -4.015 0.8984038099 259 -4.721 -5.246 -2.007 0.000 -3.120 -4.015 0.8984037826 264 -4.721 -5.246 -2.007 -0.618 -3.120 -4.015 0.8917687076 266 -4.721 -5.246 -2.007 -0.739 -3.120 -4.015 0.8916361860 268 -4.721 -5.246 -2.007 -0.839 -3.120 -4.015 0.8915519388 270 -4.721 -5.246 -2.007 -0.841 -3.120 -4.015 0.8915506368 273 -4.721 -5.246 -2.007 -0.850 -3.120 -4.015 0.8915470955 276 -4.721 -5.246 -2.007 -0.852 -3.120 -4.015 0.8915470900 288 -4.721 -5.246 -2.007 -0.852 -3.109 -4.015 0.8915466332 290 -4.721 -5.246 -2.007 -0.852 -3.114 -4.015 0.8915461296 292 -4.721 -5.246 -2.007 -0.852 -3.117 -4.015 0.8915451581 301 -4.589 -5.457 -1.916 -0.852 -2.995 -4.015 0.8900795552 302 -4.587 -5.461 -1.914 -0.852 -2.993 -4.015 0.8900763282 303 -4.577 -5.476 -1.908 -0.852 -2.985 -4.015 0.8893080253 305 -4.552 -5.517 -1.890 -0.852 -2.962 -4.015 0.8892905767 306 -4.564 -5.498 -1.898 -0.852 -2.972 -4.015 0.8888831658 307 -4.564 -5.496 -1.899 -0.852 -2.973 -4.015 0.8888811578 308 -4.565 -5.495 -1.899 -0.852 -2.974 -4.015 0.8888794892 310 -4.567 -5.492 -1.901 -0.852 -2.976 -4.015 0.8888768525 312 -4.567 -5.493 -1.900 -0.852 -2.975 -4.015 0.8888767630 320 -4.808 -5.493 -1.900 -0.852 -2.975 -4.015 0.8861596721 322 -4.738 -5.493 -1.900 -0.852 -2.975 -4.015 0.8858049399 324 -4.755 -5.493 -1.900 -0.852 -2.975 -4.015 0.8857165241 326 -4.756 -5.493 -1.900 -0.852 -2.975 -4.015 0.8857163995 333 -4.756 -5.493 -1.900 -0.852 -2.975 -3.633 0.8848255785 335 -4.756 -5.493 -1.900 -0.852 -2.975 -3.397 0.8839628980 337 -4.756 -5.493 -1.900 -0.852 -2.975 -3.487 0.8823108288 338 -4.756 -5.493 -1.900 -0.852 -2.975 -3.503 0.8822911836 342 -4.756 -5.493 -1.900 -0.852 -2.975 -3.504 0.8822904078 343 -4.756 -5.493 -1.900 -0.852 -2.975 -3.511 0.8822872259 344 -4.756 -5.493 -1.900 -0.852 -2.975 -3.514 0.8822871889 354 -4.756 -5.493 -1.984 -0.852 -2.975 -3.514 0.8821265696 357 -4.756 -5.493 -1.986 -0.852 -2.975 -3.514 0.8821265012 358 -4.756 -5.493 -1.985 -0.852 -2.975 -3.514 0.8821264622 367 -4.756 -5.493 -1.985 -0.862 -2.975 -3.514 0.8820843174 373 -4.756 -5.493 -1.985 -0.864 -2.975 -3.514 0.8820784911 382 -4.756 -5.493 -1.985 -0.864 -3.061 -3.514 0.8817482456 383 -4.756 -5.493 -1.985 -0.864 -3.089 -3.514 0.8816346007 385 -4.756 -5.493 -1.985 -0.864 -3.095 -3.514 0.8816159100 386 -4.756 -5.493 -1.985 -0.864 -3.114 -3.514 0.8815853681 396 -4.742 -5.516 -1.975 -0.864 -3.100 -3.514 0.8808649715 398 -4.712 -5.563 -1.955 -0.864 -3.074 -3.514 0.8802415504 399 -4.711 -5.566 -1.954 -0.864 -3.072 -3.514 0.8802261469 402 -4.712 -5.564 -1.954 -0.864 -3.073 -3.514 0.8802062223 411 -4.726 -5.564 -1.954 -0.864 -3.073 -3.514 0.8801464793 413 -4.725 -5.564 -1.954 -0.864 -3.073 -3.514 0.8801430451 414 -4.723 -5.564 -1.954 -0.864 -3.073 -3.514 0.8801416488 424 -4.723 -5.564 -1.954 -0.864 -3.073 -3.537 0.8797056467 427 -4.723 -5.564 -1.954 -0.864 -3.073 -3.528 0.8796875350 429 -4.723 -5.564 -1.954 -0.864 -3.073 -3.529 0.8796875237 438 -4.723 -5.564 -2.138 -0.864 -3.073 -3.529 0.8792605006 439 -4.723 -5.564 -2.097 -0.864 -3.073 -3.529 0.8792189181 440 -4.723 -5.564 -2.096 -0.864 -3.073 -3.529 0.8792172166 442 -4.723 -5.564 -2.075 -0.864 -3.073 -3.529 0.8792105710 443 -4.723 -5.564 -2.083 -0.864 -3.073 -3.529 0.8792063166 444 -4.723 -5.564 -2.084 -0.864 -3.073 -3.529 0.8792062570 455 -4.723 -5.564 -2.084 -0.865 -3.073 -3.529 0.8791969776 457 -4.723 -5.564 -2.084 -0.868 -3.073 -3.529 0.8791709581 467 -4.723 -5.564 -2.084 -0.868 -3.284 -3.529 0.8791041869 468 -4.723 -5.564 -2.084 -0.868 -3.186 -3.529 0.8790761246 469 -4.723 -5.564 -2.084 -0.868 -3.208 -3.529 0.8790698711 471 -4.723 -5.564 -2.084 -0.868 -3.201 -3.529 0.8790677684 472 -4.723 -5.564 -2.084 -0.868 -3.200 -3.529 0.8790677165 480 -4.735 -5.545 -2.092 -0.868 -3.211 -3.529 0.8790017857 482 -4.730 -5.553 -2.089 -0.868 -3.206 -3.529 0.8788183396 483 -4.729 -5.555 -2.088 -0.868 -3.205 -3.529 0.8787960346 484 -4.727 -5.558 -2.087 -0.868 -3.203 -3.529 0.8787355575 485 -4.725 -5.561 -2.086 -0.868 -3.202 -3.529 0.8787025539 486 -4.725 -5.562 -2.085 -0.868 -3.201 -3.529 0.8786832075 494 -4.768 -5.562 -2.085 -0.868 -3.201 -3.529 0.8786548630 495 -4.756 -5.562 -2.085 -0.868 -3.201 -3.529 0.8786118579 496 -4.749 -5.562 -2.085 -0.868 -3.201 -3.529 0.8785727240 497 -4.740 -5.562 -2.085 -0.868 -3.201 -3.529 0.8785444724 500 -4.739 -5.562 -2.085 -0.868 -3.201 -3.529 0.8785443088 513 -4.739 -5.562 -2.085 -0.868 -3.201 -3.528 0.8785387512 523 -4.739 -5.562 -2.134 -0.868 -3.201 -3.528 0.8783954126 525 -4.739 -5.562 -2.152 -0.868 -3.201 -3.528 0.8783512720 526 -4.739 -5.562 -2.154 -0.868 -3.201 -3.528 0.8783503718 527 -4.739 -5.562 -2.155 -0.868 -3.201 -3.528 0.8783498651 550 -4.739 -5.562 -2.155 -0.868 -3.218 -3.528 0.8783033514 554 -4.739 -5.562 -2.155 -0.868 -3.220 -3.528 0.8783031079 577 -4.779 -5.562 -2.155 -0.868 -3.220 -3.528 0.8782079426 578 -4.799 -5.562 -2.155 -0.868 -3.220 -3.528 0.8778735308 584 -4.798 -5.562 -2.155 -0.868 -3.220 -3.528 0.8778728195 621 -4.798 -5.562 -2.155 -0.861 -3.220 -3.528 0.8778713836 631 -4.798 -5.562 -2.155 -0.861 -3.323 -3.528 0.8772660846 634 -4.798 -5.562 -2.155 -0.861 -3.336 -3.528 0.8772396825 635 -4.798 -5.562 -2.155 -0.861 -3.337 -3.528 0.8772395775 636 -4.798 -5.562 -2.155 -0.861 -3.338 -3.528 0.8772395146 638 -4.798 -5.562 -2.155 -0.861 -3.339 -3.528 0.8772394740 641 -4.798 -5.562 -2.155 -0.861 -3.341 -3.528 0.8772394405 666 -4.793 -5.562 -2.155 -0.861 -3.341 -3.528 0.8771950939 668 -4.790 -5.562 -2.155 -0.861 -3.341 -3.528 0.8771875724 691 -4.790 -5.562 -2.180 -0.861 -3.341 -3.528 0.8771233311 692 -4.790 -5.562 -2.226 -0.861 -3.341 -3.528 0.8770454060 694 -4.790 -5.562 -2.276 -0.861 -3.341 -3.528 0.8770380578 695 -4.790 -5.562 -2.255 -0.861 -3.341 -3.528 0.8770055091 697 -4.790 -5.562 -2.257 -0.861 -3.341 -3.528 0.8770046553 699 -4.790 -5.562 -2.260 -0.861 -3.341 -3.528 0.8770038088 700 -4.790 -5.562 -2.261 -0.861 -3.341 -3.528 0.8770034815 755 -4.791 -5.562 -2.261 -0.861 -3.341 -3.528 0.8769999501 756 -4.793 -5.562 -2.261 -0.861 -3.341 -3.528 0.8769982550 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 0.989643 1 -25.0 -25.0 25.0 1.047706 2 -25.0 25.0 -25.0 1.016318 3 -25.0 25.0 25.0 1.017329 4 25.0 -25.0 -25.0 1.040654 5 25.0 -25.0 25.0 1.054433 6 25.0 25.0 -25.0 1.023861 7 25.0 25.0 25.0 1.047844 REL: 8 0.876998 8.237787 1.029723 rel = 0.851683 Number of iterations 8 Min cost was 0.876998 Number of FunctionCalls 825 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 5.414000 sec Parameters at optimum (transmm) -4.79263 -5.56205 -2.26082 Parameters at optimum (rotdeg) -0.86104 -3.34058 -3.52818 Final costs ---------------- Number of surface hits 2126 WM Intensity 645.1948 +/- 159.5417 Ctx Intensity 642.0433 +/- 180.6185 Pct Contrast -2.2498 +/- 24.9484 Cost 0.8770 RelCost 1.0539 Reg at min cost was 0.996 0.049 0.079 -0.519; -0.070 -0.158 0.985 12.165; 0.061 -0.986 -0.154 -6.752; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/002/tmp.bbregister.2424/bbr.pass1.dat, type = 14 Original Reg 1.000 0.001 0.009 2.908; -0.009 -0.140 0.990 18.024; 0.003 -0.990 -0.140 -4.398; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.004 -0.048 -0.070 3.427; 0.061 0.018 0.005 5.860; -0.058 -0.004 0.014 2.354; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 7.594739 Computing change in rh position Surface RMS Diff (mm) 8.396193 12.293218 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/002/tmp.bbregister.2424/template.nii --init-reg bold/002/tmp.bbregister.2424/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --cur-reg bold/002/tmp.bbregister.2424/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12 mri_segreg --mov bold/002/tmp.bbregister.2424/template.nii --init-reg bold/002/tmp.bbregister.2424/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --cur-reg bold/002/tmp.bbregister.2424/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname BOTANICA machine x86_64 user michelle movvol bold/002/tmp.bbregister.2424/template.nii regfile bold/002/tmp.bbregister.2424/bbr.pass1.dat subject ld12 dof 6 outregfile bold/002/register.dof6.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 1318435964 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.996 0.049 0.079 -0.519; -0.070 -0.158 0.985 12.165; 0.061 -0.986 -0.154 -6.752; 0.000 0.000 0.000 1.000; Loading mov 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 1.040878 1 -25.0 -25.0 25.0 1.041341 2 -25.0 25.0 -25.0 1.060495 3 -25.0 25.0 25.0 1.030719 4 25.0 -25.0 -25.0 1.057704 5 25.0 -25.0 25.0 1.030588 6 25.0 25.0 -25.0 1.018981 7 25.0 25.0 25.0 1.054988 REL: 8 0.932622 8.335694 1.041962 rel = 0.895064 Initial costs ---------------- Number of surface hits 211611 WM Intensity 650.5061 +/- 154.6862 Ctx Intensity 646.4481 +/- 176.1329 Pct Contrast -2.5002 +/- 23.3037 Cost 0.9326 RelCost 0.8951 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8795 0.8795 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8783 0.8783 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8782 0.8782 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.8777 0.8777 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8775 0.8775 0.0 28 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.8773 0.8773 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.8767 0.8767 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.8767 0.8767 0.0 275 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.8766 0.8766 0.0 Brute Force -------------------------- Min cost was 0.876649 Number of iterations 729 Search time 3.784000 sec Parameters at best (transmm, rotdeg) 0.000 -0.100 0.000 -0.100 0.000 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -0.1 2 0 3 -0.1 4 0 5 0.1 2 1.000 -0.100 0.000 -0.100 0.000 0.100 0.9254586169 5 1.618 -0.100 0.000 -0.100 0.000 0.100 0.9249231645 7 1.497 -0.100 0.000 -0.100 0.000 0.100 0.9247911807 8 1.419 -0.100 0.000 -0.100 0.000 0.100 0.9247025960 11 1.418 -0.100 0.000 -0.100 0.000 0.100 0.9247024068 12 1.414 -0.100 0.000 -0.100 0.000 0.100 0.9247020210 19 1.415 -1.718 0.000 -0.100 0.000 0.100 0.9224773946 20 1.415 -1.069 0.000 -0.100 0.000 0.100 0.9209245565 24 1.415 -1.071 0.000 -0.100 0.000 0.100 0.9209013305 26 1.415 -1.113 0.000 -0.100 0.000 0.100 0.9208511776 29 1.415 -1.105 0.000 -0.100 0.000 0.100 0.9208361045 37 1.415 -1.105 -0.618 -0.100 0.000 0.100 0.9186836741 40 1.415 -1.105 -0.638 -0.100 0.000 0.100 0.9186739762 43 1.415 -1.105 -0.650 -0.100 0.000 0.100 0.9186725160 47 1.415 -1.105 -0.651 0.900 0.000 0.100 0.9073203262 50 1.415 -1.105 -0.651 1.518 0.000 0.100 0.9059638992 52 1.415 -1.105 -0.651 1.627 0.000 0.100 0.9059155295 53 1.415 -1.105 -0.651 1.642 0.000 0.100 0.9058717355 55 1.415 -1.105 -0.651 1.685 0.000 0.100 0.9058489019 58 1.415 -1.105 -0.651 1.695 0.000 0.100 0.9058420273 61 1.415 -1.105 -0.651 1.697 0.000 0.100 0.9058395807 65 1.415 -1.105 -0.651 1.697 1.000 0.100 0.9032531653 69 1.415 -1.105 -0.651 1.697 0.618 0.100 0.9022241584 70 1.415 -1.105 -0.651 1.697 0.624 0.100 0.9022184903 71 1.415 -1.105 -0.651 1.697 0.672 0.100 0.9022167380 73 1.415 -1.105 -0.651 1.697 0.649 0.100 0.9022081616 76 1.415 -1.105 -0.651 1.697 0.647 0.100 0.9022080433 83 1.415 -1.105 -0.651 1.697 0.647 0.482 0.9014466291 91 1.415 -1.105 -0.651 1.697 0.647 0.483 0.9014435090 92 2.831 -2.110 -1.301 3.494 1.294 0.866 0.8983265144 110 2.329 -2.723 -0.651 1.697 0.647 0.483 0.8975993039 111 2.329 -2.025 -0.651 1.697 0.647 0.483 0.8937599423 115 2.329 -2.060 -0.651 1.697 0.647 0.483 0.8937504211 128 2.329 -2.060 -0.269 1.697 0.647 0.483 0.8933775713 129 2.329 -2.060 -0.381 1.697 0.647 0.483 0.8932248547 130 2.329 -2.060 -0.403 1.697 0.647 0.483 0.8932188125 131 2.329 -2.060 -0.408 1.697 0.647 0.483 0.8932185306 132 2.329 -2.060 -0.410 1.697 0.647 0.483 0.8932185054 133 2.329 -2.060 -0.411 1.697 0.647 0.483 0.8932184782 136 2.329 -2.060 -0.424 1.697 0.647 0.483 0.8932184640 137 2.329 -2.060 -0.417 1.697 0.647 0.483 0.8932182375 138 2.329 -2.060 -0.418 1.697 0.647 0.483 0.8932182242 139 2.329 -2.060 -0.419 1.697 0.647 0.483 0.8932182008 142 2.329 -2.060 -0.419 2.697 0.647 0.483 0.8927406185 146 2.329 -2.060 -0.419 2.315 0.647 0.483 0.8918155820 148 2.329 -2.060 -0.419 2.079 0.647 0.483 0.8917315382 149 2.329 -2.060 -0.419 2.151 0.647 0.483 0.8917250630 152 2.329 -2.060 -0.419 2.175 0.647 0.483 0.8917234303 154 2.329 -2.060 -0.419 2.166 0.647 0.483 0.8917139090 157 2.329 -2.060 -0.419 2.165 0.647 0.483 0.8917108673 159 2.329 -2.060 -0.419 2.165 1.647 0.483 0.8848008645 164 2.329 -2.060 -0.419 2.165 1.662 0.483 0.8847906401 165 2.329 -2.060 -0.419 2.165 1.733 0.483 0.8847638057 170 2.329 -2.060 -0.419 2.165 1.740 0.483 0.8847633427 172 2.329 -2.060 -0.419 2.165 1.738 0.483 0.8847633077 176 2.329 -2.060 -0.419 2.165 1.737 1.483 0.8758836682 181 2.329 -2.060 -0.419 2.165 1.737 1.621 0.8758327430 182 2.329 -2.060 -0.419 2.165 1.737 1.581 0.8758122084 183 2.329 -2.060 -0.419 2.165 1.737 1.572 0.8757858115 189 3.244 -3.014 -0.188 2.632 2.827 2.662 0.8449690151 192 4.723 -4.559 0.186 3.389 4.591 4.424 0.7824046582 197 4.604 -4.434 0.156 3.328 4.449 4.282 0.7820722326 198 4.633 -4.465 0.163 3.343 4.484 4.318 0.7819598930 200 4.636 -4.468 0.164 3.344 4.487 4.320 0.7819545156 202 4.636 -4.469 0.164 3.345 4.488 4.322 0.7819497583 204 5.636 -4.469 0.164 3.345 4.488 4.322 0.7778344653 208 5.255 -4.469 0.164 3.345 4.488 4.322 0.7756023448 210 5.248 -4.469 0.164 3.345 4.488 4.322 0.7756012860 211 5.246 -4.469 0.164 3.345 4.488 4.322 0.7756011953 212 5.245 -4.469 0.164 3.345 4.488 4.322 0.7756011290 216 5.244 -4.469 0.164 3.345 4.488 4.322 0.7756011076 223 5.244 -4.087 0.164 3.345 4.488 4.322 0.7735965642 225 5.244 -4.074 0.164 3.345 4.488 4.322 0.7735721251 231 5.244 -4.073 0.164 3.345 4.488 4.322 0.7735630239 234 5.244 -4.073 1.164 3.345 4.488 4.322 0.7251340873 235 5.244 -4.073 2.782 3.345 4.488 4.322 0.6874483248 240 5.244 -4.073 2.871 3.345 4.488 4.322 0.6872420317 241 5.244 -4.073 2.924 3.345 4.488 4.322 0.6871955464 243 5.244 -4.073 2.917 3.345 4.488 4.322 0.6871950812 244 5.244 -4.073 2.920 3.345 4.488 4.322 0.6871948123 251 5.244 -4.073 2.921 2.727 4.488 4.322 0.6840939702 253 5.244 -4.073 2.921 2.902 4.488 4.322 0.6835014729 257 5.244 -4.073 2.921 2.891 4.488 4.322 0.6834965525 258 5.244 -4.073 2.921 2.896 4.488 4.322 0.6834896422 268 5.244 -4.073 2.921 2.896 4.378 4.322 0.6833665436 269 5.244 -4.073 2.921 2.896 4.407 4.322 0.6833416389 272 5.244 -4.073 2.921 2.896 4.403 4.322 0.6833410379 273 5.244 -4.073 2.921 2.896 4.405 4.322 0.6833410336 281 5.007 -3.826 2.861 2.775 4.123 4.039 0.6777057795 282 5.012 -3.831 2.862 2.778 4.129 4.046 0.6776900246 283 5.023 -3.842 2.865 2.784 4.142 4.058 0.6776577032 286 5.035 -3.855 2.868 2.790 4.156 4.072 0.6776163074 287 5.038 -3.857 2.868 2.791 4.159 4.076 0.6776084327 288 5.044 -3.864 2.870 2.794 4.167 4.084 0.6775864219 290 5.043 -3.863 2.870 2.794 4.165 4.082 0.6775756294 301 5.058 -3.863 2.870 2.794 4.165 4.082 0.6775735252 302 5.053 -3.863 2.870 2.794 4.165 4.082 0.6775732765 303 5.054 -3.863 2.870 2.794 4.165 4.082 0.6775732599 310 5.054 -3.481 2.870 2.794 4.165 4.082 0.6745134683 311 5.054 -3.544 2.870 2.794 4.165 4.082 0.6744786401 312 5.054 -3.523 2.870 2.794 4.165 4.082 0.6744439225 322 5.054 -3.523 3.252 2.794 4.165 4.082 0.6706091005 323 5.054 -3.523 3.453 2.794 4.165 4.082 0.6705022687 324 5.054 -3.523 3.369 2.794 4.165 4.082 0.6703652836 325 5.054 -3.523 3.367 2.794 4.165 4.082 0.6703652063 333 5.054 -3.523 3.367 2.978 4.165 4.082 0.6697609480 338 5.054 -3.523 3.367 2.983 4.165 4.082 0.6697523570 339 5.054 -3.523 3.367 2.981 4.165 4.082 0.6697483623 340 5.054 -3.523 3.367 2.982 4.165 4.082 0.6697478511 346 5.054 -3.523 3.367 2.982 4.547 4.082 0.6682334813 347 5.054 -3.523 3.367 2.982 4.456 4.082 0.6679084226 348 5.054 -3.523 3.367 2.982 4.433 4.082 0.6678924669 349 5.054 -3.523 3.367 2.982 4.431 4.082 0.6678899458 361 4.985 -3.451 3.350 2.947 4.349 4.000 0.6675246030 365 4.985 -3.450 3.349 2.946 4.348 3.999 0.6675235279 374 5.046 -3.450 3.349 2.946 4.348 3.999 0.6674098496 375 5.058 -3.450 3.349 2.946 4.348 3.999 0.6673979268 378 5.069 -3.450 3.349 2.946 4.348 3.999 0.6673939404 387 5.069 -3.415 3.349 2.946 4.348 3.999 0.6673691749 395 5.069 -3.416 3.349 2.946 4.348 3.999 0.6673672463 402 5.069 -3.416 3.372 2.946 4.348 3.999 0.6673526722 403 5.069 -3.416 3.379 2.946 4.348 3.999 0.6673516469 404 5.069 -3.416 3.380 2.946 4.348 3.999 0.6673516222 406 5.069 -3.416 3.381 2.946 4.348 3.999 0.6673516079 424 5.069 -3.416 3.381 2.946 4.445 3.999 0.6671436610 425 5.069 -3.416 3.381 2.946 4.444 3.999 0.6671436392 426 5.069 -3.416 3.381 2.946 4.443 3.999 0.6671434827 428 5.069 -3.416 3.381 2.946 4.429 3.999 0.6671409619 442 5.063 -3.409 3.379 2.943 4.422 3.991 0.6671268952 443 5.061 -3.407 3.379 2.942 4.420 3.989 0.6671259861 444 5.060 -3.406 3.378 2.942 4.419 3.988 0.6671209732 455 5.044 -3.406 3.378 2.942 4.419 3.988 0.6671106192 456 5.037 -3.406 3.378 2.942 4.419 3.988 0.6671105901 457 5.040 -3.406 3.378 2.942 4.419 3.988 0.6671103028 468 5.039 -3.408 3.378 2.942 4.419 3.988 0.6671097219 477 5.039 -3.408 3.379 2.942 4.419 3.988 0.6671097125 496 5.039 -3.408 3.380 2.942 4.452 3.988 0.6670873280 497 5.039 -3.408 3.380 2.942 4.451 3.988 0.6670868725 498 5.039 -3.408 3.380 2.942 4.445 3.988 0.6670839065 523 5.035 -3.408 3.380 2.942 4.443 3.988 0.6670835115 524 5.034 -3.408 3.380 2.942 4.443 3.988 0.6670834778 542 5.033 -3.409 3.380 2.942 4.443 3.988 0.6670793329 550 5.033 -3.409 3.373 2.942 4.443 3.988 0.6670784288 551 5.033 -3.409 3.374 2.942 4.443 3.988 0.6670784122 622 5.033 -3.409 3.374 2.942 4.443 3.988 0.6670784066 643 5.033 -3.409 3.374 2.942 4.445 3.988 0.6670783709 721 5.032 -3.408 3.372 2.941 4.443 3.987 0.6670766557 730 5.033 -3.408 3.372 2.941 4.443 3.987 0.6670766382 742 5.033 -3.409 3.372 2.941 4.443 3.987 0.6670711792 751 5.033 -3.409 3.373 2.941 4.443 3.987 0.6670711366 752 5.033 -3.409 3.374 2.941 4.443 3.987 0.6670711332 787 5.032 -3.408 3.374 2.941 4.442 3.986 0.6670691387 797 5.033 -3.408 3.374 2.941 4.442 3.986 0.6670691022 818 5.033 -3.408 3.373 2.941 4.442 3.986 0.6670690984 841 5.033 -3.408 3.373 2.941 4.446 3.986 0.6670689421 842 5.033 -3.408 3.373 2.941 4.444 3.986 0.6670689036 885 5.033 -3.408 3.374 2.941 4.444 3.986 0.6670688793 Powell done niters = 11 Computing relative cost 0 -25.0 -25.0 -25.0 1.047532 1 -25.0 -25.0 25.0 1.058974 2 -25.0 25.0 -25.0 1.039151 3 -25.0 25.0 25.0 1.049674 4 25.0 -25.0 -25.0 1.033510 5 25.0 -25.0 25.0 1.019266 6 25.0 25.0 -25.0 1.026128 7 25.0 25.0 25.0 1.054206 REL: 8 0.667069 8.328442 1.041055 rel = 0.640762 Number of iterations 11 Min cost was 0.667069 Number of FunctionCalls 923 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 165.573000 sec Parameters at optimum (transmm) 5.03304 -3.40793 3.37505 Parameters at optimum (rotdeg) 2.94072 4.44377 3.98552 Final costs ---------------- Number of surface hits 222482 WM Intensity 656.8441 +/- 146.5641 Ctx Intensity 668.7982 +/- 166.5877 Pct Contrast 0.2325 +/- 19.7123 Cost 0.6671 RelCost 0.8951 Reg at min cost was 1.000 -0.020 0.002 3.176; -0.004 -0.109 0.994 8.988; -0.020 -0.994 -0.109 -2.685; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/002/register.dof6.dat, type = 14 Original Reg 0.996 0.049 0.079 -0.519; -0.070 -0.158 0.985 12.165; 0.061 -0.986 -0.154 -6.752; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.004 0.070 0.077 -3.694; -0.066 -0.049 -0.009 3.177; 0.081 0.008 -0.045 -4.067; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 10.615536 Computing change in rh position Surface RMS Diff (mm) 8.598681 16.397632 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done Cleaning up Started at Mon Oct 3 15:39:31 EDT 2011 Ended at Mon Oct 3 15:43:34 EDT 2011 BBR-Run-Time-Sec 243 bbregister Done To check results, run: tkregister2 --mov bold/002/template.nii --reg bold/002/register.dof6.dat --surf Mon Oct 3 15:43:34 EDT 2011 register-sess completed sj12 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -per-run Logfile is /usr/local/freesurfer/subjects/retinotopy/log/mc-sj12-bold.log ------------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 RunList: 001 002 ------- ************************** ----------- ------- Motion Correcting Run 001 ----------- ------- ************************** ----------- sess = sj12 Mon Oct 3 15:43:34 EDT 2011 mc-afni2 --i 001/f.nii --t 001/template.nii --o 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_info --nframes --o /tmp/mriinfo.2691 001/template.nii log file is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is 001/tmp.mc-afni2.2691 #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 001/template.nii 001/tmp.mc-afni2.2691/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 001/template.nii 001/tmp.mc-afni2.2691/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 001/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 001/tmp.mc-afni2.2691/tempvol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 001/f.nii 001/tmp.mc-afni2.2691/invol.nii.gz -odt float mri_convert 001/f.nii 001/tmp.mc-afni2.2691/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 001/tmp.mc-afni2.2691/invol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat -base 001/tmp.mc-afni2.2691/tempvol.nii.gz -prefix 001/tmp.mc-afni2.2691/outvol.nii.gz 001/tmp.mc-afni2.2691/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 001/tmp.mc-afni2.2691/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:001/tmp.mc-afni2.2691/tempvol.nii.gz is 8.185852 degrees from plumb. ++ Reading in base dataset 001/tmp.mc-afni2.2691/tempvol.nii.gz ++ Oblique dataset:001/tmp.mc-afni2.2691/invol.nii.gz is 8.185852 degrees from plumb. ++ VERSION CHECK! This program = AFNI_2008_07_18_1710 ++ Current AFNI website = AFNI_2011_05_26_1457 ++ Reading input dataset 001/tmp.mc-afni2.2691/invol.nii.gz ++ Edging: x=3 y=3 z=1 ++ Creating mask for -maxdisp + Automask has 41509 voxels + 6423 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 148 sub-bricks: 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.. ++ CPU time for realignment=6.49 s [=0.0439 s/sub-brick] ++ Min : roll=-0.158 pitch=-0.041 yaw=-0.050 dS=-0.474 dL=-0.102 dP=-0.031 ++ Mean: roll=-0.020 pitch=+0.017 yaw=-0.008 dS=-0.003 dL=-0.020 dP=+0.017 ++ Max : roll=+0.012 pitch=+0.097 yaw=+0.022 dS=+0.186 dL=+0.015 dP=+0.377 ++ Max displacements (mm) for each sub-brick: 0.86 0.26 0.26 0.23 0.24 0.22 0.23 0.21 0.22 0.24 0.21 0.22 0.23 0.20 0.24 0.21 0.20 0.21 0.19 0.19 0.20 0.17 0.17 0.16 0.15 0.17 0.15 0.15 0.17 0.13 0.16 0.14 0.14 0.14 0.12 0.11 0.12 0.11 0.10 0.12 0.10 0.11 0.11 0.10 0.11 0.14 0.14 0.13 0.14 0.11 0.19 0.16 0.10 0.08 0.06 0.05 0.05 0.04 0.03 0.02 0.04 0.04 0.04 0.05 0.04 0.03 0.04 0.02 0.05 0.03 0.03 0.05 0.03 0.03 0.00 0.01 0.05 0.03 0.07 0.07 0.06 0.08 0.06 0.06 0.08 0.06 0.08 0.08 0.04 0.08 0.04 0.06 0.08 0.05 0.05 0.06 0.04 0.04 0.06 0.08 0.10 0.08 0.10 0.07 0.07 0.08 0.06 0.07 0.05 0.06 0.06 0.06 0.07 0.07 0.08 0.08 0.08 0.11 0.09 0.11 0.12 0.10 0.13 0.11 0.16 0.12 0.16 0.20 0.19 0.21 0.21 0.21 0.27 0.21 0.18 0.21 0.20 0.17 0.19 0.22 0.19 0.19 0.23 0.19 0.22 0.22 0.20 0.23 ++ Max displacement in automask = 0.86 (mm) at sub-brick 0 ++ Wrote dataset to disk in 001/tmp.mc-afni2.2691/outvol.nii.gz ** Warning: overwriting file 001/fmcpr.mcdat #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 001/tmp.mc-afni2.2691/outvol.nii.gz 001/fmcpr.nii.gz --in_like 001/template.nii mri_convert 001/tmp.mc-afni2.2691/outvol.nii.gz 001/fmcpr.nii.gz --in_like 001/template.nii reading info from 001/template.nii... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 001/tmp.mc-afni2.2691/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 001/fmcpr.nii.gz... ... cleaning up .... Mon Oct 3 15:44:13 EDT 2011 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 001/fmcpr.mcdat --o 001/mcprextreg Mon Oct 3 15:44:13 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12/bold /usr/local/freesurfer/fsfast/bin/mcdat2mcextreg --i 001/fmcpr.mcdat --o 001/mcprextreg freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux mri_glmfit --table /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/table.dat --glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/glm --osgm --y-out /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/y.out.nii --pca $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_glmfit --table /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/table.dat --glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/glm --osgm --y-out /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/y.out.nii --pca sysname Linux hostname BOTANICA machine x86_64 user michelle FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/table.dat logyflag 0 usedti 0 glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/glm Loading y from /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/table.dat Found 6 data colums Found 148 data rows Saving design matrix to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 147 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=-35.5196 F=285.213 at index 4 0 0 seed=1318103254 Measure:MC osgm Tx -16.081 Ty 18.512 Tz -7.819 Rx -0.181 Ry -35.520 Rz 7.245 Computing PCA (148) mri_glmfit done ninputs = 1 Checking inputs nframestot = 148 Allocing output Done allocing nframes = 148 Computing PCA Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/tmpdir.mcdat2extreg.2787/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 002 ----------- ------- ************************** ----------- sess = sj12 Mon Oct 3 15:44:13 EDT 2011 mc-afni2 --i 002/f.nii --t 002/template.nii --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_info --nframes --o /tmp/mriinfo.2852 002/template.nii log file is 002/fmcpr.nii.gz.mclog mcdat file is 002/fmcpr.mcdat tmp dir is 002/tmp.mc-afni2.2852 #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 002/template.nii 002/tmp.mc-afni2.2852/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 002/template.nii 002/tmp.mc-afni2.2852/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 002/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 002/tmp.mc-afni2.2852/tempvol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 002/f.nii 002/tmp.mc-afni2.2852/invol.nii.gz -odt float mri_convert 002/f.nii 002/tmp.mc-afni2.2852/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 002/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 002/tmp.mc-afni2.2852/invol.nii.gz... #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold 3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.2852/tempvol.nii.gz -prefix 002/tmp.mc-afni2.2852/outvol.nii.gz 002/tmp.mc-afni2.2852/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 002/tmp.mc-afni2.2852/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:002/tmp.mc-afni2.2852/tempvol.nii.gz is 8.185852 degrees from plumb. ++ Reading in base dataset 002/tmp.mc-afni2.2852/tempvol.nii.gz ++ Oblique dataset:002/tmp.mc-afni2.2852/invol.nii.gz is 8.185852 degrees from plumb. ++ Reading input dataset 002/tmp.mc-afni2.2852/invol.nii.gz ++ Edging: x=3 y=3 z=1 ++ Creating mask for -maxdisp + Automask has 41560 voxels + 6421 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 148 sub-bricks: 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.. ++ CPU time for realignment=5.45 s [=0.0368 s/sub-brick] ++ Min : roll=-0.060 pitch=-0.056 yaw=-0.030 dS=-0.503 dL=-0.035 dP=-0.052 ++ Mean: roll=+0.001 pitch=+0.003 yaw=-0.001 dS=-0.012 dL=+0.007 dP=+0.002 ++ Max : roll=+0.026 pitch=+0.050 yaw=+0.025 dS=+0.125 dL=+0.052 dP=+0.311 ++ Max displacements (mm) for each sub-brick: 0.71 0.17 0.16 0.11 0.13 0.15 0.13 0.13 0.12 0.11 0.12 0.13 0.12 0.13 0.13 0.12 0.12 0.13 0.12 0.13 0.13 0.14 0.14 0.12 0.13 0.17 0.15 0.14 0.17 0.15 0.12 0.14 0.14 0.15 0.13 0.13 0.12 0.08 0.13 0.12 0.11 0.10 0.09 0.09 0.09 0.05 0.06 0.05 0.05 0.10 0.04 0.07 0.04 0.04 0.03 0.04 0.03 0.02 0.04 0.03 0.02 0.02 0.07 0.03 0.05 0.07 0.06 0.05 0.04 0.04 0.03 0.05 0.02 0.01 0.00 0.06 0.05 0.07 0.07 0.04 0.06 0.04 0.05 0.04 0.07 0.08 0.05 0.06 0.05 0.05 0.04 0.07 0.05 0.04 0.06 0.07 0.07 0.07 0.07 0.07 0.07 0.14 0.12 0.17 0.11 0.09 0.09 0.06 0.07 0.07 0.05 0.06 0.06 0.05 0.04 0.04 0.06 0.05 0.07 0.04 0.05 0.05 0.05 0.06 0.05 0.04 0.03 0.04 0.04 0.08 0.06 0.12 0.11 0.09 0.12 0.09 0.08 0.14 0.13 0.14 0.14 0.13 0.20 0.14 0.12 0.16 0.12 0.13 ++ Max displacement in automask = 0.71 (mm) at sub-brick 0 ++ Wrote dataset to disk in 002/tmp.mc-afni2.2852/outvol.nii.gz ** Warning: overwriting file 002/fmcpr.mcdat #@# -------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold mri_convert 002/tmp.mc-afni2.2852/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii mri_convert 002/tmp.mc-afni2.2852/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii reading info from 002/template.nii... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 002/tmp.mc-afni2.2852/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-0.999888, -0.00451677, -0.0142828) j_ras = (-0.00650041, 0.989893, 0.141666) k_ras = (-0.0134986, -0.141743, 0.989811) writing to 002/fmcpr.nii.gz... ... cleaning up .... Mon Oct 3 15:44:49 EDT 2011 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg Mon Oct 3 15:44:49 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy/sj12/bold /usr/local/freesurfer/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux mri_glmfit --table /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/table.dat --glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/glm --osgm --y-out /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/y.out.nii --pca $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy/sj12/bold cmdline mri_glmfit --table /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/table.dat --glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/glm --osgm --y-out /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/y.out.nii --pca sysname Linux hostname BOTANICA machine x86_64 user michelle FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/table.dat logyflag 0 usedti 0 glmdir /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/glm Loading y from /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/table.dat Found 6 data colums Found 148 data rows Saving design matrix to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 147 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=5.4175 F=23.0628 at index 4 0 0 seed=1318655341 Measure:MC osgm Tx 0.400 Ty 1.373 Tz -0.346 Rx -1.548 Ry 5.418 Rz 0.264 Computing PCA (148) mri_glmfit done ninputs = 1 Checking inputs nframestot = 148 Allocing output Done allocing nframes = 148 Computing PCA Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/tmpdir.mcdat2extreg.2945/pca.nii mcdat2mcextreg done Mon Oct 3 15:44:50 EDT 2011 mc-sess completed SUCCESSFULLY sj12 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -self instem fmcpr outstem fmcpr.sm5.self.hemi ------------------------------ 1/1 sj12 1/1 sj12 001 lh --------- Mon Oct 3 15:44:50 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11051 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz Dim: 146530 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 110484 values in range Counting number of voxels Found 110484 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11051 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.lh.nii.gz Dim: 146530 1 1 mris_fwhm --s ld12 --hemi lh --smooth-only --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.lh.nii.gz --fwhm 5 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.lh.nii.gz --mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz ld12 lh white Number of vertices 146530 Number of faces 293056 Total area 94675.898438 GroupSurface 0 AvgVtxArea 0.646120 AvgVtxDist 0.878464 StdVtxDist 0.276589 Loading mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz Found 110484 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 Only smoothing, so saving and exiting now 1/1 sj12 002 lh --------- Mon Oct 3 15:46:27 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11111 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz Dim: 146530 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 110668 values in range Counting number of voxels Found 110668 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11111 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.lh.nii.gz Dim: 146530 1 1 mris_fwhm --s ld12 --hemi lh --smooth-only --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.lh.nii.gz --fwhm 5 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.lh.nii.gz --mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz ld12 lh white Number of vertices 146530 Number of faces 293056 Total area 94675.898438 GroupSurface 0 AvgVtxArea 0.646120 AvgVtxDist 0.878464 StdVtxDist 0.276589 Loading mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz Found 110668 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 Only smoothing, so saving and exiting now 1/1 sj12 001 rh --------- Mon Oct 3 15:48:05 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11459 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz Dim: 148246 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 113849 values in range Counting number of voxels Found 113849 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11459 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.rh.nii.gz Dim: 148246 1 1 mris_fwhm --s ld12 --hemi rh --smooth-only --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.rh.nii.gz --fwhm 5 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm5.self.rh.nii.gz --mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz ld12 rh white Number of vertices 148246 Number of faces 296488 Total area 96597.914062 GroupSurface 0 AvgVtxArea 0.651606 AvgVtxDist 0.882506 StdVtxDist 0.270838 Loading mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz Found 113849 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 Only smoothing, so saving and exiting now 1/1 sj12 002 rh --------- Mon Oct 3 15:49:47 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11508 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz Dim: 148246 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 114049 values in range Counting number of voxels Found 114049 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11508 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.rh.nii.gz Dim: 148246 1 1 mris_fwhm --s ld12 --hemi rh --smooth-only --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.rh.nii.gz --fwhm 5 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm5.self.rh.nii.gz --mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz ld12 rh white Number of vertices 148246 Number of faces 296488 Total area 96597.914062 GroupSurface 0 AvgVtxArea 0.651606 AvgVtxDist 0.882506 StdVtxDist 0.270838 Loading mask /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz Found 114049 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=14 Only smoothing, so saving and exiting now Mon Oct 3 15:51:26 EDT 2011 rawfunc2surf-sess completed ---------------------------------------- Started at Mon Oct 3 15:34:45 EDT 2011 Ended at Mon Oct 3 15:51:26 EDT 2011 preproc-sess done BOTANICA:/usr/local/freesurfer/subjects/retinotopy> selxavg3-sess -a rtopy.self.lh -s sj12 -force Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /usr/local/freesurfer/subjects/retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-111003155312.log -------------------------------------------------------------- preproc-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -a rtopy.self.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ michelle setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/preproc-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -a rtopy.self.lh -nolog Mon Oct 3 15:53:12 EDT 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sj12 Template ----------------------------- mktemplate-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -nolog -update Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:53:12 EDT 2011 Detected input format at nii sj12 Update not needed Run: 001 ---------------- Mon Oct 3 15:53:12 EDT 2011 sj12 001 Update not needed Run: 002 ---------------- Mon Oct 3 15:53:12 EDT 2011 sj12 002 Update not needed Mon Oct 3 15:53:12 EDT 2011 mktemplate-sess completed sj12 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -nolog -update ------------------------------------------------ /usr/local/freesurfer/subjects/retinotopy/sj12 Mon Oct 3 15:53:12 EDT 2011 sj12 Update not needed for session-level mask sj12 Update not needed for run 001 mask sj12 Update not needed for run 001 meanval sj12 Update not needed for run 002 mask sj12 Update not needed for run 002 meanval Mon Oct 3 15:53:13 EDT 2011 mkbrainmask-sess done sj12 Registration ----------------------------- register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Oct 3 15:53:13 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:53:13 EDT 2011 Run: 001 ---------------- Mon Oct 3 15:53:13 EDT 2011 Update not needed Run: 002 ---------------- Mon Oct 3 15:53:13 EDT 2011 Update not needed Mon Oct 3 15:53:13 EDT 2011 register-sess completed sj12 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 RunList: 001 002 sj12 001 Update not needed sj12 002 Update not needed Mon Oct 3 15:53:13 EDT 2011 mc-sess completed SUCCESSFULLY sj12 To Surface ----------------------------- rawfunc2surf-sess -fwhm 0 -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -hemi lh -self -nolog -update instem fmcpr outstem fmcpr.sm0.self.hemi ------------------------------ 1/1 sj12 1/1 sj12 001 lh --------- Mon Oct 3 15:53:13 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11051 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz Dim: 146530 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.lh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 110484 values in range Counting number of voxels Found 110484 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm0.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11051 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm0.self.lh.nii.gz Dim: 146530 1 1 1/1 sj12 002 lh --------- Mon Oct 3 15:53:31 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11111 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz Dim: 146530 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.lh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 110668 values in range Counting number of voxels Found 110668 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi lh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm0.self.lh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11111 Masking with /usr/local/freesurfer/subjects/ld12/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm0.self.lh.nii.gz Dim: 146530 1 1 Mon Oct 3 15:53:49 EDT 2011 rawfunc2surf-sess completed ---------------------------------------- Started at Mon Oct 3 15:53:12 EDT 2011 Ended at Mon Oct 3 15:53:49 EDT 2011 preproc-sess done ------------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 Mon Oct 3 15:53:49 EDT 2011 anadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2011 The MathWorks, Inc. R2011b (7.13.0.564) 64-bit (glnxa64) August 13, 2011 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sj12 ############################### /usr/local/freesurfer/subjects/retinotopy/sj12 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /usr/local/freesurfer/subjects/retinotopy Extension format = nii.gz INFO: key unrecognized, line 3, skipping Excluding 4 points nruns = 2 autostimdur = outanadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh INFO: key unrecognized, line 3, skipping Excluding 4 points INFO: key unrecognized, line 3, skipping Excluding 4 points Found 119265/158944 (75.0) voxels in mask Creating Design Matrix ... creation time = 0.014 sec DoMCFit = 1 ntptot = 296, nX = 38, DOF = 258 Saving X matrix to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/Xtmp.mat XCond = 4.51436 (normalized) Computing contrast matrices OLS Beta Pass run 1 t= 0.1 Global Mean 690.26 run 2 t= 3.6 Global Mean 688.81 Global In-Mask Mean = 689.537 (660.982) Rescale Target = 100 RescaleFactor = 0.145025 OLS Residual Pass run 1 t= 0.0 Saving rho1 run 2 t= 9.3 Saving rho1 Found 0 voxels with corrected AR1 > 0.90 Not Whitening Found 39679 zero-valued voxels Computing contrasts Starting contrasts eccen J=2 ------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen exists, deleting Computing CES Magnitude Testing Motion Correction Parameters 0.12 0.15 2.40 0.16 0.75 3.58 0.34 0.33 0.51 0.15 0.78 0.03 2.84 2.08 0.34 0.31 0.34 0.33 polar J=2 ------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar exists, deleting Computing CES Magnitude Testing Motion Correction Parameters 3.58 0.87 0.79 0.14 3.10 0.21 1.77 1.82 2.28 1.08 1.10 0.18 3.18 0.40 1.79 1.83 1.76 1.81 fast_selxavg3 done for /usr/local/freesurfer/subjects/retinotopy/sj12 >> >> >> >> ------------------------------------------ Started at Mon Oct 3 15:53:12 EDT 2011 Ended at Mon Oct 3 15:54:39 EDT 2011 selxavg3-sess completed BOTANICA:/usr/local/freesurfer/subjects/retinotopy> selxavg3-sess -a rtopy.self.rh -s sj12 -force Surface data self rh -------------------------------------------------------------- selxavg3-sess logfile is /usr/local/freesurfer/subjects/retinotopy/log/selxavg3-sess-bold-rtopy.self.rh-111003155606.log -------------------------------------------------------------- preproc-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -a rtopy.self.rh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ michelle setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/preproc-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -a rtopy.self.rh -nolog Mon Oct 3 15:56:07 EDT 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sj12 Template ----------------------------- mktemplate-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -nolog -update Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:56:07 EDT 2011 Detected input format at nii sj12 Update not needed Run: 001 ---------------- Mon Oct 3 15:56:07 EDT 2011 sj12 001 Update not needed Run: 002 ---------------- Mon Oct 3 15:56:07 EDT 2011 sj12 002 Update not needed Mon Oct 3 15:56:07 EDT 2011 mktemplate-sess completed sj12 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -nolog -update ------------------------------------------------ /usr/local/freesurfer/subjects/retinotopy/sj12 Mon Oct 3 15:56:07 EDT 2011 sj12 Update not needed for session-level mask sj12 Update not needed for run 001 mask sj12 Update not needed for run 001 meanval sj12 Update not needed for run 002 mask sj12 Update not needed for run 002 meanval Mon Oct 3 15:56:07 EDT 2011 mkbrainmask-sess done sj12 Registration ----------------------------- register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Oct 3 15:56:07 EDT 2011 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/retinotopy /usr/local/freesurfer/fsfast/bin/register-sess -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Session: /usr/local/freesurfer/subjects/retinotopy/sj12 ---------------- Mon Oct 3 15:56:07 EDT 2011 Run: 001 ---------------- Mon Oct 3 15:56:07 EDT 2011 Update not needed Run: 002 ---------------- Mon Oct 3 15:56:07 EDT 2011 Update not needed Mon Oct 3 15:56:07 EDT 2011 register-sess completed sj12 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 RunList: 001 002 sj12 001 Update not needed sj12 002 Update not needed Mon Oct 3 15:56:07 EDT 2011 mc-sess completed SUCCESSFULLY sj12 To Surface ----------------------------- rawfunc2surf-sess -fwhm 0 -s sj12 -d /usr/local/freesurfer/subjects/retinotopy -fsd bold -hemi rh -self -nolog -update instem fmcpr outstem fmcpr.sm0.self.hemi ------------------------------ 1/1 sj12 1/1 sj12 001 rh --------- Mon Oct 3 15:56:07 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11459 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz Dim: 148246 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/masks/brain.self.rh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 113849 values in range Counting number of voxels Found 113849 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm0.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11459 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/001/fmcpr.sm0.self.rh.nii.gz Dim: 148246 1 1 1/1 sj12 002 rh --------- Mon Oct 3 15:56:25 EDT 2011 mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp nearest --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/masks/brain.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11508 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz Dim: 148246 1 1 mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_binarize --i /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz --min .00001 --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz sysname Linux hostname BOTANICA machine x86_64 user michelle input /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz frame 0 nErode3d 0 nErode2d 0 output /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/masks/brain.self.rh.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 Found 114049 values in range Counting number of voxels Found 114049 voxels in final mask mri_binarize done mri_vol2surf --mov /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii --reg /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat --trgsubject ld12 --interp trilin --projfrac 0.5 --hemi rh --o /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm0.self.rh.nii.gz --noreshape --cortex srcvol = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.nii srcreg = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ld12 surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/ld12/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/ld12/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11508 Masking with /usr/local/freesurfer/subjects/ld12/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/002/fmcpr.sm0.self.rh.nii.gz Dim: 148246 1 1 Mon Oct 3 15:56:44 EDT 2011 rawfunc2surf-sess completed ---------------------------------------- Started at Mon Oct 3 15:56:07 EDT 2011 Ended at Mon Oct 3 15:56:44 EDT 2011 preproc-sess done ------------------------------------------- /usr/local/freesurfer/subjects/retinotopy/sj12 Mon Oct 3 15:56:44 EDT 2011 anadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2011 The MathWorks, Inc. R2011b (7.13.0.564) 64-bit (glnxa64) August 13, 2011 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sj12 ############################### /usr/local/freesurfer/subjects/retinotopy/sj12 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /usr/local/freesurfer/subjects/retinotopy Extension format = nii.gz INFO: key unrecognized, line 3, skipping Excluding 4 points nruns = 2 autostimdur = outanadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh INFO: key unrecognized, line 3, skipping Excluding 4 points INFO: key unrecognized, line 3, skipping Excluding 4 points Found 122907/160448 (76.6) voxels in mask Creating Design Matrix ... creation time = 0.016 sec DoMCFit = 1 ntptot = 296, nX = 38, DOF = 258 Saving X matrix to /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/Xtmp.mat XCond = 4.51436 (normalized) Computing contrast matrices OLS Beta Pass run 1 t= 0.1 Global Mean 690.26 run 2 t= 3.7 Global Mean 688.81 Global In-Mask Mean = 689.537 (655.813) Rescale Target = 100 RescaleFactor = 0.145025 OLS Residual Pass run 1 t= 0.0 Saving rho1 run 2 t= 8.5 Saving rho1 Found 0 voxels with corrected AR1 > 0.90 Not Whitening Found 37541 zero-valued voxels Computing contrasts Starting contrasts eccen J=2 ------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen exists, deleting Computing CES Magnitude Testing Motion Correction Parameters 0.12 0.15 2.40 0.16 0.75 3.58 0.34 0.33 0.51 0.15 0.78 0.03 2.84 2.08 0.34 0.31 0.34 0.33 polar J=2 ------------- /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar exists, deleting Computing CES Magnitude Testing Motion Correction Parameters 3.58 0.87 0.79 0.14 3.10 0.21 1.77 1.82 2.28 1.08 1.10 0.18 3.18 0.40 1.79 1.83 1.76 1.81 fast_selxavg3 done for /usr/local/freesurfer/subjects/retinotopy/sj12 >> >> >> >> ------------------------------------------ Started at Mon Oct 3 15:56:06 EDT 2011 Ended at Mon Oct 3 15:57:28 EDT 2011 selxavg3-sess completed BOTANICA:/usr/local/freesurfer/subjects/retinotopy> ieldsign-sess -a rtopy.self.lh -occip -s sj12 -force ieldsign-sess: Command not found. BOTANICA:/usr/local/freesurfer/subjects/retinotopy> fieldsign-sess -a rtopy.self.lh -occip -s sj12 -force ERROR: Flag -force unrecognized. -a rtopy.self.lh -occip -s sj12 -force BOTANICA:/usr/local/freesurfer/subjects/retinotopy> fieldsign-sess -a rtopy.self.lh -occip -s sj12 /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii.gz --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii.gz --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat $Id: mri_fieldsign.c,v 1.14 2011/03/02 00:04:15 nicks Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii.gz --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii.gz --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat sysname Linux hostname BOTANICA machine x86_64 user michelle eccen real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii.gz eccen imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii.gz polar real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii.gz polar imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii.gz patch occip.patch.flat subject ld12 hemi lh fwhm -1.000000 nsmooth -1 fieldsign /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii usenew 0 Reading /usr/local/freesurfer/subjects/ld12/surf/lh.sphere Reading /usr/local/freesurfer/subjects/ld12/surf/lh.occip.patch.flat Reading /usr/local/freesurfer/subjects/ld12/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) Complex Ripping Zeros ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. Rot (rad): 0 0 surfer: compute_fieldsign() mri_fieldsign done ------------------- Mon Oct 3 15:58:54 EDT 2011 mkfieldsign-sess completed BOTANICA:/usr/local/freesurfer/subjects/retinotopy> fieldsign-sess -a rtopy.self.rh -occip -s sj12 /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log mri_fieldsign --s ld12 --hemi rh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/imag.nii.gz --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/imag.nii.gz --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/fieldsign/fieldsign.nii --patch occip.patch.flat $Id: mri_fieldsign.c,v 1.14 2011/03/02 00:04:15 nicks Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_fieldsign --s ld12 --hemi rh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/imag.nii.gz --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/real.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/imag.nii.gz --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/fieldsign/fieldsign.nii --patch occip.patch.flat sysname Linux hostname BOTANICA machine x86_64 user michelle eccen real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/real.nii.gz eccen imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/eccen/imag.nii.gz polar real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/real.nii.gz polar imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/polar/imag.nii.gz patch occip.patch.flat subject ld12 hemi rh fwhm -1.000000 nsmooth -1 fieldsign /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.rh/fieldsign/fieldsign.nii usenew 0 Reading /usr/local/freesurfer/subjects/ld12/surf/rh.sphere Reading /usr/local/freesurfer/subjects/ld12/surf/rh.occip.patch.flat Reading /usr/local/freesurfer/subjects/ld12/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) Complex Ripping Zeros ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. Rot (rad): 0 0 surfer: compute_fieldsign() mri_fieldsign done ------------------- Mon Oct 3 15:59:09 EDT 2011 mkfieldsign-sess completed BOTANICA:/usr/local/freesurfer/subjects/retinotopy>