/usr/local/freesurfer/dev/bin/defect-seg --s 099 $Id: defect-seg,v 1.2 2008/11/26 00:26:24 greve Exp $ Tue Dec 9 17:49:22 EST 2008 Linux ukase 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099 setenv SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion mri_surfcluster --in surf/lh.defect_labels --thmin .5 --hemi lh --surf orig.nofix --subject 099 --sum /tmp/defect-seg.2858.lh.sum thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.41 2008/07/15 16:42:59 greve Exp $ hemi = lh srcid = surf/lh.defect_labels srcsubjid = 099 srcsurf = orig.nofix srcframe = 0 thsign = abs thmin = 0.5 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = /tmp/defect-seg.2858.lh.sum subjectsdir = /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/transforms/talairach.xfm 1.067 -0.007 0.024 -2.347; 0.087 1.126 0.336 7.607; -0.051 -0.323 1.215 0.393; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.orig.nofix Done reading source surface Computing metric properties Loading source values number of voxels in search space = 109206 Done loading source values (nvtxs = 109206) overall max = 40 at vertex 107158 overall min = 0 at vertex 0 surface nvertices 109206 surface area 109271.999843 surface area 109272.000000 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=0.500000 (0.500000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 41 clusters Max cluster size 1026.833374 INFO: fixing MNI talairach coordinates mri_surf2vol --identity 099 --surf orig.nofix --template mri/orig.mgz --surfval surf/lh.defect_labels --hemi lh --o mri/surface.defects.mgz --add 1000 gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: ------------------------------ -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; -------------------------------------------------- subjects dir /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion surface value path surf/lh.defect_labels hemi lh mksurfmask 0 projfrac 0 outvol path mri/surface.defects.mgz template path mri/orig.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = 0.000000 0.000000 0.000000 Gdiag_no -1 Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.orig.nofix Done reading source surface INFO: reading surf/lh.defect_labels as curv Done loading source values (nvtxs = 109206) INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 109206 voxels in the volume Adding 1000.000000 to non-zero voxels INFO: writing output volume to mri/surface.defects.mgz done mris_seg2annot --seg surf/lh.defect_labels --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h lh --o lh.defects.nofix.annot --surf orig.nofix $Id: mris_seg2annot.c,v 1.8 2008/11/25 23:15:55 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099 cmdline mris_seg2annot --seg surf/lh.defect_labels --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h lh --o lh.defects.nofix.annot --surf orig.nofix sysname Linux hostname ukase machine i686 user sita subject 099 hemi lh surfseg surf/lh.defect_labels ctab /usr/local/freesurfer/dev/DefectLUT.txt annotfile lh.defects.nofix.annot Reading ctab /usr/local/freesurfer/dev/DefectLUT.txt Reading surface seg surf/lh.defect_labels Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.orig.nofix Writing annot to lh.defects.nofix.annot writing colortable into annotation file... mri_surf2surf --s 099 --sval surf/lh.defect_labels --tval surf/lh.defect_labels.fix.mgz --hemi lh --srcsurfreg orig.nofix --trgsurfreg orig --mapmethod nnf Source registration surface changed to orig.nofix Target registration surface changed to orig srcsubject = 099 srcval = surf/lh.defect_labels srctype = trgsubject = 099 trgval = surf/lh.defect_labels.fix.mgz trgtype = srcsurfreg = orig.nofix trgsurfreg = orig srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.orig.nofix Loading source data Reading target surface reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.orig Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (106495) Surf2Surf: Dividing by number of hits (106495) INFO: nSrcLost = 21108 nTrg121 = 106495, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 71810, nSrcLost = 21108, nSrcMulti = 37396, MnSrcMultiHits = 0.927506 Saving target data mris_seg2annot --seg surf/lh.defect_labels.fix.mgz --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h lh --o lh.defects.fix.annot $Id: mris_seg2annot.c,v 1.8 2008/11/25 23:15:55 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099 cmdline mris_seg2annot --seg surf/lh.defect_labels.fix.mgz --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h lh --o lh.defects.fix.annot sysname Linux hostname ukase machine i686 user sita subject 099 hemi lh surfseg surf/lh.defect_labels.fix.mgz ctab /usr/local/freesurfer/dev/DefectLUT.txt annotfile lh.defects.fix.annot Reading ctab /usr/local/freesurfer/dev/DefectLUT.txt Reading surface seg surf/lh.defect_labels.fix.mgz Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/lh.white Writing annot to lh.defects.fix.annot writing colortable into annotation file... mri_surfcluster --in surf/rh.defect_labels --thmin .5 --hemi rh --surf orig.nofix --subject 099 --sum /tmp/defect-seg.2858.rh.sum thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.41 2008/07/15 16:42:59 greve Exp $ hemi = rh srcid = surf/rh.defect_labels srcsubjid = 099 srcsurf = orig.nofix srcframe = 0 thsign = abs thmin = 0.5 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = /tmp/defect-seg.2858.rh.sum subjectsdir = /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/transforms/talairach.xfm 1.067 -0.007 0.024 -2.347; 0.087 1.126 0.336 7.607; -0.051 -0.323 1.215 0.393; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.orig.nofix Done reading source surface Computing metric properties Loading source values number of voxels in search space = 111898 Done loading source values (nvtxs = 111898) overall max = 48 at vertex 111553 overall min = 0 at vertex 0 surface nvertices 111898 surface area 111979.999852 surface area 111980.000000 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=0.500000 (0.500000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 48 clusters Max cluster size 1515.333374 INFO: fixing MNI talairach coordinates mri_surf2vol --identity 099 --surf orig.nofix --template mri/orig.mgz --surfval surf/rh.defect_labels --hemi rh --o mri/surface.defects.mgz --add 2000 --merge mri/surface.defects.mgz gdiagno = -1 Using merge volume as template Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: ------------------------------ -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; -------------------------------------------------- subjects dir /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion surface value path surf/rh.defect_labels hemi rh mksurfmask 0 projfrac 0 outvol path mri/surface.defects.mgz template path mri/surface.defects.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = 0.000000 0.000000 0.000000 Gdiag_no -1 Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.orig.nofix Done reading source surface INFO: reading surf/rh.defect_labels as curv Done loading source values (nvtxs = 111898) INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 111898 voxels in the volume Adding 2000.000000 to non-zero voxels INFO: writing output volume to mri/surface.defects.mgz done mris_seg2annot --seg surf/rh.defect_labels --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h rh --o rh.defects.nofix.annot --surf orig.nofix $Id: mris_seg2annot.c,v 1.8 2008/11/25 23:15:55 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099 cmdline mris_seg2annot --seg surf/rh.defect_labels --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h rh --o rh.defects.nofix.annot --surf orig.nofix sysname Linux hostname ukase machine i686 user sita subject 099 hemi rh surfseg surf/rh.defect_labels ctab /usr/local/freesurfer/dev/DefectLUT.txt annotfile rh.defects.nofix.annot Reading ctab /usr/local/freesurfer/dev/DefectLUT.txt Reading surface seg surf/rh.defect_labels Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.orig.nofix Writing annot to rh.defects.nofix.annot writing colortable into annotation file... mri_surf2surf --s 099 --sval surf/rh.defect_labels --tval surf/rh.defect_labels.fix.mgz --hemi rh --srcsurfreg orig.nofix --trgsurfreg orig --mapmethod nnf Source registration surface changed to orig.nofix Target registration surface changed to orig srcsubject = 099 srcval = surf/rh.defect_labels srctype = trgsubject = 099 trgval = surf/rh.defect_labels.fix.mgz trgtype = srcsurfreg = orig.nofix trgsurfreg = orig srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.orig.nofix Loading source data Reading target surface reg /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.orig Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (107607) Surf2Surf: Dividing by number of hits (107607) INFO: nSrcLost = 22852 nTrg121 = 107607, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 72763, nSrcLost = 22852, nSrcMulti = 39135, MnSrcMultiHits = 0.890354 Saving target data mris_seg2annot --seg surf/rh.defect_labels.fix.mgz --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h rh --o rh.defects.fix.annot $Id: mris_seg2annot.c,v 1.8 2008/11/25 23:15:55 greve Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099 cmdline mris_seg2annot --seg surf/rh.defect_labels.fix.mgz --ctab /usr/local/freesurfer/dev/DefectLUT.txt --s 099 --h rh --o rh.defects.fix.annot sysname Linux hostname ukase machine i686 user sita subject 099 hemi rh surfseg surf/rh.defect_labels.fix.mgz ctab /usr/local/freesurfer/dev/DefectLUT.txt annotfile rh.defects.fix.annot Reading ctab /usr/local/freesurfer/dev/DefectLUT.txt Reading surface seg surf/rh.defect_labels.fix.mgz Reading surface /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/surf/rh.white Writing annot to rh.defects.fix.annot writing colortable into annotation file... Tue Dec 9 17:52:24 EST 2008 defect-seg done