vivi vivi-ThinkStation-C20X Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 20 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 12323948 3758164 8565784 0 280480 1758976 -/+ buffers/cache: 1718708 10605240 Swap: 12571644 0 12571644 #------------------------------------- /media/vivi/code/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Apr 4 18:12:03 CEST 2012 mri_convert /media/vivi/images/freesurfer/000000112288/dwi.nii /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288/dwi.nii /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/vivi/images/freesurfer/000000112288/dwi.nii... TR=15000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.nii.gz... cp /media/vivi/images/freesurfer/bvec.txt /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.mghdti.bvecs cp /media/vivi/images/freesurfer/bval.bval /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.mghdti.bvals flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -13.806 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.nii.gz x y z /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.nii.gz INFO: found /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.mghdti.bvecs /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs mv -f /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.mghdti.bvals /media/vivi/images/freesurfer/000000112288Proc/dmri/bvals eddy_correct /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_orig_flip.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.nii.gz 0 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0000 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0001 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0002 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0003 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0004 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0005 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0006 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0007 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0008 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0009 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0010 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0011 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0012 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0013 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0014 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0015 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0016 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0017 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0018 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0019 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0020 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0021 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0022 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0023 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0024 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0025 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0026 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0027 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0028 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0029 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0030 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0031 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0032 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0033 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0034 processing /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_tmp0035 mv -f /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs.norot xfmrot /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.ecclog /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs.norot /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs fslroi /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz 0 4 fslmaths /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -Tmean /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz bet /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb_brain_mask.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff #------------------------------------- #@# Intra-subject registration Wed Apr 4 18:16:39 CEST 2012 mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/brain.mgz /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/brain.mgz /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/vivi/images/freesurfer/000000112288Proc/mri/brain.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz... flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz tkregister2 --mov /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz --targ /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2anat.mat --reg /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2anatorig.dat tkregister_tcl /media/vivi/code/freesurfer/tktools/tkregister2.tcl target volume /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz movable volume /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz reg file /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2anatorig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 1.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.000; 0.000 1.000 0.000 1.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -1 convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2anatorig.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2anat.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb_brain.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb_brain_anat.flt.nii.gz -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2anat.flt.mat -cost mutualinfo convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2diff.flt.mat -concat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2anatorig.flt.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2diff.flt.mat #------------------------------------- #@# Inter-subject registration Wed Apr 4 18:17:01 CEST 2012 flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_mni.nii.gz -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/mni2anat.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat -concat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/mni2diff.flt.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2mni.mat -concat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2anat.mat convert_xfm -omat /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/mni2anatorig.mat -inverse /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anatorig2mni.mat #------------------------------------- #@# Masks Wed Apr 4 18:18:33 CEST 2012 mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 5 0 2 1 7 2 41 3 46 4 77 binval 1 binvalnot 0 Found 511090 values in range Counting number of voxels Found 511090 voxels in final mask mri_binarize done mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter++.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 8 0 2 1 7 2 41 3 46 4 77 5 28 6 60 7 16 binval 1 binvalnot 0 Found 541891 values in range Counting number of voxels Found 541891 voxels in final mask mri_binarize done mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz Binarizing based on matching values nMatch 2 0 4 1 43 binval 0 binvalnot 1 Found 4631 values in range Counting number of voxels Found 4631 voxels in final mask mri_binarize done mri_aparc2aseg --s 000000112288Proc --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz SUBJECTS_DIR /media/vivi/images/freesurfer subject 000000112288Proc outvol /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 Reading lh white surface /media/vivi/images/freesurfer/000000112288Proc/surf/lh.white Reading lh pial surface /media/vivi/images/freesurfer/000000112288Proc/surf/lh.pial Loading lh annotations from /media/vivi/images/freesurfer/000000112288Proc/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /media/vivi/images/freesurfer/000000112288Proc/surf/rh.white Reading rh pial surface /media/vivi/images/freesurfer/000000112288Proc/surf/rh.pial Loading rh annotations from /media/vivi/images/freesurfer/000000112288Proc/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /media/vivi/images/freesurfer/000000112288Proc/mri/ribbon.mgz Loading filled from /media/vivi/images/freesurfer/000000112288Proc/mri/filled.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/vivi/images/freesurfer/000000112288Proc/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1018937 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 2 clusters 0 k 1.000000 1 k 1140.000000 Fixing Parahip RH WM Found 3 clusters 0 k 1.000000 1 k 1.000000 2 k 1127.000000 Writing output aseg to /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex.nii.gz Binarizing based on threshold min 1000 max 2999 binval 1 binvalnot 0 Found 538618 values in range Counting number of voxels Found 538618 voxels in final mask mri_binarize done mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz Binarizing based on threshold min 1000 max 4999 binval 1 binvalnot 0 Found 830388 values in range Counting number of voxels Found 830388 voxels in final mask mri_binarize done mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 16 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/Brain-Stem.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/vivi/code/freesurfer cmdline mri_binarize --i /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz --match 16 --o /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/Brain-Stem.nii.gz sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi input /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/Brain-Stem.nii.gz Binarizing based on matching values nMatch 1 0 16 binval 1 binvalnot 0 Found 22303 values in range Counting number of voxels Found 22303 voxels in final mask mri_binarize done fslmaths /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz -add /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/Brain-Stem.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm+bs.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/brainmask.mgz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/brainmask.mgz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/vivi/images/freesurfer/000000112288Proc/mri/brainmask.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz... fslmaths /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz -mul /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask-vent.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/vivi/images/freesurfer/000000112288Proc/mri/aparc+aseg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz... fslmaths /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg_mask.nii.gz flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/White-Matter.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/White-Matter.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter++.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter++.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/White-Matter++.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter++.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter++.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter++.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/White-Matter++.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/notventricles.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/notventricles.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/notventricles.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/notventricles.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/notventricles.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/notventricles.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/notventricles.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/cortex.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/cortex.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/cortex+2mm.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm+bs.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm+bs.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm+bs.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm+bs.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm+bs.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/cortex+2mm+bs.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/aparc+aseg.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg+2mm.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg+2mm.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg+2mm.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/aparc+aseg+2mm.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg_mask.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg_mask.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg_mask.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg_mask.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/aparc+aseg_mask.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour flip4fsl /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask-vent.nii.gz /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask-vent.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 fslswapdim /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask-vent.nii.gz fslorient -forceradiological /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask-vent.nii.gz flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/lowb.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/anat_brain_mask-vent.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/anat2mni.mat -interp nearestneighbour fslstats -t /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.nii.gz -k /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}' > /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi_snr.txt flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour flirt -in /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/lowb_brain_mask.nii.gz -ref /media/vivi/images/freesurfer/000000112288Proc/dmri/brain_anat_orig.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour #------------------------------------- #@# Tensor fit Wed Apr 4 18:24:00 CEST 2012 dtifit -k /media/vivi/images/freesurfer/000000112288Proc/dmri/dwi.nii.gz -m /media/vivi/images/freesurfer/000000112288Proc/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /media/vivi/images/freesurfer/000000112288Proc/dmri/bvecs -b /media/vivi/images/freesurfer/000000112288Proc/dmri/bvals -o /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit 0 128 0 128 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_FA.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_L1.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_L1.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_L2.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_L2.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_L3.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_L3.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_MD.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_MD.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_MO.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_MO.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat flirt -in /media/vivi/images/freesurfer/000000112288Proc/dmri/dtifit_S0.nii.gz -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz -out /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_S0.flt.nii.gz -applyxfm -init /media/vivi/images/freesurfer/000000112288Proc/dmri/xfms/diff2mni.flt.mat #------------------------------------- #@# Priors Wed Apr 4 18:24:07 CEST 2012 /media/vivi/code/freesurfer/bin/dmri_train --outdir /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.000000112288Proc.16360.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz --fa /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug cwd /media/vivi/code/freesurfer cmdline /media/vivi/code/freesurfer/bin/dmri_train --outdir /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.000000112288Proc.16360.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz --fa /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug sysname Linux hostname vivi-ThinkStation-C20X machine x86_64 user vivi Output directory: /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni Output base: lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt Training subject directory list: /tmp/subj33.000000112288Proc.16360.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz Number of control points for initial spline: 5 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 0 Loading brain mask of output subject from /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc001/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc002/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc003/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc004/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc005/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc006/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc007/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc008/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc009/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc010/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc011/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc012/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc013/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc014/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc015/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc016/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc017/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc018/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc019/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc020/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc021/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc022/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc023/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc024/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc025/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc026/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc027/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc028/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc029/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc030/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc031/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012