[root@dhcp-129-105-146-127 freesurfer]# mri_convert -it afni -ot cor /root/U_Chicago/Anil3DVolume/Volume+orig.BRIK /root/U_Chicago/Anil3DVolume/Output.cor mri_convert -it afni -ot cor /root/U_Chicago/Anil3DVolume/Volume+orig.BRIK /root/U_Chicago/Anil3DVolume/Output.cor reading from /root/U_Chicago/Anil3DVolume/Volume+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 120) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 0, verify 0 ORIGIN : (-119.531197, -119.531197, -88.506248) DELTA : (0.937500, 0.937500, 1.487500) IDCODE_STRING : XYZ_nftQGLeg_tbZnwTm6HlmAw BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min -32768.000000 max 32512.000000 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.000000 ==================================================================== BRICK_STATS min = -32768.000000 <--> actual min = -32768.000000 BRICK_STATS max = 32512.000000 <--> actual max = 32512.000000 TR=0.00, 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) Original Data has (0.9375, 0.9375, 1.4875) mm size and (256, 256, 120) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /root/U_Chicago/Anil3DVolume/Output.cor... [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Anil3DVolume/Output.cor -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 55982 Feb 8 13:13 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 mri_convert /root/U_Chicago/Anil3DVolume/Output.cor /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz mri_convert /root/U_Chicago/Anil3DVolume/Output.cor /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Anil3DVolume/Output.cor... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Feb 8 13:16:45 CST 2007 Found 1 runs /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/rawavg.mgz /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 mri_convert /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/rawavg.mgz /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig.mgz --conform mri_convert /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/rawavg.mgz /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig.mgz --conform reading from /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig.mgz... mri_add_xform_to_header -c /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig.mgz /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Thu Feb 8 13:16:58 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri /usr/local/freesurfer/bin//mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux Thu Feb 8 13:16:58 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.11590 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11590/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11590/nu0.mnc Can't find the talairach xform '/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.11590/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Feb 8 13:17:07 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.11590/nu0.mnc ./tmp.mri_nu_correct.mni.11590/nu1.mnc [root@dhcp-129-105-146-127.speech.northwestern.edu:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/] [2007-02-08 13:17:07] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_11640/ ./tmp.mri_nu_correct.mni.11590/nu0.mnc ./tmp.mri_nu_correct.mni.11590/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 8 CV of field change: 0.00091532 [root@dhcp-129-105-146-127.speech.northwestern.edu:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/] [2007-02-08 13:17:32] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11590/nu0.mnc /usr/tmp/nu_correct_11640//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Feb 8 13:17:39 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.11590/nu1.mnc ./tmp.mri_nu_correct.mni.11590/nu2.mnc [root@dhcp-129-105-146-127.speech.northwestern.edu:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/] [2007-02-08 13:17:40] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_11784/ ./tmp.mri_nu_correct.mni.11590/nu1.mnc ./tmp.mri_nu_correct.mni.11590/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.00085611 [root@dhcp-129-105-146-127.speech.northwestern.edu:/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/] [2007-02-08 13:17:51] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11590/nu1.mnc /usr/tmp/nu_correct_11784//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.11590/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11590/nu2.mnc nu.mgz --like orig.mgz Can't find the talairach xform '/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from ./tmp.mri_nu_correct.mni.11590/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz Talairach transform /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm writing to nu.mgz... Thu Feb 8 13:18:14 CST 2007 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Thu Feb 8 13:18:14 CST 2007 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri /usr/local/freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux Thu Feb 8 13:18:14 CST 2007 tmpdir is transforms/tmp.talairach.11897 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri mri_convert nu.mgz transforms/tmp.talairach.11897/src.mnc mri_convert nu.mgz transforms/tmp.talairach.11897/src.mnc Can't find the talairach xform '/root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from nu.mgz... Talairach transform /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.11897/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.11897/src.mnc transforms/talairach.auto.xfm Thu Feb 8 13:19:06 CST 2007 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Intensity Normalization Thu Feb 8 13:19:07 CST 2007 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri mri_normalize -g 1 nu.mgz T1.mgz WM removal version using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.454 -0.030 0.001 2.330; 0.035 0.531 -0.003 -25.453; -0.001 0.003 0.582 22.210; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 6 minutes and 5 seconds. white matter peak found at 110 gm peak at 54 (54), valley at 40 (40) csf peak at 18, setting threshold to 42 white matter peak found at 110 gm peak at 55 (55), valley at 42 (42) csf peak at 18, setting threshold to 42 #-------------------------------------------- #@# Skull Stripping Thu Feb 8 13:25:14 CST 2007 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri mri_watershed T1.mgz brainmask.auto.mgz ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 9751272 Find the largest 110-component...mriSegmentReallocateVoxels: could not alloc 6190043 voxels for sno 116 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Feb 8 13:25:30 CST 2007