None of the text in bold is of concern. It appears that mri_ca_register was running, which can take many hours to complete.
Nick On Mon, 2013-02-04 at 22:55 +0100, std...@virgilio.it wrote: > Hi list, > > > I'm running : > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject > $SUBJECTS_DIR/hptu_sub001 > In bold the error that I'm visualizing: > > > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR > is /Applications/freesurfer/subjects/subject_prova/Diff01 > Actual FREESURFER_HOME /Applications/freesurfer > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu > Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 > \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading > from /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998454, 0.00426797, -0.0554224) > j_ras = (0.0151969, 0.980022, -0.198308) > k_ras = (-0.0534688, 0.198844, 0.978572) > writing > to > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Mon Feb 4 20:34:08 CET 2013 > Found 1 runs > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > Checking for (invalid) multi-frame inputs... > 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. > \n > cp > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > \n > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 > \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > --conform \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > --conform > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading > from > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998454, 0.00426797, -0.0554224) > j_ras = (0.0151969, 0.980022, -0.198308) > k_ras = (-0.0534688, 0.198844, 0.978572) > Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing > to > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz... > \n mri_add_xform_to_header > -c > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > \n > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Mon Feb 4 20:34:17 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n > \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n > #-------------------------------------------- > #@# Talairach Failure Detection Mon Feb 4 20:34:49 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > talairach_afd: Talairach Transform: transforms/talairach.xfm OK > (p=0.4903, pval=0.1531 >= threshold=0.0050) > \n awk > -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log > \n > TalAviQA: 0.96699 > z-score: -2 > #-------------------------------------------- > #@# Nu Intensity Correction Mon Feb 4 20:34:50 CET 2013 > \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar > transforms/talairach.xfm --n 2 \n > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > /Applications/freesurfer/bin/mri_nu_correct.mni > --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu > Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > Mon Feb 4 20:34:50 CET 2013 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by nschmans@W0084482 > (i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56 > tmpdir is ./tmp.mri_nu_correct.mni.17691 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17691/nu0.mnc -odt float > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17691/nu0.mnc -odt > float > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from orig.mgz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 1.86265e-09, 7.45058e-09) > j_ras = (1.11759e-08, -5.96046e-08, -1) > k_ras = (1.86265e-09, 1, -2.98023e-08) > changing data type from uchar to float (noscale = 0)... > writing to ./tmp.mri_nu_correct.mni.17691/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Mon Feb 4 20:34:53 CET 2013 > nu_correct > -clobber ./tmp.mri_nu_correct.mni.17691/nu0.mnc > ./tmp.mri_nu_correct.mni.17691/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.17691/0/ > [Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] > [2013-02-04 20:34:53] running: > /Applications/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 ./tmp.mri_nu_correct.mni.17691/0/ > ./tmp.mri_nu_correct.mni.17691/nu0.mnc ./tmp.mri_nu_correct.mni.17691/nu1.imp > > > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Number of iterations: 44 > CV of field change: 0.000967614 > [Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] > [2013-02-04 20:35:16] running: > /Applications/freesurfer/mni/bin/make_template -quiet -shrink > 3 ./tmp.mri_nu_correct.mni.17691/nu0.mnc > ./tmp.mri_nu_correct.mni.17691/0//template.mnc > > > Transforming > slices:......................................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Transforming > slices:................................................................................................................................................................................................................................................................Done > > > -------------------------------------------------------- > Iteration 2 Mon Feb 4 20:35:21 CET 2013 > nu_correct > -clobber ./tmp.mri_nu_correct.mni.17691/nu1.mnc > ./tmp.mri_nu_correct.mni.17691/nu2.mnc -tmpdir > ./tmp.mri_nu_correct.mni.17691/1/ > [Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] > [2013-02-04 20:35:21] running: > /Applications/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 ./tmp.mri_nu_correct.mni.17691/1/ > ./tmp.mri_nu_correct.mni.17691/nu1.mnc ./tmp.mri_nu_correct.mni.17691/nu2.imp > > > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Processing:.................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Number of iterations: 20 > CV of field change: 0.000999692 > [Stefano@iMac-di-Stefano.local:/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/] > [2013-02-04 20:35:32] running: > /Applications/freesurfer/mni/bin/make_template -quiet -shrink > 3 ./tmp.mri_nu_correct.mni.17691/nu1.mnc > ./tmp.mri_nu_correct.mni.17691/1//template.mnc > > > Transforming > slices:......................................................................................Done > Not implemented yet in cache_volume_range_has_changed() > Transforming > slices:................................................................................................................................................................................................................................................................Done > > > > mri_binarize --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --min -1 > --o ./tmp.mri_nu_correct.mni.17691/ones.mgz > > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --min > -1 --o ./tmp.mri_nu_correct.mni.17691/ones.mgz > sysname Darwin > hostname iMac-di-Stefano.local > machine x86_64 > user Stefano > > > input ./tmp.mri_nu_correct.mni.17691/nu2.mnc > frame 0 > nErode3d 0 > nErode2d 0 > output ./tmp.mri_nu_correct.mni.17691/ones.mgz > Binarizing based on threshold > min -1 > max +infinity > binval 1 > binvalnot 0 > Found 16777216 values in range > Counting number of voxels > Found 16777216 voxels in final mask > mri_binarize done > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i > orig.mgz --sum ./tmp.mri_nu_correct.mni.17691/sum.junk > --avgwf ./tmp.mri_nu_correct.mni.17691/input.mean.dat > > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > cwd > cmdline mri_segstats --id 1 > --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz --i orig.mgz > --sum ./tmp.mri_nu_correct.mni.17691/sum.junk > --avgwf ./tmp.mri_nu_correct.mni.17691/input.mean.dat > sysname Darwin > hostname iMac-di-Stefano.local > machine x86_64 > user Stefano > Loading ./tmp.mri_nu_correct.mni.17691/ones.mgz > Loading orig.mgz > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 16777216 1.67772e+07 > > > Reporting on 1 segmentations > Computing spatial average of each frame > 0 > Writing to ./tmp.mri_nu_correct.mni.17691/input.mean.dat > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz > --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc > --sum ./tmp.mri_nu_correct.mni.17691/sum.junk > --avgwf ./tmp.mri_nu_correct.mni.17691/output.mean.dat > > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > cwd > cmdline mri_segstats --id 1 > --seg ./tmp.mri_nu_correct.mni.17691/ones.mgz > --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc > --sum ./tmp.mri_nu_correct.mni.17691/sum.junk > --avgwf ./tmp.mri_nu_correct.mni.17691/output.mean.dat > sysname Darwin > hostname iMac-di-Stefano.local > machine x86_64 > user Stefano > Loading ./tmp.mri_nu_correct.mni.17691/ones.mgz > Loading ./tmp.mri_nu_correct.mni.17691/nu2.mnc > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 16777216 1.67772e+07 > > > Reporting on 1 segmentations > Computing spatial average of each frame > 0 > Writing to ./tmp.mri_nu_correct.mni.17691/output.mean.dat > mris_calc > -o ./tmp.mri_nu_correct.mni.17691/nu2.mnc > ./tmp.mri_nu_correct.mni.17691/nu2.mnc mul .98419113815649368597 > Saving result to './tmp.mri_nu_correct.mni.17691/nu2.mnc' (type = > MINC ) [ ok ] > mri_convert ./tmp.mri_nu_correct.mni.17691/nu2.mnc nu.mgz --like > orig.mgz > mri_convert ./tmp.mri_nu_correct.mni.17691/nu2.mnc nu.mgz --like > orig.mgz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from ./tmp.mri_nu_correct.mni.17691/nu2.mnc... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 1.86265e-09, 7.45058e-09) > j_ras = (1.11759e-08, -5.96046e-08, -1) > k_ras = (1.86265e-09, 1, -2.98023e-08) > INFO: transform src into the like-volume: orig.mgz > writing to nu.mgz... > mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz > type change took 0 minutes and 6 seconds. > mapping (14, 168) to ( 3, 110) > > > Mon Feb 4 20:36:08 CET 2013 > mri_nu_correct.mni done > #-------------------------------------------- > #@# Intensity Normalization Mon Feb 4 20:36:08 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n mri_normalize -g 1 nu.mgz T1.mgz \n > using max gradient = 1.000 > reading from nu.mgz... > normalizing image... > talairach transform > 1.063 -0.036 0.068 -2.289; > 0.026 1.120 -0.133 -8.875; > -0.088 0.148 1.191 -31.505; > 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 2 minutes and 50 seconds. > MRIsplineNormalize(): npeaks = 19 > Starting OpenSpline(): npoints = 19 > white matter peak found at 111 > white matter peak found at 109 > gm peak at 84 (84), valley at 71 (71) > csf peak at 40, setting threshold to 69 > white matter peak found at 111 > white matter peak found at 110 > gm peak at 85 (85), valley at 57 (57) > csf peak at 33, setting threshold to 67 > #-------------------------------------------- > #@# Skull Stripping Mon Feb 4 20:38:59 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n mri_em_register -skull > nu.mgz /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta \n > aligning to atlas containing skull, setting unknown_nbr_spacing = 5 > reading 1 input volumes... > logging results to talairach_with_skull.log > reading > '/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca'... > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > average std = 23.1 using min determinant for regularization = 53.4 > 0 singular and 5702 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > freeing gibbs priors...done. > bounding unknown intensity as < 20.2 or > 943.7 > total sample mean = 92.0 (1443 zeros) > ************************************************ > spacing=8, using 3481 sample points, tol=1.00e-05... > ************************************************ > register_mri: find_optimal_transform > find_optimal_transform: nsamples 3481, passno 0, spacing 8 > resetting wm mean[0]: 117 --> 126 > resetting gm mean[0]: 74 --> 74 > input volume #1 is the most T1-like > using real data threshold=13.0 > skull bounding box = (48, 49, 39) --> (210, 226, 213) > using (102, 108, 126) as brain centroid... > mean wm in atlas = 126, using box (82,86,105) --> (121, 129,147) to > find MRI wm > before smoothing, mri peak at 105 > after smoothing, mri peak at 105, scaling input intensities by 1.200 > scaling channel 0 by 1.2 > initial log_p = -10395.9 > ************************************************ > First Search limited to translation only. > ************************************************ > Found translation: (-7.4, -13.1, -6.3): log p = -10344.984 > **************************************** > Nine parameter search. iteration 0 nscales = 0 ... > **************************************** > Result so far: scale 1.000: max_log_p=-10343.3, old_max_log_p > =-10345.0 (thresh=-10334.6) > 0.983 0.131 0.129 -29.663; > -0.129 0.991 -0.017 7.223; > -0.140 0.000 1.066 -2.456; > 0.000 0.000 0.000 1.000; > reducing scale to 0.2500 > **************************************** > Nine parameter search. iteration 1 nscales = 1 ... > **************************************** > Result so far: scale 0.250: max_log_p=-10331.8, old_max_log_p > =-10343.3 (thresh=-10332.9) > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > **************************************** > Nine parameter search. iteration 2 nscales = 1 ... > **************************************** > Result so far: scale 0.250: max_log_p=-10331.8, old_max_log_p > =-10331.8 (thresh=-10321.5) > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > reducing scale to 0.0625 > **************************************** > Nine parameter search. iteration 3 nscales = 2 ... > **************************************** > Result so far: scale 0.062: max_log_p=-10331.8, old_max_log_p > =-10331.8 (thresh=-10321.5) > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > min search scale 0.025000 reached > *********************************************** > Computing MAP estimate using 3481 samples... > *********************************************** > dt = 5.00e-06, momentum=0.80, tol=1.00e-05 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 1.00929 0.06752 0.12102 -29.00327; > -0.08608 0.98449 0.16623 -21.03892; > -0.11966 -0.16323 1.07352 15.91519; > 0.00000 0.00000 0.00000 1.00000; > nsamples 3481 > Quasinewton: input matrix > 1.00929 0.06752 0.12102 -29.00327; > -0.08608 0.98449 0.16623 -21.03892; > -0.11966 -0.16323 1.07352 15.91519; > 0.00000 0.00000 0.00000 1.00000; > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: > 006: -log(p) = 10331.8 tol 0.000010 > Resulting transform: > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > > > pass 1, spacing 8: log(p) = -10331.8 (old=-10395.9) > transform before final EM align: > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > > > ************************************************** > EM alignment process ... > Computing final MAP estimate using 382743 samples. > ************************************************** > dt = 5.00e-06, momentum=0.80, tol=1.00e-07 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 1.00929 0.06752 0.12102 -29.00327; > -0.08608 0.98449 0.16623 -21.03892; > -0.11966 -0.16323 1.07352 15.91519; > 0.00000 0.00000 0.00000 1.00000; > nsamples 382743 > Quasinewton: input matrix > 1.00929 0.06752 0.12102 -29.00327; > -0.08608 0.98449 0.16623 -21.03892; > -0.11966 -0.16323 1.07352 15.91519; > 0.00000 0.00000 0.00000 1.00000; > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: > 008: -log(p) = 1145838.5 tol 0.000000 > final transform: > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > > > writing output transformation to > transforms/talairach_with_skull.lta... > registration took 14 minutes and 43 seconds. > \n mri_watershed -T1 > -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n > > > Mode: T1 normalized volume > Mode: Use the information of atlas (default parms, --help for > details) > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > > > ********************************************************* > The input file is T1.mgz > The output file is brainmask.auto.mgz > Weighting the input with atlas information before watershed > > > *************************WATERSHED************************** > Sorting... > first estimation of the COG coord: x=131 y=121 z=129 r=76 > first estimation of the main basin volume: 1870432 voxels > Looking for seedpoints > 2 found in the cerebellum > 17 found in the rest of the brain > global maximum in x=96, y=112, z=94, Imax=255 > CSF=12, WM_intensity=110, WM_VARIANCE=5 > WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 > preflooding height equal to 10 percent > done. > Analyze... > > > main basin size=361193305 voxels, voxel volume =1.000 > = 361193305 mmm3 = 361193.312 cm3 > done. > PostAnalyze...Basin Prior > 44 basins merged thanks to atlas > ***** 0 basin(s) merged in 1 iteration(s) > ***** 0 voxel(s) added to the main basin > done. > Weighting the input with prior template > > > ****************TEMPLATE DEFORMATION**************** > > > second estimation of the COG coord: x=129,y=130, z=117, r=9449 > iterations > ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ > > > GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = > -1072089698 > RIGHT_CER CSF_MIN=0, CSF_intensity=25, CSF_MAX=47 , nb = > -1035635533 > LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = > -1086068051 > RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = > 1065522184 > LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = > -1036263885 > OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 387 > > CSF_MAX TRANSITION GM_MIN GM > GLOBAL > before analyzing : 22, 18, 6, 87 > after analyzing : 18, 22, 25, 38 > RIGHT_CER > before analyzing : 47, 40, 17, 93 > after analyzing : 35, 40, 40, 53 > LEFT_CER > before analyzing : 23, 65, 82, 90 > after analyzing : 23, 76, 82, 79 > RIGHT_BRAIN > before analyzing : 21, 22, 28, 85 > after analyzing : 21, 26, 28, 40 > LEFT_BRAIN > before analyzing : 22, 20, 13, 89 > after analyzing : 20, 23, 25, 39 > OTHER > before analyzing : 19, 16, 6, 87 > after analyzing : 16, 22, 25, 38 > mri_strip_skull: done peeling brain > highly tesselated surface with 10242 vertices > matching...65 iterations > > > *********************VALIDATION********************* > curvature mean = -0.013, std = 0.009 > curvature mean = 74.494, std = 5.862 > > > No Rigid alignment: -atlas Mode Off (basic atlas / no registration) > before rotation: sse = 6.45, sigma = 10.96 > after rotation: sse = 6.45, sigma = 10.96 > Localization of inacurate regions: Erosion-Dilation steps > the sse mean is 7.59, its var is 13.01 > before Erosion-Dilatation 5.37% of inacurate vertices > after Erosion-Dilatation 8.52% of inacurate vertices > Validation of the shape of the surface done. > Scaling of atlas fields onto current surface fields > > > ********FINAL ITERATIVE TEMPLATE DEFORMATION******** > Compute Local values csf/gray > Fine Segmentation...38 iterations > > > mri_strip_skull: done peeling brain > > > Brain Size = 1931109 voxels, voxel volume = 1.000 mm3 > = 1931109 mmm3 = 1931.109 cm3 > > > > > ****************************** > Saving brainmask.auto.mgz > done > \n cp brainmask.auto.mgz brainmask.mgz \n > #------------------------------------- > #@# EM Registration Mon Feb 4 20:54:11 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n mri_em_register -uns 3 -mask brainmask.mgz > nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca > transforms/talairach.lta \n > aligning to atlas containing skull, setting unknown_nbr_spacing = 3 > using MR volume brainmask.mgz to mask input volume... > reading 1 input volumes... > logging results to talairach.log > reading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > average std = 6.9 using min determinant for regularization = 4.7 > 0 singular and 1812 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > freeing gibbs priors...done. > bounding unknown intensity as < 14.9 or > 790.2 > total sample mean = 84.4 (994 zeros) > ************************************************ > spacing=8, using 2772 sample points, tol=1.00e-05... > ************************************************ > register_mri: find_optimal_transform > find_optimal_transform: nsamples 2772, passno 0, spacing 8 > resetting wm mean[0]: 102 --> 107 > resetting gm mean[0]: 64 --> 64 > input volume #1 is the most T1-like > using real data threshold=20.0 > skull bounding box = (61, 59, 39) --> (198, 225, 209) > using (107, 114, 124) as brain centroid... > mean wm in atlas = 107, using box (90,94,103) --> (123, 134,144) to > find MRI wm > before smoothing, mri peak at 105 > after smoothing, mri peak at 105, scaling input intensities by 1.019 > scaling channel 0 by 1.01905 > initial log_p = -7523.2 > ************************************************ > First Search limited to translation only. > ************************************************ > Found translation: (-4.0, -8.5, -13.1): log p = -7211.725 > **************************************** > Nine parameter search. iteration 0 nscales = 0 ... > **************************************** > Result so far: scale 1.000: max_log_p=-7211.7, old_max_log_p =-7211.7 > (thresh=-7204.5) > 1.000 0.000 0.000 -3.977; > 0.000 1.000 0.000 -8.523; > 0.000 0.000 1.000 -13.068; > 0.000 0.000 0.000 1.000; > reducing scale to 0.2500 > **************************************** > Nine parameter search. iteration 1 nscales = 1 ... > **************************************** > Result so far: scale 0.250: max_log_p=-7125.6, old_max_log_p =-7211.7 > (thresh=-7204.5) > 0.976 0.068 0.060 -16.633; > -0.069 1.052 -0.073 2.558; > -0.065 0.065 0.996 -8.572; > 0.000 0.000 0.000 1.000; > **************************************** > Nine parameter search. iteration 2 nscales = 1 ... > **************************************** > Result so far: scale 0.250: max_log_p=-7125.6, old_max_log_p =-7125.6 > (thresh=-7118.5) > 0.976 0.068 0.060 -16.633; > -0.069 1.052 -0.073 2.558; > -0.065 0.065 0.996 -8.572; > 0.000 0.000 0.000 1.000; > reducing scale to 0.0625 > **************************************** > Nine parameter search. iteration 3 nscales = 2 ... > **************************************** > Result so far: scale 0.062: max_log_p=-7094.4, old_max_log_p =-7125.6 > (thresh=-7118.5) > 0.976 0.085 0.059 -18.687; > -0.085 1.055 -0.075 3.581; > -0.065 0.065 0.996 -9.040; > 0.000 0.000 0.000 1.000; > **************************************** > Nine parameter search. iteration 4 nscales = 2 ... > **************************************** > Result so far: scale 0.062: max_log_p=-7093.2, old_max_log_p =-7094.4 > (thresh=-7087.3) > 0.976 0.085 0.059 -18.687; > -0.085 1.057 -0.075 3.311; > -0.065 0.065 0.996 -9.040; > 0.000 0.000 0.000 1.000; > min search scale 0.025000 reached > *********************************************** > Computing MAP estimate using 2772 samples... > *********************************************** > dt = 5.00e-06, momentum=0.80, tol=1.00e-05 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > nsamples 2772 > Quasinewton: input matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: > 007: -log(p) = 7093.2 tol 0.000010 > Resulting transform: > 0.976 0.085 0.059 -18.687; > -0.085 1.057 -0.075 3.311; > -0.065 0.065 0.996 -9.040; > 0.000 0.000 0.000 1.000; > > > pass 1, spacing 8: log(p) = -7093.2 (old=-7523.2) > transform before final EM align: > 0.976 0.085 0.059 -18.687; > -0.085 1.057 -0.075 3.311; > -0.065 0.065 0.996 -9.040; > 0.000 0.000 0.000 1.000; > > > ************************************************** > EM alignment process ... > Computing final MAP estimate using 312841 samples. > ************************************************** > dt = 5.00e-06, momentum=0.80, tol=1.00e-07 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > nsamples 312841 > Quasinewton: input matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > dfp_em_step_func: 008: -log(p) = 844596.4 > after pass:transform: ( 0.98, 0.09, 0.06, -18.69) > ( -0.08, 1.06, -0.07, 3.31) > ( -0.07, 0.06, 1.00, -9.04) > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through > quasi-newton minimization... > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH > ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR > GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: > 010: -log(p) = 844596.4 tol 0.000000 > final transform: > 0.984 0.092 0.065 -18.687; > -0.079 1.063 -0.069 3.311; > -0.066 0.064 0.996 -9.040; > 0.000 0.000 0.000 1.000; > > > writing output transformation to transforms/talairach.lta... > registration took 14 minutes and 23 seconds. > #-------------------------------------- > #@# CA Normalize Mon Feb 4 21:08:34 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz > nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca > transforms/talairach.lta norm.mgz \n > writing control point volume to ctrl_pts.mgz > using MR volume brainmask.mgz to mask input volume... > reading 1 input volumes > reading atlas from > '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > reading transform from 'transforms/talairach.lta'... > reading input volume from nu.mgz... > resetting wm mean[0]: 102 --> 107 > resetting gm mean[0]: 64 --> 64 > input volume #1 is the most T1-like > using real data threshold=20.0 > skull bounding box = (61, 59, 39) --> (198, 225, 209) > using (107, 114, 124) as brain centroid... > mean wm in atlas = 107, using box (90,94,103) --> (123, 134,144) to > find MRI wm > before smoothing, mri peak at 105 > after smoothing, mri peak at 105, scaling input intensities by 1.019 > scaling channel 0 by 1.01905 > using 244171 sample points... > INFO: compute sample coordinates transform > 0.984 0.092 0.065 -18.687; > -0.079 1.063 -0.069 3.311; > -0.066 0.064 0.996 -9.040; > 0.000 0.000 0.000 1.000; > INFO: transform used > finding control points in Left_Cerebral_White_Matter.... > found 41584 control points for structure... > bounding box (124, 63, 35) --> (195, 177, 204) > Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 182.0 > 2 of 1837 (0.1%) samples deleted > finding control points in Right_Cerebral_White_Matter.... > found 40735 control points for structure... > bounding box (61, 61, 35) --> (132, 173, 203) > Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 182.0 > 0 of 2081 (0.0%) samples deleted > finding control points in Left_Cerebellum_White_Matter.... > found 3012 control points for structure... > bounding box (129, 138, 56) --> (176, 182, 110) > Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 182.0 > 0 of 77 (0.0%) samples deleted > finding control points in Right_Cerebellum_White_Matter.... > found 2764 control points for structure... > bounding box (79, 138, 52) --> (129, 178, 109) > Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 182.0 > 0 of 99 (0.0%) samples deleted > finding control points in Brain_Stem.... > found 3520 control points for structure... > bounding box (108, 135, 87) --> (142, 199, 122) > Brain_Stem: limiting intensities to 100.0 --> 182.0 > 0 of 247 (0.0%) samples deleted > using 4341 total control points for intensity normalization... > bias field = 0.965 +- 0.075 > 2 of 4339 control points discarded > finding control points in Left_Cerebral_White_Matter.... > found 41584 control points for structure... > bounding box (124, 63, 35) --> (195, 177, 204) > Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 146.0 > 2 of 2231 (0.1%) samples deleted > finding control points in Right_Cerebral_White_Matter.... > found 40735 control points for structure... > bounding box (61, 61, 35) --> (132, 173, 203) > Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 146.0 > 0 of 2411 (0.0%) samples deleted > finding control points in Left_Cerebellum_White_Matter.... > found 3012 control points for structure... > bounding box (129, 138, 56) --> (176, 182, 110) > Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 146.0 > 11 of 109 (10.1%) samples deleted > finding control points in Right_Cerebellum_White_Matter.... > found 2764 control points for structure... > bounding box (79, 138, 52) --> (129, 178, 109) > Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 146.0 > 11 of 115 (9.6%) samples deleted > finding control points in Brain_Stem.... > found 3520 control points for structure... > bounding box (108, 135, 87) --> (142, 199, 122) > Brain_Stem: limiting intensities to 88.0 --> 146.0 > 8 of 315 (2.5%) samples deleted > using 5181 total control points for intensity normalization... > bias field = 1.018 +- 0.054 > 12 of 5149 control points discarded > finding control points in Left_Cerebral_White_Matter.... > found 41584 control points for structure... > bounding box (124, 63, 35) --> (195, 177, 204) > Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 140.0 > 2 of 2274 (0.1%) samples deleted > finding control points in Right_Cerebral_White_Matter.... > found 40735 control points for structure... > bounding box (61, 61, 35) --> (132, 173, 203) > Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 140.0 > 2 of 2331 (0.1%) samples deleted > finding control points in Left_Cerebellum_White_Matter.... > found 3012 control points for structure... > bounding box (129, 138, 56) --> (176, 182, 110) > Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 140.0 > 31 of 121 (25.6%) samples deleted > finding control points in Right_Cerebellum_White_Matter.... > found 2764 control points for structure... > bounding box (79, 138, 52) --> (129, 178, 109) > Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 140.0 > 28 of 144 (19.4%) samples deleted > finding control points in Brain_Stem.... > found 3520 control points for structure... > bounding box (108, 135, 87) --> (142, 199, 122) > Brain_Stem: limiting intensities to 84.0 --> 140.0 > 13 of 307 (4.2%) samples deleted > using 5177 total control points for intensity normalization... > bias field = 1.015 +- 0.043 > 14 of 5101 control points discarded > writing normalized volume to norm.mgz... > writing control points to ctrl_pts.mgz > freeing GCA...done. > normalization took 1 minutes and 49 seconds. > #-------------------------------------- > #@# CA Reg Mon Feb 4 21:10:23 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n mri_ca_register -nobigventricles -T transforms/talairach.lta > -align-after -mask brainmask.mgz > norm.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca > transforms/talairach.m3z \n > not handling expanded ventricles... > using previously computed transform transforms/talairach.lta > renormalizing sequences with structure alignment, equivalent to: > -renormalize > -regularize_mean 0.500 > -regularize 0.500 > using MR volume brainmask.mgz to mask input volume... > reading 1 input volumes... > logging results to talairach.log > reading input volume 'norm.mgz'... > reading GCA > '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > freeing gibbs priors...done. > average std[0] = 5.0 > label assignment complete, 0 changed (0.00%) > det(m_affine) = 1.06 (predicted orig area = 7.6) > label assignment complete, 0 changed (0.00%) > **************** pass 1 of 1 ************************ > setting smoothness coefficient to 0.039 > blurring input image with Gaussian with sigma=2.000... > 0000: dt=0.000, rms=0.876, neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 18445.328 ms > 0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19654.701 ms > 0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19650.012 ms > 0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19766.332 ms > 0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=766 > 0005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=766 > 0006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=766 > 0007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=766 > 0008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 > > > Thanks, > > > > > Stefano > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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