Hi list, I'm running :recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_sub001In bold the error that I'm visualizing: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01Actual FREESURFER_HOME /Applications/freesurferDarwin 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 \nmri_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=0.00i_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 2013Found 1 runs/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgzChecking for (invalid) multi-frame inputs...WARNING: only one run found. This is OK, but motioncorrection cannot be performed on one run, so I'llcopy 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 \nmri_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=0.00i_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 directionschanging 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 \nINFO: 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 \ntalairach_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 \nTalAviQA: 0.96699z-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 2nIters 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_64Mon Feb 4 20:34:50 CET 2013Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nschmans@W0084482 (i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56tmpdir is ./tmp.mri_nu_correct.mni.17691/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mrimri_convert orig.mgz ./tmp.mri_nu_correct.mni.17691/nu0.mnc -odt floatmri_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=0.00i_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 2013nu_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:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot 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:......................................................................................DoneNot implemented yet in cache_volume_range_has_changed()Transforming slices:................................................................................................................................................................................................................................................................Done --------------------------------------------------------Iteration 2 Mon Feb 4 20:35:21 CET 2013nu_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:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot implemented yet in cache_volume_range_has_changed()Processing:.................................................................DoneNot 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:......................................................................................DoneNot 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/mricmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17691/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17691/ones.mgz sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user Stefano input ./tmp.mri_nu_correct.mni.17691/nu2.mncframe 0nErode3d 0nErode2d 0output ./tmp.mri_nu_correct.mni.17691/ones.mgzBinarizing based on thresholdmin -1max +infinitybinval 1binvalnot 0Found 16777216 values in rangeCounting number of voxelsFound 16777216 voxels in final maskmri_binarize donemri_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 Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoLoading ./tmp.mri_nu_correct.mni.17691/ones.mgzLoading orig.mgzVoxel Volume is 1 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentationsComputing spatial average of each frame 0Writing to ./tmp.mri_nu_correct.mni.17691/input.mean.datmri_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 Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoLoading ./tmp.mri_nu_correct.mni.17691/ones.mgzLoading ./tmp.mri_nu_correct.mni.17691/nu2.mncVoxel Volume is 1 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentationsComputing spatial average of each frame 0Writing to ./tmp.mri_nu_correct.mni.17691/output.mean.datmris_calc -o ./tmp.mri_nu_correct.mni.17691/nu2.mnc ./tmp.mri_nu_correct.mni.17691/nu2.mnc mul .98419113815649368597Saving 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.mgzmri_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=0.00i_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.mgzwriting to nu.mgz...mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgztype change took 0 minutes and 6 seconds.mapping (14, 168) to ( 3, 110) Mon Feb 4 20:36:08 CET 2013mri_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 \nusing max gradient = 1.000reading 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_305building Voronoi diagram...performing soap bubble smoothing...3d normalization pass 1 of 2building Voronoi diagram...performing soap bubble smoothing...3d normalization pass 2 of 2building Voronoi diagram...performing soap bubble smoothing...writing output to T1.mgz3D bias adjustment took 2 minutes and 50 seconds.MRIsplineNormalize(): npeaks = 19Starting OpenSpline(): npoints = 19white matter peak found at 111white matter peak found at 109gm peak at 84 (84), valley at 71 (71)csf peak at 40, setting threshold to 69white matter peak found at 111white matter peak found at 110gm 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 \naligning to atlas containing skull, setting unknown_nbr_spacing = 5reading 1 input volumes...logging results to talairach_with_skull.logreading '/Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0average std = 23.1 using min determinant for regularization = 53.40 singular and 5702 ill-conditioned covariance matrices regularizedreading '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_transformfind_optimal_transform: nsamples 3481, passno 0, spacing 8resetting wm mean[0]: 117 --> 126resetting gm mean[0]: 74 --> 74input volume #1 is the most T1-likeusing real data threshold=13.0skull 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 wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.200scaling channel 0 by 1.2initial 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-05l_intensity = 1.0000Aligning 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 3481Quasinewton: 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 0.000010Resulting 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-07l_intensity = 1.0000Aligning 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 382743Quasinewton: 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 0.000000final 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 volumeMode: Use the information of atlas (default parms, --help for details)gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0 *********************************************************The input file is T1.mgzThe output file is brainmask.auto.mgzWeighting 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 percentdone.Analyze... main basin size=361193305 voxels, voxel volume =1.000 = 361193305 mmm3 = 361193.312 cm3done.PostAnalyze...Basin Prior 44 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basindone.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 = 0.009curvature 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 = 10.96Localization 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/grayFine 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.mgzdone\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 \naligning to atlas containing skull, setting unknown_nbr_spacing = 3using MR volume brainmask.mgz to mask input volume...reading 1 input volumes...logging results to talairach.logreading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0average std = 6.9 using min determinant for regularization = 4.70 singular and 1812 ill-conditioned covariance matrices regularizedreading '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_transformfind_optimal_transform: nsamples 2772, passno 0, spacing 8resetting wm mean[0]: 102 --> 107resetting gm mean[0]: 64 --> 64input volume #1 is the most T1-likeusing real data threshold=20.0skull 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 wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.019scaling channel 0 by 1.01905initial 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-05l_intensity = 1.0000Aligning 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 2772Quasinewton: 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 0.000010Resulting 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-07l_intensity = 1.0000Aligning 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 312841Quasinewton: 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) = 844596.4after 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 0.000000final 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 \nwriting control point volume to ctrl_pts.mgzusing MR volume brainmask.mgz to mask input volume...reading 1 input volumesreading atlas from '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0reading transform from 'transforms/talairach.lta'...reading input volume from nu.mgz...resetting wm mean[0]: 102 --> 107resetting gm mean[0]: 64 --> 64input volume #1 is the most T1-likeusing real data threshold=20.0skull 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 wmbefore smoothing, mri peak at 105after smoothing, mri peak at 105, scaling input intensities by 1.019scaling channel 0 by 1.01905using 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 usedfinding 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 --> 182.02 of 1837 (0.1%) samples deletedfinding 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 --> 182.00 of 2081 (0.0%) samples deletedfinding 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 --> 182.00 of 77 (0.0%) samples deletedfinding 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 --> 182.00 of 99 (0.0%) samples deletedfinding 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 --> 182.00 of 247 (0.0%) samples deletedusing 4341 total control points for intensity normalization...bias field = 0.965 +- 0.0752 of 4339 control points discardedfinding 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 --> 146.02 of 2231 (0.1%) samples deletedfinding 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 --> 146.00 of 2411 (0.0%) samples deletedfinding 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 --> 146.011 of 109 (10.1%) samples deletedfinding 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 --> 146.011 of 115 (9.6%) samples deletedfinding 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 --> 146.08 of 315 (2.5%) samples deletedusing 5181 total control points for intensity normalization...bias field = 1.018 +- 0.05412 of 5149 control points discardedfinding 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 --> 140.02 of 2274 (0.1%) samples deletedfinding 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 --> 140.02 of 2331 (0.1%) samples deletedfinding 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 --> 140.031 of 121 (25.6%) samples deletedfinding 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 --> 140.028 of 144 (19.4%) samples deletedfinding 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 --> 140.013 of 307 (4.2%) samples deletedusing 5177 total control points for intensity normalization...bias field = 1.015 +- 0.04314 of 5101 control points discardedwriting normalized volume to norm.mgz...writing control points to ctrl_pts.mgzfreeing 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 \nnot handling expanded ventricles...using previously computed transform transforms/talairach.ltarenormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500using MR volume brainmask.mgz to mask input volume...reading 1 input volumes...logging results to talairach.logreading input volume 'norm.mgz'...reading GCA '/Applications/freesurfer/average/RB_all_2008-03-26.gca'...gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0freeing gibbs priors...done.average std[0] = 5.0label 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 0.039blurring input image with Gaussian with sigma=2.000...0000: dt=0.000, rms=0.876, neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 18445.328 ms0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19654.701 ms0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19650.012 ms0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19766.332 ms0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=7660005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=7660006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=7660007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=7660008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 Thanks,

Stefano