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, stdp82@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 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 basin done. Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=129,y=130, z=117, r=9449iterations ^^^^^^^^ 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 GLOBALbefore 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 brainBrain 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