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()
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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()
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Not implemented yet in cache_volume_range_has_changed()
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Not implemented yet in cache_volume_range_has_changed()
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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