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#--------------------------------------------
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
********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
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;************************************************** 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;
**************** 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_______________________________________________
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