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

#--------------------------------------------

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

********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

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;

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;

**************************************************

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)

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;

**************** 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