Dear all,
I am new freesurfer user (version 5.0.0 installed to windows using virtual
machine),
during the installation i was trying to test the installation, following the
recommended steps.
The recon-all -s terminated with errors, andi can't find the bug.
I send you the command line and the report including the error message to
help you.
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FREESURFER_HOME /home/virtualuser/freesurfer
SUBJECTS_DIR /home/virtualuser/freesurfer/subjects
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FreeSurfer:~> recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i
$SUBJECTS_DIR/sample-002.mgz -autorecon1
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects
Actual FREESURFER_HOME /home/virtualuser/freesurfer
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
/home/virtualuser/freesurfer/subjects/ernie
mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz...
/home/virtualuser/freesurfer/subjects/ernie
mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz...
#--------------------------------------------
#@# MotionCor Mon Apr 23 04:55:18 EDT 2012
Found 2 runs
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#-----------------------------------------------
/home/virtualuser/freesurfer/subjects/ernie
mri_robust_template --mov
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1
--template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale --iscaleout
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt
--subsample 200 --lta
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as
movable/source volume.
--mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as
movable/source volume.
Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz
as template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source
'/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'...
reading source
'/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'...
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 ,
epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 (
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz )
to TP 1 (
/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz )
Registration::setSourceAndTarget ...
Mov: (1, 1, 1.32812)mm and dim (256, 256, 128)
Dst: (1, 1, 1.32812)mm and dim (256, 256, 128)
Asserting both images: 1mm isotropic and (256, 256, 170) voxels
Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels.
Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels.
Reslicing using trilinear interpolation
Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels.
Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels.
Reslicing using trilinear interpolation
Registration::findSaturation
- Gaussian Pyramid
- Gaussian Pyramid
- Max Resolution used: 2
-- gpS ( 64 , 64 , 42 )
-- gpT ( 64 , 64 , 42 )
- computing centroids
- computing initial transform
-- using translation info
- running loop to estimate saturation parameter:
-- Iteration: 1 trying sat: 16
min sat: 0 ( -1 ), max sat: 16 ( 0.0356683 ), sat diff: 16
-- Iteration: 2 trying sat: 8
min sat: 0 ( -1 ), max sat: 8 ( 0.132346 ), sat diff: 8
-- Iteration: 3 trying sat: 4
min sat: 4 ( 0.391276 ), max sat: 8 ( 0.132346 ), sat diff: 4
-- Iteration: 4 trying sat: 6
min sat: 6 ( 0.21266 ), max sat: 8 ( 0.132346 ), sat diff: 2
-- Iteration: 5 trying sat: 7
min sat: 6 ( 0.21266 ), max sat: 7 ( 0.16739 ), sat diff: 1
-- Iteration: 6 trying sat: 6.5
- final SAT: 7 ( it: 6 , weight check 0.16739 <= 0.175 )
Registration::computeMultiresRegistration
- computing centroids
- computing initial transform
-- using translation info
- initial transform:
Ti = [ ...
1.0000000000000 0 0 -0.0652797588760
0 1.0000000000000 0 0.2680379336344
0 0 1.0000000000000 0.4401045835282
0 0 0 1.0000000000000 ]
- initial iscale: Ii =1
Resolution: 3 S( 32 32 21 ) T( 32 32 21 )
Iteration(f): 1 -- diff. to prev. transform: 0.706674
Iteration(f): 2 -- diff. to prev. transform: 0.0752789
Iteration(f): 3 -- diff. to prev. transform: 0.0228908
Iteration(f): 4 -- diff. to prev. transform: 0.0664109
Iteration(f): 5 -- diff. to prev. transform: 0.0548568 max it: 5
reached!
Resolution: 2 S( 64 64 42 ) T( 64 64 42 )
Iteration(f): 1 -- diff. to prev. transform: 0.192344
Iteration(f): 2 -- diff. to prev. transform: 0.0308604
Iteration(f): 3 -- diff. to prev. transform: 0.0187651
Iteration(f): 4 -- diff. to prev. transform: 0.00839767 < 0.01 :-)
Resolution: 1 S( 128 128 85 ) T( 128 128 85 )
Iteration(f): 1 -- diff. to prev. transform: 0.128598
Iteration(f): 2 -- diff. to prev. transform: 0.0134286
Iteration(f): 3 -- diff. to prev. transform: 0.00837132 < 0.01 :-)
Resolution: 0 S( 256 256 170 ) T( 256 256 170 )
Iteration(f): 1 (subsample 200) terminate called after throwing an instance
of 'std::bad_alloc'
what(): std::bad_alloc
Abort
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
recon-all -s ernie exited with ERRORS at Mon Apr 23 04:56:44 EDT 2012
FreeSurfer:~> which freesurfer
/home/virtualuser/freesurfer/bin/freesurfer
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Thanks in advanced,
Stratos
