Hello All,
I wanted to test the Freesurfer installation by running recon-all but I
received an error saying flirt no found. Can someone point me to the cause
of this problem, is it a missing library or some other issue?
I have posted the output from running recon-all on bert below.
Thanks,
Anil.
[EMAIL PROTECTED] freesurfer]# recon-all -s bert -autorecon1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-rw- 1 root root 657949 Aug 18 23:25
/usr/local/freesurfer/subjects/bert/scripts/recon-all.log
Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386
GNU/Linux
flirt: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /space/freesurfer/build/pub-releases/freesurfer
#--------------------------------------------
[EMAIL PROTECTED] MotionCor Mon Nov 26 16:17:47 CST 2007
Found 3 runs
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
#-----------------------------------------------
/usr/local/freesurfer/subjects/bert
mri_motion_correct.fsl -o
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz -wild
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
tmpdir is
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009
--------------------------------------------------------------
mri_motion_correct.fsl logfile is
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log
--------------------------------------------------------------
-----------------------------------------
Converting /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
Mon Nov 26 16:18:28 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img...
Analyze Output Matrix
-1.000 0.000 -0.000 134.400;
-0.000 0.000 1.000 -111.000;
-0.000 -1.000 -0.000 129.000;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
Mon Nov 26 16:18:33 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img...
Analyze Output Matrix
-1.000 0.000 -0.000 134.400;
-0.000 0.000 1.000 -111.000;
-0.000 -1.000 -0.000 129.000;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Converting /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
Mon Nov 26 16:18:40 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
3.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
3.img...
Analyze Output Matrix
-1.000 0.000 -0.000 134.400;
-0.000 0.000 1.000 -111.000;
-0.000 -1.000 -0.000 129.000;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to -1
-----------------------------------------
Motion Correcting
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img
Mon Nov 26 16:18:45 CST 2007
/usr/local/freesurfer/subjects/bert
fsl_rigid_register -maxangle 90 -r
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img -i
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img -o
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/resampled.img
-tmpdir
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009
-cleanup
$Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $
Mon Nov 26 16:18:46 CST 2007
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/resampled.img
--------------------------------------
/usr/local/freesurfer/subjects/bert
mri_convert
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii
mri_convert
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii...
--------------------------------------
/usr/local/freesurfer/subjects/bert
mri_convert
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii
mri_convert
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii...
--------------------------------------
/usr/local/freesurfer/subjects/bert
tkregister2_cmdl --targ
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img --mov
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img --reg
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/tkregister.dat
--fslregout
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/initxfm.fslmat
--regheader --noedit --s doesnotmatter
target volume
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img
movable volume
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img
reg file
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/tkregister.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.86.2.1 2007/08/15 15:39:42 nicks Exp $
Diagnostic Level -1
INFO: loading target
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img
Tmov: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
subject = doesnotmatter
RegMat ---------------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
register: file
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/tkregister.dat
written
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -1, ref det = -1
Init FSL Mat based on geometry -------------------
1.00000000 -0.00000000 -0.00000000 -0.00000000
-0.00000000 1.00000000 -0.00000000 -0.00000000
-0.00000000 -0.00000000 1.00000000 -0.00000000
0.00000000 0.00000000 0.00000000 1.00000000
-------------------------------------------------
--------------------------------------
/usr/local/freesurfer/subjects/bert
calling eval flirt -in
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.hdr
-out
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.hdr
-bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-interp trilinear -dof 6 -ref
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.hdr
-init
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/initxfm.fslmat
-omat
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.fslmat
flirt: Command not found.
ERROR: running flirt
Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386
GNU/Linux
recon-all exited with ERRORS at Mon Nov 26 16:18:55 CST 2007
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