The FSL library or the path to FSL is missing.
regards,
Pedro Paulo Oliveira Jr.
-- mens. original --
Assunto: [Freesurfer] recon-all Flirt Error
De: "Anil Roy" <[EMAIL PROTECTED]>
Data: 26/11/2007 22:38
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
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