Hi,
I have got the same error with freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz that I have downloaded yesterday.
Thanks
Ozlem
----------------------------------------------------------------------
Sarah,
Indeed you are correct! The rh9 freesurfer v4.0.1 distribution is missing the fsl tools. I don't know how this happened, as the other dists have it, but I have re-posted freesurfer-Linux-rh9-stable-pub-v4.0.1.tar.gz, containing the fsl tools (actually, a subset of the full fsl distribution).
recon-all will work without the fsl tool 'flirt' if there is just one structural scan. flirt is used to motion correct two or more scans.
Also, the FS-FAST tools use some of the fsl tools.
Apologies again, and also to Anil,
Nick
On Wed, 2007-11-28 at 14:03 -0600, [EMAIL PROTECTED] wrote:
i have installed version freesurfer-Linux-rh9-stable-pub-v4.0.1
and i do not see a dir for fsl, only fsafd and fsfast. i tend to get the flirt error but this does not seem to affect the completion of recon-all so i've ignored it 'til now. but just wondering why i don't see an fsl directory if there is meant to be one in the distribution package...
thanks sarah
---- Original message ----
Date: Mon, 26 Nov 2007 19:38:45 -0500 From: Nick Schmansky <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] recon-all Flirt Error To: Anil Roy <[EMAIL PROTECTED]> Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Anil,
flirt is an FSL utility that is included in the freesurfer
distribution
in the $FREESURFER_HOME/fsl directory (in bin). Normally,
freesurfer
will setup a path to it. Make sure it is in your path.
Nick
On Mon, 2007-11-26 at 16:26 -0600, Anil Roy wrote:
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 MailScanner has detected a possible
fraud attempt
from "1.86.2.1" claiming to beMailScanner warning:
numerical links are
often malicious: 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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