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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ozlem,
I'm not sure what it is about our rh9 platform that doesnt like FSL, but as you noticed, the 'flirt' binary is missing from the rh9 v4.0.2 tarball. I've updated the rh9 tarball (.tar.gz) file on the download site so that it now contains it, but it would be easier for you to just get 'flirt' from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/rh9
Copy it to your $FREESURFER_HOME/bin and type: chmod a+x flirt
FYI, beginning with release 4.0.2, the FSL tools are no longer included, as really only 'flirt' is needed by recon-all (and so only 'flirt' is included in the freesurfer/bin dir). If you use FS-FAST, then you may need to get the entire FSL download from their site.
Sorry for the hassle.
Nick
On Fri, 2008-01-11 at 14:24 +0200, özlem özmen okur wrote:
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 "MailScanner has detected a possible fraud attempt from "1.86.2.1" claiming to be MailScanner warning: numerical links are often malicious: 1.86.2.1" claiming to beMailScanner warning:
numerical links are
often malicious: MailScanner has detected a possible fraud attempt from "1.86.2.1" claiming to be MailScanner 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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