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 warning: numerical links are often malicious: 1.86.2.1" claiming to beMailScanner warning:
> numerical links are
> >> often malicious: 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
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >_______________________________________________
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> _______________________________________________
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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