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
>
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