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
