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 > > >> > > >> _______________________________________________ > > >> 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 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
