A new set of Linux 'dev' distributions has been uploaded which contain the recon-all bug fix. That link is:
https://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D You can either get that new distribution, or just copy the recon-all taken from Doug's link below to your $FREESURFER_HOME/bin directory. On Wed, 2005-09-07 at 23:43 -0400, Doug Greve wrote: > That's due to a problem I created a few days ago. Fixes are at: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve > > doug > > > On Thu, 8 Sep 2005, Fornito, Alexander wrote: > > > Hi, > > We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz > > distribution on our systems, which run Debian 3.1. I noticed that unpacking > > the distribution did not place the perl5 directory in > > $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then > > downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the > > $FREESURFER_HOME/lib/mni/lib directory, and set the environment > > appropriately. When I source the environment, I get: > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer-dev20050905 > > FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast > > SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects > > FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions > > MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin > > MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni/lib > > PERL5LIB /usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5 > > GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl > > QTDIR /usr/local/freesurfer-dev20050905/lib/qt > > TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib > > FSL_DIR /usr/local/fsl > > > > However, when I try to run autorecon, I get a message saying "cmd: > > Undefined variable." I get this whether the environment is set to link to > > perl5 in $FREESURFER_HOME/lib/mni/lib/ or in > > /usr/pubsw/packages/mni/current/lib/. > > I don't even know if it's the perl library that's the problem. Could > > someone please help out? As far as we're aware, all the environments are > > set correctly, so we're not sure what Undefined variable is referring to. > > The entire output is below: > > > > recon-all -autorecon1 -subjid 27_new -hemi lh > > INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects > > Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 > > Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux > > ######################################## > > program versions used > > $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ > > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > > mri_convert --version > > $ > > $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 > > 2005/03/16 19:02:52 bert Exp $ > > minctracc.c > > $Header: > > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v > > 96.11 2004/02/12 05:54:22 rotor Exp $ > > $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 > > 2005/03/16 19:02:51 bert Exp $ > > $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 > > 2005/03/16 19:02:49 bert Exp $ > > $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ > > mri_convert --version > > $ > > # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ > > Program nu_correct, built from: > > Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] > > (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40 > > ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v 1.36 > > 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v > > 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: > > $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27 > > 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ > > TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 > > 14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux > > PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v > > 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: > > $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13 > > 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v 1.28 > > 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: > > $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 > > 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_fix_topology.c,v > > 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_euler_number.c,v > > 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_make_surfaces.c,v > > 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: > > $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 > > 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_register.c,v 1.30 > > 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: > > $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mrisp_paint.c,v 1.6 > > 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_label2label.c,v > > 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ > > TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 > > 19:45:07 nicks Exp $ User: UNKNOWN Machine: flanders Platform: Linux > > PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_em_register.c,v > > 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_normalize.c,v > > 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_register.c,v > > 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: flanders > > Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: > > 30200 > > ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: > > $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_label.c,v 1.62 > > 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: flanders Platform: > > Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 > > ####################################### > > GCA RB40_talairach_2005-07-20.gca > > AvgCurvTif average.curvature.filled.buckner40.tif > > GCS curvature.buckner40.filled.desikan_killiany.gcs > > ####################################### > > /data/flanders/work/alex/freesurfer/subjects/27_new > > Using COR format > > --------------------------------------------- > > MotionCor Thu Sep 8 11:59:54 EST 2005 > > > > INFO: no runs were found in > > /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX, > > however, there is a volume in > > /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig, > > so I am just going to proceed with that as the input. > > cmd: Undefined variable. > > > > > > _______________________________________________ > > 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
