Hi Bruce and Doug, When you say it can be done automatically,does that mean it wouldn't require additional editing? Does it use edits that are already performed (eg., in creating surfaces with the dev version)? If so, do you know how long it would roughly take to re-create them in this way? Thanks again, Alex
-----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 9/8/2005 10:45 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? Hi Alex, you probably want to regenerate everything. Note that this can be done automatically through recon-all (Doug can tell you the switches). cheers, Bruce On Thu, 8 Sep 2005, Fornito, Alexander wrote: > Seems to be working now. Thanks Doug, you're a lifesaver!! > As an aside, will surfaces created using the 20050509 dev version be > compatible with those created using the upcoming stable release? > > -----Original Message----- > From: Doug Greve [mailto:[EMAIL PROTECTED] > Sent: Thu 9/8/2005 1:43 PM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Intstallation problems on new dev? > > > > > 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 > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > > > _______________________________________________ > 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
