Freesurfer September 2005

freesurfer@nmr.mgh.harvard.edu

44 participants
91 discussions

recon-all
by Keyma Prince 08 Sep '05

08 Sep '05

Hello, I tried running one of my subjects through the whole autorecon stream and I noticed more of the basal ganglia region was filled in then was described in the previous tutorial. Is this extra filling ok? The data I ran it on is located in /space/engram/11/users/rk_fmri_struc/Y24_010705a_STRUC. Thanks, Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

2 1

Intstallation problems on new dev?
by Fornito, Alexander 08 Sep '05

08 Sep '05

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 nicks@martinos01 (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.

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RE: [Freesurfer] Intstallation problems on new dev?
by Fornito, Alexander 08 Sep '05

08 Sep '05

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:greve@nmr.mgh.harvard.edu] Sent: Thu 9/8/2005 1:43 PM To: Fornito, Alexander Cc: freesurfer(a)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 nicks@martinos01 (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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

talairach transform problem
by Michele Perry 07 Sep '05

07 Sep '05

I ran recon-all -stage1 -nomotioncor -subjid <subjectID> It exited with errors during mri_fill: mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... I ran -stage1 again with rh, lh, cc, and pons seed points. It finished without errors but the cc cut was still incorrect (wm in the rh was incorrectly labelled lh wm). I opened "brain" in tkmedit and loaded the talairach transform. The talairach is really off. When I choose "corornal" view, I get horizonal view. Increasing slice numbers go superior to inferior When I choose "horizontal" view, I get an upside-down coronal view, increasing slice numbers go anterior to posterior When I choose "sagittal" view, I get a sagittal view rotated 90 degrees counter-clockwise. Increasing slice numbers go right to left. How do I fix this?

3 2

new 'dev' release for Linux rh9, centos4 and centos4_x86_64
by Nick Schmansky 07 Sep '05

07 Sep '05

Freesurfer community, For those who wish to install a 'development' release of Freesurfer on Linux RedHat 9, CentOS 4 or CentOS 4 x86_64 platforms, distribution files are now posted at: http://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D On this distribution site, a README is available: freesurfer-Linux-platform-dev20050905-full.README.txt The new distributions include: freesurfer-Linux-rh9-dev20050905-full.tar.gz freesurfer-Linux-centos4-dev20050905-full.tar.gz freesurfer-Linux-centos4_x86_64-dev20050905-full.tar.gz The 'dev' release contains all the functionality of the upcoming 'stable' release, but has not been fully tested, particularly in regards to installation issues. This 'dev' release is intended for those who wish to attempt an installation on their Linux platform, and are willing to give feedback on possible installation problems. This 'dev' release contains most of the libraries that Freesurfer requires: the MINC toolkit, Tcl/Tk/Tix and BLT libraries, GSL and Qt, as well as sample MRI data. The release may be installed in any directory. A Mac OS X 'dev' build is not available just yet. Please direct comments or questions to this mailing list.

2 4

segmentation fault during make_average_surface
by Marie Schaer 07 Sep '05

07 Sep '05

Hello, I'm trying to make an average surface using the latest version of make_average_surface (2005/08/02 19:14:20 nicks Exp), and I got the same error as posted in the following message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01135.html, with a segmentation fault when mris_average_surface is called (I get the same segmentation fault when running mris_average_surface alone): mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_test subj1 subj2 processing subject subj1... The following must be revisited******************************************* Segmentation fault I did not find in the mailing list how to solve this, thank you very much for your help, Marie Schaer

1 0

RE: [Freesurfer] mri_convert with *.IMG
by Thomas, Adam (NIH/NIMH) 06 Sep '05

06 Sep '05

Hi Michele, It might not be the most direct way of converting your data to COR format, but AFNI has a good utility for dealing with GE data: http://afni.nimh.nih.gov/pub/dist/doc/program_help/Ifile.html Then you can use mri_convert to get from AFNI to COR format. Here's an example: [antimony:07129] (nmr-dev-env) ls 008 I.001 I.014 I.027 I.040 I.053 I.066 I.079 I.092 I.105 I.118 I.002 I.015 I.028 I.041 I.054 I.067 I.080 I.093 I.106 I.119 I.003 I.016 I.029 I.042 I.055 I.068 I.081 I.094 I.107 I.120 I.004 I.017 I.030 I.043 I.056 I.069 I.082 I.095 I.108 I.121 I.005 I.018 I.031 I.044 I.057 I.070 I.083 I.096 I.109 I.122 I.006 I.019 I.032 I.045 I.058 I.071 I.084 I.097 I.110 I.123 I.007 I.020 I.033 I.046 I.059 I.072 I.085 I.098 I.111 I.124 I.008 I.021 I.034 I.047 I.060 I.073 I.086 I.099 I.112 SERHDR.008 I.009 I.022 I.035 I.048 I.061 I.074 I.087 I.100 I.113 I.010 I.023 I.036 I.049 I.062 I.075 I.088 I.101 I.114 I.011 I.024 I.037 I.050 I.063 I.076 I.089 I.102 I.115 I.012 I.025 I.038 I.051 I.064 I.077 I.090 I.103 I.116 I.013 I.026 I.039 I.052 I.065 I.078 I.091 I.104 I.117 [antimony:07129] (nmr-dev-env) Ifile 008/I.* ++ using time stamp. ++ using slice pattern alt+z ++ using output directory afni ++ Expanding file list ... ++ found 124 '*/I.*' files ++ Scanning GE headers ++ 124 files are good images ++ File time threshold = 10 s RUN 01: 008/I.001 .. 008/I.124 124 images 1 Volume(s) Found 1 complete scans. Run GERT_Reco to create AFNI bricks. [antimony:07129] (nmr-dev-env) ./GERT_Reco Will use OutBrick_r1 for this data set. Forming image list ... >From 008/I.001 ... to 008/I.124 Done with File List. on to To3D ... Now Running: to3d -save_outliers OutBrick_r1_Outliers.1D -epan -prefix OutBrick_r1 -time:zt 124 1 0 alt+z -@ < ./PangaList to3d: 2D slices into 3D datasets for AFNI, by RW Cox ++ WARNING: TR expressed in milliseconds will be converted to TR=0.000000s Illegal value of nt after -time: option Counting images: total=124 2D slices Reading images: ......................................... 3D dataset written to disk Done with To3D. READY. \012Either execute: cd afni afni & Or <rescan this> in afni [antimony:07129] (nmr-dev-env) ls afni/ OutBrick_r1+orig.BRIK OutBrick_r1+orig.HEAD [antimony:07129] (nmr-dev-env) mkdir COR [antimony:07129] (nmr-dev-env) mri_convert afni/OutBrick_r1+orig.BRIK COR/ mri_convert afni/OutBrick_r1+orig.BRIK COR/ reading from afni/OutBrick_r1+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 124) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (-126.031197, -122.851402, -46.322140) DELTA : (0.937500, 0.937500, 1.000000) IDCODE_STRING : XYZ_2zCmhd23DSvVbCOGq0klwg BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 668.000000 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.000000 ==================================================================== BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 668.000000 <--> actual max = 668.000000 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) Original Data has (0.9375, 0.9375, 1) mm size and (256, 256, 124) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to COR/... [antimony:07129] (nmr-dev-env) Hope that helps, -a --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 -----Original Message----- From: Michele Perry [mailto:mperry@ucsd.edu] Sent: Thursday, September 01, 2005 5:35 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert with *.IMG Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have tried to convert from .IMG to COR using mri_convert -it <see below> -ot cor /path/001.IMG $SUBJECTS_DIR/subjid/mri/orig Here's what I get... -it anaylze -ot cor (I get errors if I don't give an output type) (result: reading from /path/001.IMG... analyzeRead(): cannot find any files for /path/001.IMG) -it ge -ot cor (result: reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG) -it gelx -ot cor reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG I have tried running this with the .IMG files in their own separate directory and in a directory with the .HDRs and .TIFs. I've also tried running it without specifing the .IMG file, just the directory. Any ideas what I'm doing wrong? Michele _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all problem
by Paul Aparicio 06 Sep '05

06 Sep '05

Hello all, I run recon-all and get this problem: --------------------------------------------- Nu Intensity Correction Tue Sep 6 13:04:59 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, -0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/pubsw/packages/perl/5.6.0/lib/5.6.0/i686-l inux /usr/pubsw/packages/perl/5.6.0/lib/5.6.0 /usr/pubsw/packages/perl/5.6.0/lib/site_perl/5.6.0/i6 86-linux /usr/pubsw/packages/perl/5.6.0/lib/site_perl/5.6.0 /usr/pubsw/packages/perl/5.6.0/lib/site _perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct Anyone know how I might fix this? Thanks!

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Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and
by Sebastian Moeller 06 Sep '05

06 Sep '05

Hi Nick, thanks for the nice software. On 6. Sep 2005, at 05:58 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Date: Mon, 05 Sep 2005 16:32:33 -0400 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] new 'dev' release for Linux rh9, centos4 and > centos4_x86_64 > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1125952353.25463.24.camel(a)minerva.nmr.mgh.harvard.edu> > Content-Type: text/plain > > Freesurfer community, > > For those who wish to install a 'development' release > of Freesurfer on Linux RedHat 9, CentOS 4 or CentOS 4 x86_64 > platforms, distribution files are now posted at: > > http://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D > > On this distribution site, a README is available: > > freesurfer-Linux-platform-dev20050905-full.README.txt > > The new distributions include: > > freesurfer-Linux-rh9-dev20050905-full.tar.gz > > freesurfer-Linux-centos4-dev20050905-full.tar.gz > > freesurfer-Linux-centos4_x86_64-dev20050905-full.tar.gz In Bremen we are using SuSE Linux 9.3 x86_64, do you think it will be possible for you to supply a version running on that system as well. Otherwise I will try to make the centos4 x86_64 work, but it would be much nicer to have a matching version to the system, even though differences between redhat and suse should be really small. Anyway thanks for supplying such a capable system as freesurfer/fs-fast to the comunity. On a related note, will the new version alsao run on macosx 10.3 aka panther or will it reqire tiger (10.4)? Ahoi Sebastian > > The 'dev' release contains all the functionality of > the upcoming 'stable' release, but has not been fully > tested, particularly in regards to installation issues. > > This 'dev' release is intended for those who wish to > attempt an installation on their Linux platform, and are > willing to give feedback on possible installation problems. > > This 'dev' release contains most of the libraries that > Freesurfer requires: the MINC toolkit, Tcl/Tk/Tix and BLT > libraries, GSL and Qt, as well as sample MRI data. > > The release may be installed in any directory. > > A Mac OS X 'dev' build is not available just yet. > > Please direct comments or questions to this mailing list. > > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 06 Sep '05

06 Sep '05

Hi, I tried both of those. Here is what I did in order: >source freesurfer/dev/SetUpFreeSurfer.csh FREESURFER_HOME /home/people/xmeadow/freesurfer/dev FSFAST_HOME /home/people/xmeadow/freesurfer/dev/fsfast SUBJECTS_DIR /home/people/xmeadow/freesurfer/dev/subjects FUNCTIONALS_DIR /home/people/xmeadow/freesurfer/dev/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >setenv TCLLIBPATH $FREESURFER_HOME/lib/tcltktixblt/tk8.4 >csurf But I still got the same problems. Then I opened up a new terminal and did the same thing except used setenv TCL_LIBRARY $FREESURFER_HOME/lib/tcltktixblt/tk8.4 instead of TCLLIBPATH. Is there a way I can send a log of the entire errors printed in the logs to you? Because it looks as though there are many errors that are being written but are scrolling off the screen before I can read them. Thanks very much. >Xander ---- Original message ---- >Date: Fri, 02 Sep 2005 17:04:46 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: Xander Meadow <xmeadow(a)uchicago.edu> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Xander, > >Can you try setting the TCLLIBPATH var, like this: > > setenv TCLLIBPATH $FREESURFER_HOME/lib/tcltktixblt/tk8.4 > >and failing that: > > setenv TCL_LIBRARY $FREESURFER_HOME/lib/tcltktixblt/tk8.4 > >Nick > > >On Fri, 2005-09-02 at 15:50 -0500, Xander Meadow wrote: >> The files were in $FREESURFER_HOME/subjects/<subject>/scripts. I've >> removed the . that preceeds the files so my mail client wouldn't have >> problems. >> >> >Xander >> >> >> >> On Sep 2, 2005, at 3:36 PM, Nick Schmansky wrote: >> >> > Xander, >> > >> > Tksurfer and Tkmedit will generate debug files called .xdebug_tksurfer >> > and .xdebug_tkmedit in the directory in which the program is started. >> > Can you send me the contents of those files? >> > >> > Thanks, >> > >> > Nick >> > >> > >> > >> > On Sat, 2005-09-03 at 02:43 +0700, xmeadow(a)uchicago.edu wrote: >> >> Hi, >> >> >> >> I tried what you said, and after setting up the path and >> >> checking that $FREESURFER_HOME/lib/tcltktixblt/bin is at the >> >> front of the path I tried running tkmedit <subject> orig. >> >> When I did that a window popped up that had 'Medit:' in the >> >> title bar. The window had nothing but a gray background. The >> >> window stays open for about 7 seconds, and then the title >> >> switches from 'Medit:' to the name of the subject, but then >> >> the window closes. There are no error messages produced, the >> >> window just closes. >> >> >> >>> Xander >> >> >> >> ---- Original message ---- >> >>> Date: Fri, 02 Sep 2005 15:09:33 -0400 >> >>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>> Subject: Re: [Freesurfer] Lib prob? >> >>> To: Xander Meadow <xmeadow(a)uchicago.edu> >> >>> Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, >> >> Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> >>> Xander, >> >>> >> >>> Can you try executing these two statements after issuing the >> >> source >> >>> SetUpFreeSurfer.csh command? >> >>> >> >>> set path = ( $FREESURFER_HOME/lib/tcltktixblt/bin $path ) >> >>> rehash >> >>> >> >>> This will add to the binary search path the location of the >> >> tcl-tk-tix- >> >>> blt tools. I noticed it is missing from the >> >> FreeSurferEnv.csh setup >> >>> script. It is possible that the problem you are seeing is >> >> because some >> >>> of the old tools are being used (from prior installed search >> >> paths). >> >>> >> >>> Can you then try running tkmedit, such as like this: >> >>> >> >>> tkmedit <subjectname> orig >> >>> >> >>> (replacing <subjectname> with your subject id). >> >>> >> >>> Thanks, >> >>> >> >>> Nick >> >>> >> >>> >> >>> On Fri, 2005-09-02 at 11:39 -0500, Xander Meadow wrote: >> >>>> Hi, >> >>>> >> >>>> Everything was just as you predicted, but I still get the >> >> tcl and tk >> >>>> errors. >> >>>> >> >>>>> source freesurfer/dev/SetUpFreeSurfer.csh >> >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> >>>> FREESURFER_HOME /home/people/xmeadow/freesurfer/dev >> >>>> FSFAST_HOME /home/people/xmeadow/freesurfer/dev/fsfast >> >>>> SUBJECTS_DIR /home/people/xmeadow/freesurfer/dev/subjects >> >>>> FUNCTIONALS_DIR /home/people/xmeadow/freesurfer/dev/sessions >> >>>> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin >> >>>> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib >> >>>> PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >> >>>> >> >>>> >> >>>>> echo $LD_LIBRARY_PATH >> >>>> >> >> /usr/pubsw/packages/mni/current/lib:/home/people/xmeadow/freesurfer/ >> >> >> >>>> dev/lib/tclt >> >>>> ktixblt/lib:/home/people/xmeadow/freesurfer/dev/lib/ >> >>>> >> >>>>> which tkmedit >> >>>> /home/people/xmeadow/freesurfer/dev/bin//tkmedit >> >>>> >> >>>>> ldd `which tkmedit` >> >>>> libtix8.1.8.3.so => >> >>>> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/ >> >>>> lib/libtix8.1.8.3.so (0x005a2000) >> >>>> libtk8.4.so => >> >>>> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/l >> >>>> ibtk8.4.so (0x004c1000) >> >>>> libtcl8.4.so => >> >>>> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/ >> >>>> libtcl8.4.so (0x003b8000) >> >>>> libglut.so.3 => /usr/lib/libglut.so.3 (0x007ec000) >> >>>> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00af8000) >> >>>> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00b02000) >> >>>> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00123000) >> >>>> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x00101000) >> >>>> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00139000) >> >>>> libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x001b0000) >> >>>> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x009f9000) >> >>>> libgsl.so.0 => /usr/lib/libgsl.so.0 (0x0021e000) >> >>>> libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 >> >> (0x00382000) >> >>>> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00dad000) >> >>>> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x04a99000) >> >>>> libz.so.1 => /usr/lib/libz.so.1 (0x00ad2000) >> >>>> libm.so.6 => /lib/tls/libm.so.6 (0x00451000) >> >>>> libcrypt.so.1 => /lib/libcrypt.so.1 (0x03e64000) >> >>>> libc.so.6 => /lib/tls/libc.so.6 (0x008a3000) >> >>>> libdl.so.2 => /lib/libdl.so.2 (0x009f3000) >> >>>> libXext.so.6 => /usr/X11R6/lib/libXext.so.6 >> >> (0x00ac2000) >> >>>> libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 >> >> (0x003b2000) >> >>>> libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x005dc000) >> >>>> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00ce0000) >> >>>> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00cd6000) >> >>>> libpthread.so.0 => /lib/tls/libpthread.so.0 >> >> (0x00ae4000) >> >>>> /lib/ld-linux.so.2 (0x0088a000) >> >>>> >> >>>> Also, I am using the rh9 installation, because it is the >> >> latest redhat >> >>>> installation available, but the machine is currently >> >> running Enterprise >> >>>> version 4. >> >>>> >> >>>> Thanks very much. >> >>>> >> >>>>> Xander >> >>>> >> >>>> On Sep 2, 2005, at 10:43 AM, Nick Schmansky wrote: >> >>>> >> >>>>> Xander, >> >>>>> >> >>>>> The new download includes the tcl/tk/tix and blt >> >> libraries in the >> >>>>> $FREESURFER_HOME/lib/tcltktixblt directory, so this >> >> freesurfer should >> >>>>> not be using any prior installation of tix (such at that in >> >>>>> /usr/share). >> >>>>> >> >>>>> You do not need to delete any prior installations of >> >> tix/tcl/tk/blt. >> >>>>> The SetUpFreeSurfer.csh script (which calls >> >> FreeSurferEnv.csh) will set >> >>>>> the LD_LIBRARY_PATH to contain >> >> $FREESURFER_HOME/lib/tcltktixblt/lib. >> >>>>> You can confirm this setting by typing: >> >>>>> >> >>>>> env |grep LD_ >> >>>>> >> >>>>> and checking that the path is found in LD_LIBRARY_PATH. >> >>>>> >> >>>>> Also, can you run the following commands for me? >> >>>>> >> >>>>> which tkmedit >> >>>>> ldd `which tkmedit` >> >>>>> >> >>>>> The first will tell you which tkmedit you are using, to >> >> confirm that it >> >>>>> is the one that you installed. The second command will >> >> tell you >> >>>>> exactly >> >>>>> which libraries tkmedit uses (note: the ` character is >> >> not the ' >> >>>>> character, rather ` is in the upper left-hand corner of >> >> the keyboard, >> >>>>> usually). >> >>>>> >> >>>>> You should see something like this for a rh9 system: >> >>>>> >> >>>>> [kani:lib] (nmr-dev-env) which tkmedit >> >>>>> /usr/local/freesurfer/dev/bin//tkmedit >> >>>>> [kani:lib] (nmr-dev-env) ldd `which tkmedit` >> >>>>> libtix8.1.8.3.so >> >>>>> => >> >> /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtix8.1.8.3.so >> >>>>> (0x40017000) >> >>>>> libtk8.4.so >> >>>>> => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtk8.4.so >> >>>>> (0x40051000) >> >>>>> libtcl8.4.so >> >>>>> => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtcl8.4.so >> >>>>> (0x40111000) >> >>>>> libglut.so.3 => /usr/lib/libglut.so.3 (0x401be000) >> >>>>> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401f3000) >> >>>>> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 >> >> (0x401fc000) >> >>>>> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 >> >> (0x40214000) >> >>>>> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x4022a000) >> >>>>> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 >> >> (0x40232000) >> >>>>> libGL.so.1 => /usr/lib/tls/libGL.so.1 (0x402af000) >> >>>>> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 >> >> (0x40318000) >> >>>>> libgsl.so.0 => /usr/lib/libgsl.so.0 (0x403f7000) >> >>>>> libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 >> >> (0x40570000) >> >>>>> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x405a2000) >> >>>>> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x405c0000) >> >>>>> libz.so.1 => /usr/lib/libz.so.1 (0x40602000) >> >>>>> libm.so.6 => /lib/tls/libm.so.6 (0x40610000) >> >>>>> libcrypt.so.1 => /lib/libcrypt.so.1 (0x40632000) >> >>>>> libc.so.6 => /lib/tls/libc.so.6 (0x42000000) >> >>>>> libdl.so.2 => /lib/libdl.so.2 (0x40660000) >> >>>>> libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x40664000) >> >>>>> libXext.so.6 => /usr/X11R6/lib/libXext.so.6 >> >> (0x406b6000) >> >>>>> libstdc++.so.5 => /usr/lib/libstdc++.so.5 >> >> (0x406c4000) >> >>>>> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40777000) >> >>>>> libGLcore.so.1 => /usr/lib/tls/libGLcore.so.1 >> >> (0x40780000) >> >>>>> /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) >> >>>>> [kani:lib] (nmr-dev-env) >> >>>>> >> >>>>> Notice that the tix/tk/tcl libraries are found in the new >> >>>>> freesurfer/dev >> >>>>> installation path. It is necessary to have consistency >> >> among these >> >>>>> libraries (BLT is loaded dynamically). >> >>>>> >> >>>>> I'm curious to know the output of this for your machine. >> >> It seems to >> >>>>> be >> >>>>> difficult for us to predict exactly how a rh9 machine >> >> will respond to >> >>>>> our install. >> >>>>> >> >>>>> Thanks! And again, I appreciate your patience! We're >> >> trying to make >> >>>>> this install easier to use. >> >>>>> >> >>>>> Nick >> >>>>> >> >>>>> >> >>>>> >> >>>>> On Fri, 2005-09-02 at 22:24 +0700, xmeadow(a)uchicago.edu >> >> wrote: >> >>>>>> Hi, >> >>>>>> >> >>>>>> I installed the version you recommeneded and I had to make a >> >>>>>> few changes (for instance tix8.1 is installed in /usr/share >> >>>>>> instead of /usr/lib) on my machine. After creating some >> >> soft >> >>>>>> links to get around this I started up Freesurfer with the >> >>>>>> csurf command, and then inflated a brain. The brain came up >> >>>>>> like last time but I'm still getting errors in the logs, and >> >>>>>> the tools pallette still doesn't appear. However, >> >> Freesurfer >> >>>>>> no longer becomes unresponsive, it's just none of the tools >> >>>>>> are available. The errors I'm getting are: >> >>>>>> >> >>>>>> surfer: Error sending tcl command SelectVertex -1: invalid >> >>>>>> command name "SelectVertex" >> >>>>>> >> >>>>>> Whenever I move the mouse over the image of the brain. One >> >>>>>> thing to note, I don't have enough room on my /usr partition >> >>>>>> so I installed Freesurfer in my home space, but I did change >> >>>>>> the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any >> >>>>>> thoughts on why I'm still getting tcl errors? Thanks >> >> very much. >> >>>>>> >> >>>>>>> Xander >> >>>>>> >> >>>>>> ---- Original message ---- >> >>>>>>> Date: Thu, 01 Sep 2005 21:30:34 -0400 >> >>>>>>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>>>>>> Subject: Re: [Freesurfer] Lib prob? >> >>>>>>> To: xmeadow(a)uchicago.edu >> >>>>>>> Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, >> >>>>>> Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>>>>>> >> >>>>>>> Xander and Alex, >> >>>>>>> >> >>>>>>> The special rh9 dev release is available now to >> >> download at: >> >>>>>>> >> >>>>>>> http://surfer.nmr.mgh.harvard.edu/pub/dist/ >> >>>>>>> >> >>>>>>> Look for the file: >> >>>>>>> >> >>>>>>> freesurfer-Linux-rh9-dev20050901.tar.gz >> >>>>>>> >> >>>>>>> The installation readme is: >> >>>>>>> >> >>>>>>> freesurfer-Linux-rh9-dev20050901.README.txt >> >>>>>>> >> >>>>>>> You will also need the MINC tools if you don't already >> >> have them: >> >>>>>>> >> >>>>>>> mni-Linux2-2.3-i386.tar.gz >> >>>>>>> >> >>>>>>> and its readme is: >> >>>>>>> >> >>>>>>> mni-Linux2-README.txt >> >>>>>>> >> >>>>>>> Nick >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> On Fri, 2005-09-02 at 03:33 +0700, xmeadow(a)uchicago.edu >> >> wrote: >> >>>>>>>> Hi, >> >>>>>>>> >> >>>>>>>> I downloaded what hopefully is the correct version of >> >> blt, and >> >>>>>>>> after that ran your script and said everything was fine in >> >>>>>>>> terms of libraries. However, I did have to create two >> >> soft >> >>>>>>>> links. The first one was a softlink from libtix8.1.8.3 to >> >>>>>>>> libtix8.1.8.4 in /usr/lib. The second was a softlink from >> >>>>>>>> tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After >> >> making >> >>>>>>>> both of these changes I was able to run csurf, but when I >> >>>>>>>> tried to view an inflated brain the brain image would >> >> come up, >> >>>>>>>> but then freesurfer freezes and I can't do anything. >> >> In the >> >>>>>>>> logs I get the following errors: >> >>>>>>>> >> >>>>>>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>>>>>> varialble surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>>>>>> >> >>>>>>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>>>>>> variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 >> >>>>>>>> >> >>>>>>>> Unfortunately these error messages mean nothing to me, >> >> so I >> >>>>>>>> was wondering if anyone else had seen them before. Thanks >> >>>>>>>> very much. >> >>>>>>>> >> >>>>>>>>> Xander >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> ---- Original message ---- >> >>>>>>>>> Date: Thu, 01 Sep 2005 11:08:52 -0400 >> >>>>>>>>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>>>>>>>> Subject: Re: [Freesurfer] Lib prob? >> >>>>>>>>> To: xmeadow(a)uchicago.edu, "Fornito, Alexander" >> >>>>>>>> <Alexander.Fornito(a)wh.org.au> >> >>>>>>>>> Cc: Freesurfer Mailing List >> >> <freesurfer(a)nmr.mgh.harvard.edu> >> >>>>>>>>> >> >>>>>>>>> Alex and Xander, >> >>>>>>>>> >> >>>>>>>>>> From reading the error messages in your emails, it >> >>>>>> appears that >> >>>>>>>>> freesurfer is not able to find the tcl/tk, and tix >> >> libraries >> >>>>>>>> on your >> >>>>>>>>> platform. >> >>>>>>>>> >> >>>>>>>>> We have been working on trying to provide a seamless >> >> solution >> >>>>>>>> to the >> >>>>>>>>> problem of freesurfer finding the external libraries upon >> >>>>>>>> which it >> >>>>>>>>> depends, on the varied platforms that it supports. >> >>>>>>>>> >> >>>>>>>>> To help, later today, a new 'dev' build for rh9 that >> >> includes >> >>>>>>>> many of >> >>>>>>>>> the necessary libraries will be posted for download. >> >> This is >> >>>>>>>> not a >> >>>>>>>>> 'stable' release (which is still undergoing testing), >> >> but a >> >>>>>>>>> 'development' (dev) build, so it is still possible to >> >> have >> >>>>>>>> installation >> >>>>>>>>> problems, but hopefully it will install and work for >> >> you. I >> >>>>>>>> will email >> >>>>>>>>> you again when it is ready, and your patience is >> >> appreciated. >> >>>>>>>>> >> >>>>>>>>> In the meantime, I've attached a script, called >> >>>>>>>> 'fs_lib_check', which >> >>>>>>>>> will check your system for the libraries that freesurfer >> >>>>>>>> requires. I'm >> >>>>>>>>> curious to know the results of its output for your >> >> systems. >> >>>>>>>> Just type >> >>>>>>>>> 'fs_lib_check' to run it, and 'fs_lib_check --help' >> >> for help >> >>>>>>>> text. >> >>>>>>>>> >> >>>>>>>>> Nick >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander >> >> wrote: >> >>>>>>>>>> Hi, >> >>>>>>>>>> We've recently installed the >> >>>>>>>> freesurfer-Linux-rh9-dev20050729.tar.gz distribution >> >> along >> >>>>>>>> with fs_supportlibs.tar.gz. >> >>>>>>>>>> csurf works ok, but if i try to run tksurfer, I get the >> >>>>>>>> error message below. We'd appreciate any help as we've >> >> been >> >>>>>>>> stuck for a while. >> >>>>>>>>>> Thanks! >> >>>>>>>>>> >> >>>>>>>>>> tksurfer 1000027 rh white >> >>>>>>>>>> surfer: current subjects dir: >> >>>>>>>> /data/flanders/work/alex/freesurfer/subjects >> >>>>>>>>>> surfer: not in "scripts" dir ==> using cwd for >> >> session root >> >>>>>>>>>> surfer: session root data dir ($session) set to: >> >>>>>>>>>> surfer: /data/flanders/work/alex/freesurfer/subjects >> >>>>>>>>>> surfer: Reading header info from >> >>>>>>>> >> >>>>>> >> >> /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> >>>>>>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc >> >> cannot be >> >>>>>>>> found. >> >>>>>>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc >> >> cannot be >> >>>>>>>> found. >> >>>>>>>>>> surfer: vertices=152190, faces=304376 >> >>>>>>>>>> surfer: single buffered window >> >>>>>>>>>> Xlib: extension "XFree86-DRI" missing on display >> >> ":0.0". >> >>>>>>>>>> Tix_Init failed: version conflict for package "Tcl": >> >> have >> >>>>>>>> 8.3, need 8.4 >> >>>>>>>>>> surfer: using interface >> >>>>>>>> /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> >>>>>>>>>> Reading >> >> /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> >>>>>>>>>> Reading >> >>>>>> /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> >>>>>>>>>> Reading >> >> /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> >>>>>>>>>> couldn't load file "/usr/lib/libtix8.1.8.4.so": >> >>>>>>>> /usr/lib/libtix8.1.8.4.so: cannot open shared object >> >> file: No >> >>>>>>>> such file or directorysurfer: Error sending tcl command >> >>>>>>>> UpdateUndoItemLabel "Nothing to Undo": >> >>>>>>>>>> invalid command name "UpdateUndoItemLabel" >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> >>>>>>>>>> can't read "glMenuGroups(mg_OriginalVSetLoaded)": >> >> no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_InflatedVSetLoaded)": >> >> no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_PialVSetLoaded)": no such >> >>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_OverlayLoaded)": no such >> >>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_CurvatureLoaded)": no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_LabelLoaded)": no such >> >> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>>>>>> variable >> >>>>>>>>>> surfer: Error sending tcl command >> >>>>>>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>>>>>>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>>>>>> variable >> >>>>>>>>>> % surfer: Error sending tcl command MoveToolWindow >> >> 663 670: >> >>>>>>>>>> invalid command name "MoveToolWindow" >> >>>>>>>>>> surfer: Error sending tcl command MoveToolWindow 663 >> >> 670: >> >>>>>>>>>> invalid command name "MoveToolWindow" >> >>>>>>>>>> surfer: Error sending tcl command MoveToolWindow 663 >> >> 670: >> >>>>>>>>>> invalid command name "MoveToolWindow" >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> _______________________________________________ >> >>>>>>>>>> Freesurfer mailing list >> >>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >> >>>>>>>>>> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>> ________________ >> >>>>>>>>> fs_lib_check (4k bytes) >> >>>>>>>> >> >>>>>>>> >> >>>>>>> >> >>>>>> >> >>>>>> >> >>>>> >> >>>> >> >>>> >> >>> >> >> >> >> >> > >

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Freesurfer September 2005