Freesurfer

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

08 Sep '05

Great. Sorry, I'm a but slow on the uptake sometimes :) Thanks for your help! -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 9/9/2005 9:46 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? no, I mean just rerun all the automated steps, and retain your old edits. On Fri, 9 Sep 2005, Fornito, Alexander wrote: > Sorry, when you say "safest thing to do is to rerun everything " do you mean including doing the manual edits again? > I'm doing strcutural studies, so I want to make sure I get it right! > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Fri 9/9/2005 9:36 AM > To: Fornito, Alexander > Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Intstallation problems on new dev? > > > > probably. The safest thing to do is to rerun everything to make sure that > all your subjects were processed in the same way. This probably isn't so > important for functional studies, but can be for structural. > > On Fri, 9 Sep 2005, Fornito, Alexander wrote: > > > I understand. Good to hear I wouldn't have to do all the manual editing again. Would it still take about 24 hours from start to finish, or is much quicker on the re-run? > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Fri 9/9/2005 9:31 AM > > To: Fornito, Alexander > > Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu > > Subject: RE: [Freesurfer] Intstallation problems on new dev? > > > > > > > > we just have to test it. We've run the equivalent process many times, > > just not in the recon-all env yet. > > > > On Fri, 9 Sep 2005, Fornito, Alexander > > wrote: > > > > > Do you mean you're not sure if it will work? > > > > > > -----Original Message----- > > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > > Sent: Fri 9/9/2005 9:28 AM > > > To: Fornito, Alexander > > > Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Intstallation problems on new dev? > > > > > > > > > > > > You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. > > > > > > doug > > > > > > > > > Fornito, Alexander wrote: > > > > > > 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:fischl@nmr.mgh.harvard.edu] > > > Sent: Thu 9/8/2005 10:45 PM > > > To: Fornito, Alexander > > > Cc: Doug Greve; freesurfer(a)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: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 > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > >

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

08 Sep '05

Sorry, when you say "safest thing to do is to rerun everything " do you mean including doing the manual edits again? I'm doing strcutural studies, so I want to make sure I get it right! -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 9/9/2005 9:36 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? probably. The safest thing to do is to rerun everything to make sure that all your subjects were processed in the same way. This probably isn't so important for functional studies, but can be for structural. On Fri, 9 Sep 2005, Fornito, Alexander wrote: > I understand. Good to hear I wouldn't have to do all the manual editing again. Would it still take about 24 hours from start to finish, or is much quicker on the re-run? > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Fri 9/9/2005 9:31 AM > To: Fornito, Alexander > Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Intstallation problems on new dev? > > > > we just have to test it. We've run the equivalent process many times, > just not in the recon-all env yet. > > On Fri, 9 Sep 2005, Fornito, Alexander > wrote: > > > Do you mean you're not sure if it will work? > > > > -----Original Message----- > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: Fri 9/9/2005 9:28 AM > > To: Fornito, Alexander > > Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Intstallation problems on new dev? > > > > > > > > You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. > > > > doug > > > > > > Fornito, Alexander wrote: > > > > 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:fischl@nmr.mgh.harvard.edu] > > Sent: Thu 9/8/2005 10:45 PM > > To: Fornito, Alexander > > Cc: Doug Greve; freesurfer(a)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: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 > > > > > > > > _______________________________________________ > > 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

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

08 Sep '05

I understand. Good to hear I wouldn't have to do all the manual editing again. Would it still take about 24 hours from start to finish, or is much quicker on the re-run? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 9/9/2005 9:31 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? we just have to test it. We've run the equivalent process many times, just not in the recon-all env yet. On Fri, 9 Sep 2005, Fornito, Alexander wrote: > Do you mean you're not sure if it will work? > > -----Original Message----- > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Fri 9/9/2005 9:28 AM > To: Fornito, Alexander > Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Intstallation problems on new dev? > > > > You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. > > doug > > > Fornito, Alexander wrote: > > 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:fischl@nmr.mgh.harvard.edu] > Sent: Thu 9/8/2005 10:45 PM > To: Fornito, Alexander > Cc: Doug Greve; freesurfer(a)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: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 > > > > _______________________________________________ > 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 > > > >

3 2

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

08 Sep '05

Do you mean you're not sure if it will work? -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Fri 9/9/2005 9:28 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. doug Fornito, Alexander wrote: 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:fischl@nmr.mgh.harvard.edu] Sent: Thu 9/8/2005 10:45 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)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: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 _______________________________________________ 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

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

08 Sep '05

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:fischl@nmr.mgh.harvard.edu] Sent: Thu 9/8/2005 10:45 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)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: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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

3 2

recon-all
by Sasha Wolosin 08 Sep '05

08 Sep '05

I am having some trouble running recon-all. one thing I have observed: Freesurfer keeps searching in the /mri folder instead of the /mri/orig folder, for example, in order to run tkmedit I had to type the command as follows: tkmedit 2332 orig/orig.mgz and I had to copy the orig.mgz file from the /mri/orig folder to the /mri folder in order to run recon-all, otherwise I would get an error during the 'Nu Intensity Correction' step. Is this what it is supposed to do? I still get an error during the mri_normalize step (see below- the error is all the way at the end) Do you know what I might be missing? Thanks, Sasha [wolosin@localhost mri]# recon-all -subjid 2332 -autorecon1 -mgz INFO: SUBJECTS_DIR is /home/wolosin/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ minctracc.c $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 $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- MotionCor Thu Sep 8 16:34:35 EDT 2005 INFO: no runs were found in /home/wolosin/subjects/2332/mri, however, there is a volume /home/wolosin/subjects/2332/mri/rawavg.mgz, so I am just going to proceed with that as the input. --------------------------------------------- Nu Intensity Correction Thu Sep 8 16:34:38 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:41] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 1646/ nu0.mnc nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 22 CV of field change: 0.00094628 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:58] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu0.mnc /us r/tmp/nu_correct_1646//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu1.mnc nu2.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:01] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 1951/ nu1.mnc nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 12 CV of field change: 0.000947063 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:10] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu1.mnc /us r/tmp/nu_correct_1951//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu2.mnc nu3.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:13] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 2142/ nu2.mnc nu3.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 9 CV of field change: 0.000974347 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:20] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu2.mnc /us r/tmp/nu_correct_2142//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu3.mnc nu4.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:23] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 2295/ nu3.mnc nu4.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 8 CV of field change: 0.000890052 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:30] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu3.mnc /us r/tmp/nu_correct_2295//template.mnc Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done mri_convert nu4.mnc nu.mgz mri_convert nu4.mnc nu.mgz reading from nu4.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mgz... --------------------------------------------- Talairach Thu Sep 8 16:35:36 EDT 2005 /home/wolosin/subjects/2332/mri talairach2 2332 .mgz INFO: registering 2332 Thu Sep 8 16:35:36 EDT 2005 -------------------------------------------- mri_convert nu.mgz nu.mnc mri_convert nu.mgz nu.mnc reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm nu.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /home/wolosin/subjects/2332/mri/transforms/talairach.xfm /home/wolosin/subjects/2332/mri/orig.mgz /home/wolosin/subjects/2332/mri/orig.m gz INFO: extension is mgz Thu Sep 8 16:36:16 EDT 2005 --------------------------------------------- Intensity Normalization Thu Sep 8 16:36:16 EDT 2005 /home/wolosin/subjects/2332/mri mri_normalize nu.mgz T1.mgz reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Sep 8 16:37:02 EDT 2005 Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

1 0

image output question
by Tracy Wang 08 Sep '05

08 Sep '05

Hi all, is there anyway to change space of the images from 256 x 256 x 256 (in my case in minc format) to output to 172 x 220 x 156? Thanks! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

1 0

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.

5 4

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

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