RE: [Freesurfer] Intstallation problems on new dev? - Freesurfer

8 Sep 2005

      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@nmr.mgh.harvard.edu 
    Subject: RE: [Freesurfer] Intstallation problems on new dev?
no, I mean

On Fri, 9

> Sorry, > I'm > > > > >       To: Fornito, Alexander > > > > > > > > > > > > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       >       wrote: >       > >       > >       >       > >       > >       > >       > >       > >       > >       > >       >       > >       >       > >       >       > >       > >       >       > >       > >       >       > >       >       > >       > >       >       > >       > >       > >       > >       > >       > >       >       > >       >       > >       > >       > >       > >       > >       > >       > >       > >       >       > >       > >       > >       >       > >       > >       >       > >       > >       >       > >       >       > >       > >       >       > >       >       > >       >       > >       > >       > >       >       > >       > >       > >       > >       > >       > >       > >       >       > >       >       > >       >       > >       >       > >       > >       >       > >       > >       >       > >       > >       >       > >       >       > >       > >       >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       > >       >       > >       > >       > >       > >       > >       > >       > >       >       > >       >       > >       >       > >       > >       > >       > >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       > >       >       >       -- >       > >       > >       > >       > >       > >       >       > >       >       > >       >       > >       >       > >       > >       > >       > >       > >       > > > > > >

just rerun all the automated steps, and retain your old edits. Sep 2005, Fornito, Alexander wrote: when you say "safest thing to do is to rerun everything " do you mean including doing the manual edits again? 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 Cc: Doug Greve; freesurfer@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@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 > 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@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@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@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@nmr.mgh.harvard.edu >                               > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >                               > >                               > >                               > >                               -- >                               Douglas N. Greve, Ph.D. >                               MGH-NMR Center >                               greve@nmr.mgh.harvard.edu >                               Phone Number: 617-724-2358 >                               Fax: 617-726-7422 >                       _______________________________________________ >                       Freesurfer mailing list >                       Freesurfer@nmr.mgh.harvard.edu >                       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >       Douglas N. Greve, Ph.D. >       MGH-NMR Center >       greve@nmr.mgh.harvard.edu >       Phone Number: 617-724-2358 >       Fax: 617-726-7422