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:[EMAIL PROTECTED]
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
wrote:
> Do you mean you're not sure if it will work?
>
> -----Original Message-----
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> 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:[EMAIL PROTECTED]
> Sent: Thu 9/8/2005 10:45 PM
> To: Fornito, Alexander
> Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] Intstallation problems
on new dev?
> Hi Alex,
>
> you probably want to regenerate everything. Note that
this can be done
> automatically through recon-all (Doug can tell you the
switches).
>
> cheers,
>
> Bruce
>
>
> On Thu, 8 Sep 2005, Fornito, Alexander wrote:
>
>
>
> Seems to be working now. Thanks Doug, you're a
lifesaver!!
> As an aside, will surfaces created using the
20050509 dev version be compatible with those created using the upcoming stable
release?
>
> -----Original Message-----
> From: Doug Greve [mailto:[EMAIL
PROTECTED]
> Sent: Thu 9/8/2005 1:43 PM
> To: Fornito, Alexander
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Intstallation
problems on new dev?
>
>
>
>
> That's due to a problem I created a few
days ago. Fixes are at:
>
>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
>
> doug
>
>
> On Thu, 8 Sep 2005, Fornito, Alexander
wrote:
>
> > Hi,
> > We've recently installed the
freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run
Debian 3.1. I noticed that unpacking the distribution did not place the perl5
directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then
downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the
$FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I
source the environment, I get:
> >
> > Setting up environment for
FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME
/usr/local/freesurfer-dev20050905
> > FSFAST_HOME
/usr/local/freesurfer-dev20050905/fsfast
> > SUBJECTS_DIR
/data/flanders/work/alex/freesurfer/subjects
> > FUNCTIONALS_DIR
/usr/local/freesurfer-dev20050905/sessions
> > MINC_BIN_DIR
/usr/local/freesurfer-dev20050905/lib/mni/bin
> > MINC_LIB_DIR
/usr/local/freesurfer-dev20050905/lib/mni/lib
> > PERL5LIB
/usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5
> > GSL_DIR
/usr/local/freesurfer-dev20050905/lib/gsl
> > QTDIR
/usr/local/freesurfer-dev20050905/lib/qt
> > TCLLIBPATH
/usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib
> > FSL_DIR /usr/local/fsl
> >
> > However, when I try to run autorecon, I get a
message saying "cmd: Undefined variable." I get this whether the environment is set
to link to perl5 in $FREESURFER_HOME/lib/mni/lib/ or in /usr/pubsw/packages/mni/current/lib/.
> > I don't even know if it's the perl
library that's the problem. Could someone please help out? As far as we're aware, all
the environments are set correctly, so we're not sure what Undefined variable is
referring to. The entire output is below:
> >
> > recon-all -autorecon1 -subjid 27_new
-hemi lh
> > INFO: SUBJECTS_DIR is
/data/flanders/work/alex/freesurfer/subjects
> > Actual FREESURFER_HOME
/usr/local/freesurfer-dev20050905
> > Linux flanders 2.4.26 #2 SMP Tue Dec
14 03:07:23 EST 2004 i686 GNU/Linux
> >
########################################
> > program versions used
> > $Id: recon-all-nmr,v 1.102 2005/09/02
18:03:58 greve Exp $
> > $Id: mri_motion_correct2,v 1.9
2004/12/14 03:37:42 greve Exp $
> > mri_convert --version
> > $
> > $Header:
/software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert
Exp $
> > minctracc.c
> > $Header:
/software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11
2004/02/12 05:54:22 rotor Exp $
> > $Header:
/software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16
19:02:51 bert Exp $
> > $Header:
/software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49
bert Exp $
> > $Id: talairach2,v 1.7 2004/08/31
18:07:37 tosa Exp $
> > mri_convert --version
> > $
> > # $Id: mritotal.in,v 1.12 2004/02/12
05:55:18 rotor Exp $
> > Program nu_correct, built from:
> > Package MNI N3, version 1.10,
compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40
> > ProgramName: mri_normalize
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp
$ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mri_watershed
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mri_segment
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mri_fill
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 14:30:08 fischl Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mri_tessellate
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris_smooth
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mris_inflate
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp
$ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris_sphere
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mris_fix_topology
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris_euler_number
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris_make_surfaces
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27
fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris_sphere
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mris_register
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp
$ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mrisp_paint
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mri_label2label
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mris2rgb
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $
User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
> > ProgramName: mri_em_register
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp
$ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mri_ca_normalize
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mri_ca_register
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl
Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> > ProgramName: mri_ca_label
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
05/09/08-01:59:54-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp
$ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
> >
#######################################
> > GCA RB40_talairach_2005-07-20.gca
> > AvgCurvTif
average.curvature.filled.buckner40.tif
> > GCS
curvature.buckner40.filled.desikan_killiany.gcs
> >
#######################################
> >
/data/flanders/work/alex/freesurfer/subjects/27_new
> > Using COR format
> >
---------------------------------------------
> > MotionCor Thu Sep 8 11:59:54 EST 2005
> >
> > INFO: no runs were found in
/data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX,
> > however, there is a volume in
/data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig,
> > so I am just going to proceed with
that as the input.
> > cmd: Undefined variable.
> >
> >
> >
_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
>
>
>
