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:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:36 AM
To: Fornito, Alexander
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:[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
> >
> >
> >
> >
>
>
>
>
>
