date:20051002

[Freesurfer] recon-all error

2005-10-02 Thread Morgan Hough

I downloaded the latest freesurfer-dev and I was testing out my install
with recon-all -autorecon-all -subjid bert and I am getting this
error.

mri_convert nu4.mnc nu.mgz
mincRead(): can't find
file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc
reading from nu4.mnc...
ERROR: converting nu to COR/mgz

The file certainly isn't there and I don't see anything in mri/norm if
that is where it should be. Here's what there is:

[EMAIL PROTECTED] bert]$ find . -name *.mnc
./mri/tmp-mri_motion_correct2-32472/cor-1.mnc
./mri/tmp-mri_motion_correct2-32472/cor-2.mnc
./mri/tmp-mri_motion_correct2-32472/cor-3.mnc

[EMAIL PROTECTED] bert]$ which nu_correct
/usr/local/freesurfer/lib/mni/bin/nu_correct

Just to double check it wasn't something special about bert I created a
new directory for my one subject that I want to process and I got the
same error. 

Thanks in advance.

Cheers,

-Morgan

-- 
Morgan G. Hough, DPhil Candidate
University of Oxford, Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom
Tel:+44 (0) 1865 222545  / Fax:  +44 (0) 1865 222717
e-mail: [EMAIL PROTECTED]  / URL:  http://www.fmrib.ox.ac.uk/~mhough


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

2005-10-02 Thread Bruce Fischl


Hi Morgan,
can you send us the entire recon-all.log file?

thanks,
Bruce
On Sun, 2 Oct 2005, Morgan 
Hough wrote:



I downloaded the latest freesurfer-dev and I was testing out my install
with recon-all -autorecon-all -subjid bert and I am getting this
error.

mri_convert nu4.mnc nu.mgz
mincRead(): can't find
file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc
reading from nu4.mnc...
ERROR: converting nu to COR/mgz

The file certainly isn't there and I don't see anything in mri/norm if
that is where it should be. Here's what there is:

[EMAIL PROTECTED] bert]$ find . -name *.mnc
./mri/tmp-mri_motion_correct2-32472/cor-1.mnc
./mri/tmp-mri_motion_correct2-32472/cor-2.mnc
./mri/tmp-mri_motion_correct2-32472/cor-3.mnc

[EMAIL PROTECTED] bert]$ which nu_correct
/usr/local/freesurfer/lib/mni/bin/nu_correct

Just to double check it wasn't something special about bert I created a
new directory for my one subject that I want to process and I got the
same error.

Thanks in advance.

Cheers,

-Morgan



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error?

2005-10-02 Thread Brian Schweinsburg, Ph.D.

Title: Re: [Freesurfer] make_average_subject error?



Hi Doug,
I changed the flags to efxv as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesnt seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.

Thanks,
Brian

[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036

set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $

set PrintHelp = 0 ;
set PrintHelp = 0

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=

if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l

**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036

set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $

set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject = average
set average_subject = average

set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l

**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $

set PrintHelp = 0 ;
set PrintHelp = 0

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=

if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l





From: Doug Greve [EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 15:04:59 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?


Try editing those scripts so that the first line is:

#!/bin/tcsh -efxv

ie, adding xv

This turns on all kinds of debugging


Brian Schweinsburg, Ph.D. wrote: 
 Re: [Freesurfer] make_average_subject error? Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.

Brian

-- 
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756



From: Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Date: Tue, 27 Sep 2005 11:16:00 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

[Freesurfer] recon-all error

Re: [Freesurfer] recon-all error

Re: [Freesurfer] make_average_subject error?

3 matches

Site Navigation

Mail list logo

Footer information