We're running on a Red Hat Enterprise 4 (kernel 2.6.9-22) using Freesurfer 3 (downloaded on 3/406)

We can give you all the path for the files, but since this is not an MGH server I'm not sure this will be useful to you.

Here is the command and the output.

[tashmoo:analysis] (freesurfer-stable) tkmedit-sess -sf sessid -df sessdir -analysis localizer_sm5 -contrast avb -map sig -mgz

--------------------------------------------------------------

tkmedit-sess logfile is /space/dilks/filling-in/analysis/log/tkmedit-sess.log

--------------------------------------------------------------

setenv SUBJECTS_DIR /space/sharedProjects/subjectsDir

INFO: Found session in: /space/dilks/filling-in/data//filling-in001

grep: /space/dilks/filling-in/data//filling-in001/session.info: No such file or directory

INFO: Found session in: /space/dilks/filling-in/data//filling-in001

grep: /space/dilks/filling-in/data//filling-in001/session.info: No such file or directory

INFO: subject is filling-in001

INFO: Anatomical directory set to /space/sharedProjects/subjectsDir/filling-in001/mri/orig

------------------------

SUBJECTS_DIR /space/sharedProjects/subjectsDir

/space/dilks/filling-in/analysis

tkmedit filling-in001 orig.mgz -overlay /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5/avb/sig_000.bfloat -overlay-reg /space/dilks/filling-in/data/filling-in001/bold/register.dat -fthresh 2 -fmid 5 -fslope 1 -aux brain.mgz

------------------------

-----------------------------------------------------------------

Could not find the direction cosine information.

Will use the CORONAL orientation.

If not suitable, please provide the information in /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5/avb/sig.bhdr file

-----------------------------------------------------------------

Reading /space/analysis_tools/freesurfer/freesurfer-2006-03-05/lib/tcl/tkm_common.tcl

Reading /space/analysis_tools/freesurfer/freesurfer-2006-03-05/lib/tcl/tkm_wrappers.tcl

Talairach transform /nfs_data2/data/subjects/filling-in001/mri/transforms/talairach.xfm does not exist ...

Loading tal xfm file /space/sharedProjects/subjectsDir/filling-in001/mri/transforms/talairach.xfm

Talairach transform /nfs_data2/data/subjects/filling-in001/mri/transforms/talairach.xfm does not exist ...

Loading tal xfm file /space/sharedProjects/subjectsDir/filling-in001/mri/transforms/talairach.xfm

INFO: bvolumeRead: min = -41.5851, max = 17.3363

On May 3, 2006, at 1:36 PM, Doug Greve wrote:

hi chris,

We're going to need more info. Please consult
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

doug
Chris Baker wrote:
Hi,

I'm trying to register a set of functionals with anatomical data and am finding that even though the registration looks good when viewed in tkregister (see snapshot below), when I look at the data in tkmedit or tksurfer, the alignment is completely off (see second snapshot). It looks almost as if the size of the functional slab is being read incorrectly with respect to the anatomicals, although all the information in register.dat looks OK (see below).

Any ideas how to fix this or what the problem is? Could this be a problem with paint-sess or surf-sess. I'm using versions

$Id: paint-sess,v 1.9 2006/01/09 23:44:42 greve Exp $
$Id: surf-sess,v 1.12 2005/08/30 16:56:04 greve Exp $

Thanks for any help,

Chris.

filling-in001
3.000000
3.300000
0.100000
9.998358e-01 -8.742601e-04 7.647049e-04 8.429348e-01
-6.269891e-04 6.565273e-01 7.541288e-01 4.779076e+01
9.408451e-04 7.537801e-01 -6.573987e-01 2.930424e+01
5.640810e-12 8.807770e-12 -1.513114e-12 1.000000e+00
round
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting