Hi Doug,
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.
tkmedit-sess -sf sessid -df sessdir -analysis localizer_sm5 -contrast
avb -map sig -mgz
[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: 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
Cheers,
Chris.
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
[EMAIL PROTECTED]
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
