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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 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
Hmm, that was not too helpful. Can you do the following:
1. Run mri_info on /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5/avb/sig.bhdr and verify the voxel dimensions. If that is not correct, look at the h-offset.bhdr and h.bhdr volumes in localizer_sm5. If that is not correct, double check that all the functional volumes are correct.
2. If #1 is ok, then verify the registration with: cd /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5 tkregister2 --mov h-offset.bhdr --reg ../register.dat --surf
Chris Baker wrote:
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
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 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
freesurfer@nmr.mgh.harvard.edu
-
Chris Baker -
Doug Greve