Re: [Freesurfer] Talairach transform/coordinates not present in mgz files and/or not shown in tkmedit
Thanks Bruce. I'll give that a try. But it seems strange to me that after processing different subjects with autorecon1 that the transform info would be missing from the header of some subjects but not others. Can you think of any reason why this might happen?
Cheers, Andy
On Sun, Jul 1, 2012 at 4:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Andrew
try running:
mri_add_xform_to_header -c \ $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm \ $SUBJECTS_DIR/$subject/mri/orig.mgz \ $SUBJECTS_DIR/$subject/mri/orig.mgz
or whatever volume (instead of orig.mgz) you were viewing in tkmedit. This gets done automatically during the recon-all process, but possibly you skipped that step.
cheers Bruce
On Sun, 1 Jul 2012, Andrew R. Dykstra wrote:
Dear Freesurfers, I am experiencing a strange issue when processing some, but not all, subjects with the recommended recon stream. After autorecon1, which includes Talairach registration step, I cannot see Talairach coordinates
in
the tkmedit interface ('none' appears in the text box where the
coordinates
usually are - attached screenshot). This is despite the registration
step
supposedly succeeding (I can view and adjust the reg with tkregister2).
I
think this may be causing further problems when trying to compute the forward solution in MNE (I get messages there about not being able to
read
the coordinate transformation). Has anyone experienced an issue like
this?
Cheers, Andy
-- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg
"How small the cosmos. How paltry and puny compared to human
consciousness
. . . to a single individual recollection." - Vladimir Nabokov
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
not really, sorry. On Sun, 1 Jul 2012, Andrew R. Dykstra wrote:
Thanks Bruce. I'll give that a try. But it seems strange to me that after processing different subjects with autorecon1 that the transform info would be missing from the header of some subjects but not others. Can you think of any reason why this might happen? Cheers, Andy
On Sun, Jul 1, 2012 at 4:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Andrew
try running: mri_add_xform_to_header -c \ $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm \ $SUBJECTS_DIR/$subject/mri/orig.mgz \ $SUBJECTS_DIR/$subject/mri/orig.mgz or whatever volume (instead of orig.mgz) you were viewing in tkmedit. This gets done automatically during the recon-all process, but possibly you skipped that step. cheers Bruce On Sun, 1 Jul 2012, Andrew R. Dykstra wrote: > Dear Freesurfers, > I am experiencing a strange issue when processing some, but not all, > subjects with the recommended recon stream. After autorecon1, which > includes Talairach registration step, I cannot see Talairach coordinates in > the tkmedit interface ('none' appears in the text box where the coordinates > usually are - attached screenshot). This is despite the registration step > supposedly succeeding (I can view and adjust the reg with tkregister2). I > think this may be causing further problems when trying to compute the > forward solution in MNE (I get messages there about not being able to read > the coordinate transformation). Has anyone experienced an issue like this? > > Cheers, > Andy > > -- > Andrew R. Dykstra, PhD Auditory Cognition Lab > Neurologie und Poliklinik > Universitätsklinikum Heidelberg > Im Neuenheimer Feld 400 > 69120 Heidelberg > > "How small the cosmos. How paltry and puny compared to human consciousness > . . . to a single individual recollection." - Vladimir Nabokov > > >The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Andrew R. Dykstra, PhDAuditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg
"How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
freesurfer@nmr.mgh.harvard.edu
-
Andrew R. Dykstra -
Bruce Fischl