Just a few things to add to John's replies:
* Why are you using Colin instead of PALS? Unless you have a very
specific reason to use Colin, I would use the PALS_B12 atlas for this
purpose. In this case, you would use the average fiducial corresponding
to the stereotaxic space. You will find several of them in your
$CARET_HOME/data_files/fmri_mapping_files subdirectory. This page
describes the methods used for normalizing the 12 Buckner brains to the
* The above link also explains how FLIRT, SPM2, and SPM99 use the same
template/target, but the methods produce subtle differences
enough so that David felt it was worth having separate surfaces. I
tried to talk him out of it, mostly because I'm lazy.;-) (Notice there
is no SPM5 version yet.;-)
* The AFNI coords are the only ones we have in "true" Talairach space,
so yes -- these are the ones to use for mni2tal'd coordinates.
* I know nothing about SPM96, but the spm_templates.man file in my SPM2
distribution contains this helpful excerpt:
% In SPM96, we released a single subject brain for use as a
% template. Although the MNI gave us this data, they never
% recommended that this brain should be used as a stereotaxic
% standard. This is something that we at the FIL chose to do.
% The official standard for the ICBM stereotactic space is
% the MNI305 brain - which this was not. This brain has many
% merits for simulation but it suffers from all the single
% brain criticisms that apply to Talairach. In this release, the
% single subject T1 has been replaced by a 152 subject average. We
% (in the SPM group) chose to use the 152 subject T1-weighted
% average rather than the 305 brain average because there are also
% T2-, and PD-weighted images of the same subjects. This should
% allow much more flexibility in the range of different MR
% contrasts that can be spatially normalized to the same
% stereotaxic space (by registering to a linear combination of
% template images).
On 05/22/2006 08:55 AM, John Harwell wrote:
When mapping foci using the Map Stereotaxic Focus Dialog, the focus
entered is projected using the fiducial surface displayed in the main
window. So, the main window surface must be in the same stereotaxic
space as the focus that is being mapped. The stereotaxic space entry
on the Map Stereotaxic Focus dialog is a meta-data entry for now.
Map foci as follows:
1) As needed, change the fiducial surface in the main window so that
it is in the appropriate stereotaxic space for the focus currently
being mapped. It is okay to load multiple fiducial surfaces in Caret.
2) Save the foci projection file.
3) Exit Caret.
4) Start Caret.
5) Reopen the spec file and choose the foci projection file just
saved and choose only one of the fiducial surfaces.
Since the foci projection file stores the foci relative to a triangle
in the surface, the foci will be approximately transformed from the
other stereotaxic spaces.
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On May 22, 2006, at 12:36 AM, Fornito, Alexander wrote:
I'd like to map some foci from past studies onto the Colin surface.
I've noticed that there seems to be 2 options for selecting co-
ordinate type during this process;
1 - when loading the Colin spec file, there is the option of
choosing the SPM99, SPM2, etc fidcucial surface.
2 - in the 'studies' tab of the 'map stereotaxic focus' dialog, it
is possible to choose the stereotaxic space used in the study.
Just want to check that I've got this right:
If I chose the Colin fiducial to be SPM2, then that means the
surface has been registered to SPM2 template space. If I want to map
the focus of a study that used SPM99 space, will choosing SPM99 in
the 'map stereotaxic focus' dialog automatically convert the coords
so the focus appears in the (roughly) correct spot on the SPM2-space
If so,if a study has reported coords that have been transformed from
MNI to talairach (e.g., using Matthew Brett's method), would
choosing 'AFNI' in the 'map stereotaxic focus' dialog be the most
Finally, there are some studies that used SPM96. Does anyone know if
there are large differences between SPM96 and SPM99 spaces, or
indeed, between SPM99 and SPM2 spaces?
Thanks for your help,
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 & 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph: +61 3 8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)