Hi Alex,

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 various spaces:


* The above link also explains how FLIRT, SPM2, and SPM99 use the same template/target, but the methods produce subtle differences (http://brainvis.wustl.edu/help/mni305_diffs/arch_diffs_mni305.html) -- 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% single subject T1 has been replaced by a 152 subject average.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.

Good Luck.

John Harwell

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 surface?

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 appropriate?

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,

Alex Fornito
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

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