Sorry about all the emails anhd thanks again,
Alex
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
email: [EMAIL PROTECTED]
-----Original Message-----
From: Fornito, Alexander
Sent: Thu 5/25/2006 1:10 PM
To: Caret, SureFit, and SuMS software users; Caret, SureFit, and
SuMS software users
Subject: RE: [caret-users] Mapping foci
Never mind, I found it. Its a separate coord file - right?
Are there any surface-shape files for depth hidden anywhere, or do
I generate that myself?
Thanks again,
Alex
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
email: [EMAIL PROTECTED]
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Donna
Dierker
Sent: Tue 5/23/2006 12:45 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Mapping foci
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:
http://brainvis.wustl.edu/help/pals_volume_normalization/
* 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:
Alex,
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
[EMAIL PROTECTED]
314-362-3467
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:
Hi,
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
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
email: [EMAIL PROTECTED]
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