Hi Donna, I do have a reason for using Colin, but I would still like to have a fiddle with the PALS. I tried openinig it from the fmri_mapping directory, but I only get the surface of each of the 12 individuals. Do I need to average it myself to get the average surface, or am I missing something? Thanks, 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 In this release, the % single subject T1 has been replaced by a 152 subject average.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] >> >> >> >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
