Ok, let me see if I got this right... 1 - I loaded the Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730.spec file from the caret/data_files/fmri_mapping directory and loaded all the coord files
2 - I created the average using Surface > Average coord file and requested the standard deviation surface_shape file. 3 - I exited and reloaded the average coord file and surface_shape file. Compared to the 711-2C map, there seems to be a fair amount more variability with SPM2 (I tried to attach pics, but the messgae was to big for the list). Just wandering why this would be the case. From what I understand, the SPM2 normalization routine begins with an affine transformation, followed by a linear combination of basis functions to model nonlinear shape differences. In contrast, it seems the 711-2C stops at the affine registration. Could the greater variability in the SPM2 image result from the greater warping involved through the use of the additional basis functions? One other thing I'd like to clarify; are the surfaces for the SPM2 and 711-2C PALS atlases created after the volumes were initially registered to their repsective templates, or was some transform applied directly to the surfaces after they were reconstructed in native space? Therefore, do the maps correspond to the SD of distance each voxel moves during normalization, mapped onto the corresponding surface node, or the distance moved at some other stage? Thanks again 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] -----Original Message----- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Thu 5/25/2006 11:29 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Mapping foci On 05/25/2006 03:27 AM, Fornito, Alexander wrote: >Never mind again! >I found the surface_shape files in the tutorial, but there only seems to be >the right hemisphere ones. I'm particularly interested in the 3D variability >maps for the PALS atlas (left and right). > > 3D variability -- not depth variability, right? This shape file has both left and right hem 3D variability: Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-Variability.73730.surface_shape http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6486399 It has these columns: LoContrast AVERAGE B1-12 RIGHT DEPTH 3D VARIABILITY - RIGHT_HEM Human.PALS_B12 LoContrast AVG DEPTH B1-12 LEFT (Women + Men) 3D VARIABILITY - LEFT_HEM Human.PALS_B12 >If you don't have the left hemispher map handy, is there anyway that I'd be >able to generate one myself? > > The 3D variability is generated using Surface: Create Average Coordinate File, and checking the Create Sample Standard Deviation. Just make sure you choose the right coord files (e.g., don't mix left and right hems). If you're averaging native coordinates, then expect much higher deviation than if you're averaging AC-PC aligned, or better yet some scale-controlled space (Talairach, icbm*, or 711-2*). >Also, does it matter what space the PALS atlas is in when viewing the >variability map? There seems to be only one surface_shape file in the tutorial. > > We only generated these measures on the 711-2C surfaces (the ones we originally segmented). I wouldn't expect significant differences using the other spaces, although the SPM ones use nonlinear volume registration methods, so those differences might be vary. Try it and let us know whether you think the differences are worth worrying about. >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] >>> >>> >>> >>> >>> >>>_______________________________________________ >>>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
