> Hmmm... > I'm still a little unclear as to how the averaging works; > - The surfaces are created from 711-2C space. > - The volumetric SPM transform is applied to the 711-2C surfaces to > place them in "SPM-surface" space > - The surfaces are averaged
Good so far. > Does the variability map reflect the coord variability of the individual > surfaces in 711-2C space, or SPM-surface space? Currently, there is only a single 3d variability map and a single depth variability map. Both maps were generated using the 711-2B surfaces. >>From my understanding, the surface average procedure doesn't impplement >> any deformation to match the surfaces; it assumes the surfaces in are in >> the same space. Thus, for example, it assumes that node i in persons j >> and k should be in the same anatomical location. Let's call it corresponding locations on the PALS standard mesh surface. These are not guaranteed to be the same anatomical location. Figure 7 in David's PALS paper shows how for a given node, some subjects vote with sulcus A, whereas other subjects may vote gyral or sulcus B. >> The only point at which >> variability could be encoded (in my mind) would be in the normalization >> from 711-2C to SPM space, but I can't see where this information is used >> in the above processing steps (i.e., no transform file is used in the >> above). So I'm guessing I'm missing something; either the averaging >> procedure is more complex than I thought, or the transform info is stored >> somewhere I'm unaware of (or I have it completely wrong!). It's 9:41pm here in Milwaukee, and I've been working all day, so I probably can't explain this as well as I'd like. But it seems to me like you're starting to grapple with what David calls "the correspondence problem" -- which is a part of the learning curve of grasping exactly what it means to register one surface to another on the sphere. What I can assure you is that the step of creating the average coord file is just a simple mean of the contributing coordinates -- no magic there. The SPM *sn.mat (or something like that) does encode the nonlinear warping transformation that gets applied to the surface coordinates. If there is a big difference between the 711-2B 3D variability and the SPM2 or SPM99 3D variability, then the 24 (12x2) *sn.mat files hold the key. > > Thanks again for your help, > Alex > > PS - I cancelled the email with the pics. I can re-send it if you're still > interested. Not needed; I can look at this when I return to St. Louis, but it will be a couple of weeks, because we're preparing for a Caret course in St. Louis. (I didn't advertise this on the list, because it's already pretty full, and the facilities are less than optimal.) > > 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 > [EMAIL PROTECTED] > Sent: Fri 5/26/2006 8:39 PM > To: Caret, SureFit, and SuMS software users > Subject: RE: [caret-users] Mapping foci > >> >> >> 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 > > Loading a spec file isn't necessary to create an average coord file. (But > it is generally helpful when visualizing the resulting average coord > file.) > >> 2 - I created the average using Surface > Average coord file and >> requested >> the standard deviation surface_shape file. > > And you selected just the 12 left (or right) SPM2 coord files, excluding > the average SPM2 coord file, right? >> >> 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). > > It's awaiting moderator approval; I'll get to that next. >> >> 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? > > I suspect the nonlinear component. > >> 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? > > Actually, the surfaces were reconstructed in 711-2C space. The 711-2C > volumes were input to the various spatial normalization methods (SPM99, > SPM2, FLIRT, AFNI, and MRITOTAL), and the resulting volume transformation > applied to the surface coordinates. The link I provided in the earlier > email provides details, but I don't have it handy here in Milwaukee > (helping out with their fMRI/AFNI course). > >> 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? > > No, I wouldn't characterize it this way. It's not measuring movement > during normalization. Rather, I think of it as a measure of the spread of > the cloud of points that represents the 3D coordinates for node i for each > of the 12 PALS subjects. One can compute the average coordinate for node > i, and see how far each of the 12 subjects' coords stray from that > average. This is what the 3D variability maps measure. > > The depth variability maps, on the other hand, are a different animal. >> >> >> 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 >>>>>[email protected] >>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>>_______________________________________________ >>>>caret-users mailing list >>>>[email protected] >>>>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 >> [email protected] >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> >> >> >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://pulvinar.wustl.edu/mailman/listinfo/caret-users >
