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
Does the variability map reflect the coord variability of the individual
surfaces in 711-2C space, or SPM-surface space?
>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. 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!).
Thanks again for your help,
Alex
PS - I cancelled the email with the pics. I can re-send it if you're still
interested.
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
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>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>
>>>>
>>>_______________________________________________
>>>caret-users mailing list
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>>>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.)
>
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