[caret-users] Target space

[Chuan-Chih Yang]

Thank you, Donna,for the clarification and the helpful suggestions.
Now I got the direction to start with :)

Have a nice day!
Jackie


Am 31.08.2007 15:30 Uhr schrieb "Donna Dierker" unter
<donna at brainvis.wustl.edu>:

> Hi Jackie,
> 
> Apologies for the long reply that follows, but what you're trying to do
> is non-trivial.
> 
> I couldn't get your link to work, but I think you mean this Desai paper:
> 
> Desai R, Liebenthal E, Possing ET, Waldron E, Binder JR (2005).
> Volumetric vs. surface-based intersubject alignment for localization of
> auditory cortex activation. NeuroImage 26(4), 1019-1029.
> http://www.neuro.mcw.edu/~rhdesai/papers/neuroimage05_desai_flatmap.html
> 
> I learned a lot from this paper, and I hold Rutvik in the highest
> esteem. But I have some reservations about this approach, which is
> outdated in some respects. Consider this excerpt from Rutvik's methods:
> 
>> Working with a patch as opposed to the entire hemisphere has two main
>> advantages. First, since the patch has a limited amount of curvature,
>> it can be flattened without requiring major cuts to overcome intrinsic
>> curvature. This preserves the topology of the region. This does not 10
>> hold true for an entire hemisphere, which requires cuts to flatten
>> without major distortions. The placement of cuts changes the topology
>> of the surface, since adjacent points on the 3D surface are not
>> necessarily adjacent on the flat map. A second advantage is that the
>> computational time required to flatten and warp the patch is
>> significantly less than the time required for performing the same
>> operations on an entire hemisphere.
>> 
>> For displaying group data, we chose the template anatomy provided by
>> Holmes et al. (1998), which represents an average of 27 scans of the
>> same individual. This ³N27² or ³Colin² anatomy was processed in an
>> identical manner by preparing a surface model and cutting and
>> flattening the perisylvian patch.
> 
> 1) The patch approach requires defining boundaries. This isn't hard to
> do on any single subject, but defining clear, rater-free guidelines
> across individuals is quite challenging. And the concern about cuts is
> misplaced with spherical registration; while one might flatten as a
> means to generating an easy landmark border drawing substrate, these
> flattening cuts do NOT affect registration, except where they coincide
> with your user-defined landmarks. For example, our core 6 landmarks
> include the medial wall and calcarine sulcus, which also happen to be
> flattening cuts. But other flattening cuts (e.g., frontal, cingulate,
> temporal, and sylvian) do not affect registration in any way. Spherical
> registration operates on the CLOSED topology, which is cut-free. Also,
> now that Caret's 3D border drawing is much faster and easier than it
> used to be, one doesn't even really need to flatten. This document
> drafts a procedure for registering Freesurfer-generated surfaces without
> flattening:
> 
> http://pub:download@brainmap.wustl.edu/pub/donna/NIH/JULIA/TUTORIAL/FreeSurfer
> _to_CARET.doc
> 
> 2) Computational constraints in 2007 are not what they were in
> 2003-2004, when Rutvik probably did most of his work. Most people these
> days choose computationally expensive methods that require less user input.
> 
> 3) Rutvik chose colin because he didn't have a better alternative back
> then. Dr. Van Essen's PALS paper was published after Rutvik's. You have
> already decided to use PALS_B12 as a target.
> 
> You still might have a compelling reason for sticking with this
> approach, but be aware that flat-based registration just isn't much
> anymore -- at least not in this lab.
> 
> It's still possible to register subregions on the sphere to the PALS_B12
> atlas, but this can be done by drawing landmarks on the PALS_B12
> inflated or very inflated surfaces, using the average fiducial surface
> and your individual to carefully delineate the subregion boundaries in a
> principled way.
> 
> I can't imagine a scenario where it would make sense to generate
> flattened patches of each PALS_B12 subject; one could use the colin flat
> map deformed to PALS_B12 that comes with many of the visualization specs
> in sumsdb, but again -- I would draw in 3D, on the PALS_B12 very
> inflated surface, using PALS_B12 average fiducial surface in a Window 2
> to help sync the source and target region boundaries. Drawing on each
> PALS_B12 subject's surface is not necessary.
> 
> Another thing that isn't quite clear to me is the relationship between
> the individual and group results. If you want to compare them in
> volume-land, then yes -- both need to be in a common stereotaxic space.
> What you do then is within your analysis domain. But when mapping it
> onto the PALS_B12 atlas, put some thought into which mapping algorithm
> makes the most sense:
> 
> * most wustl.edu users prefer enclosing voxel for most applications, but
> activation that doesn't intersect the surface precisely is missed; it's
> unusual for clusters to miss it altogether, but the peak may be missed
> * max voxel or MCW Brainfish might be appropriate if you're trying to
> give the volumetric method the benefit of the doubt, to make sure peaks
> make it
> 
> But keep in mind that usually mapping group results to PALS_B12 is for
> visualization -- not direct comparison. It can be used properly for
> comparisons, but caution/thought is needed.
> 
> Donna
> 
> On 08/30/2007 01:01 PM, Chuan-Chih Yang wrote:
>> (My replies are also inline :)
>> 
>> Am 30.08.2007 18:43 Uhr schrieb "Donna Dierker" unter
>> <donna at brainvis.wustl.edu>:
>> 
>>   
>>> Hi Jackie,
>>> 
>>> See inline replies below.
>>> 
>>> Donna
>>> 
>>> On 08/30/2007 08:43 AM, Chuan-Chih Yang wrote:
>>>     
>>>> Hi Donna,
>>>> 
>>>> Thanks again for the suggestions. I decide to chagne to PALS_B12.
>>>> Is there an PALS_B12 dataset that are in native space (structural volume
>>>> scans)? 
>>>>   
>>>>       
>>> Technically, yes, those scans exist and may be part of the OASIS dataset
>>> available from Dan Marcus.  But the anatomical volumes used to generate
>>> the PALS_B12 surfaces were originally multiple (3-4) MPRAGES
>>> coregistered, averaged, and written to 711-2C atlas space in a single
>>> resampling, using Avi Snyder's imgreg.  The PALS_B12 surfaces were
>>> generated from the resulting atlas space MPRAGE, and these surfaces were
>>> subsequently registered to various atlas spaces using the procedures
>>> defined here:
>>> 
>>> http://brainvis.wustl.edu/help/pals_volume_normalization/
>>>     
>>>> I wanna use Freesurfer to generate the surface version of PALS_B12, and
>>>> then
>>>> cut & flatten the patches,
>>>>       
>>> Why?  I'm afraid I'm completely lost on what you're trying to do.
>>>     
>>>> and then use CARET to do the landmark-based
>>>> warping. (I would like to select some landmarks on the individual patch &
>>>> on
>>>> the PALS_B12 patch)
>>>>   
>>>>       
>>> Many people use Freesurfer to segment their volumes and generate
>>> surfaces, and then use Caret to register those surfaces to the PALS
>>> atlas.  But it almost sounds like you're trying to recreate the PALS
>>> atlas using Freesurfer-generated surfaces, and this goal confuses me.
>>>     
>> 
>> Dear Donna,
>> 
>> I want to compare the volumetric & surface-based alignment methods, as Desai
>> et. al in the paper in 2005. I wanna use PALS_B12 instead of N27 as the
>> template for displaying the group result.
>> 
>> Here is the link
>> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4G4XBWC-2&_us
>> er=28961&_coverDate=07%2F15%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c
>> &_acct=C000003618&_version=1&_urlVersion=0&_userid=28961&md5=aa0015307383f25
>> e8f568e8ba0675156
>> 
>> The attemp is to use Freesurfer to generate the flatten patch for both
>> individual and template. For volumetric alignment, I would like to use the
>> individual zstat and group zstat to overlay onto the individual patch & the
>> template patch, respectively.(for displaying purpose) Thanks for Desai's
>> suggestions and helpful emails.
>> 
>> For the volumetric alignment, I wanna take the zstat from FSL's flirt, (the
>> individual zstat is in native space, the group zstat is in mni152, if I
>> understanding it correctly.) For that, I will need to transform the
>> individual zstat & the individual patch into mni152 ; and directly overlay
>> the group zstat (which is already in mni152) onto the PALS_B12 patch (which
>> I will also need it to be normalized into mni152)
>> 
>> For the landmark-based alignment, I would need to select the landmarks both
>> on the individual and PALS_B12 patch, and then deform them by using CARET.
>> The group zstat which is already in mni152 will be mapped onto the PALS_B12
>> patch.(I havn't got the idea yet how to do this by using Caret, am still
>> newbies :P)
>> 
>> For the spherical alignment, I would need to use all the individual T1 to
>> create the sphere and then registrate them to fsaverage by FreeSurfer
>> standard pipeline. For transfering the warped spherical activation to the
>> template patch, one will then need SUMA to creat the std meshes for
>> individual patch & template patch (Desai, et. al)
>> 
>> Then I will need to select some ROIs on the template patches by using CARET,
>> to quantitatively compare the activations.
>>  
>>   
>>> I'm pretty sure Fischl, et. al., have put the OASIS dataset through
>>> Freesurfer processing stream, so the PALS surfaces probably do exist in
>>> Freesurfer form somewhere, but you would need to consult Dan Marcus or
>>> Fischl et. al. on getting those surfaces and establishing correspondence
>>> between the OASIS ID's and the Buckner case numbers.
>>>     
>> 
>> Shall I still need to get the correspondence between the OASIS ID's and the
>> Buckner case numbers, if my attemp is to generate the flatten patch of this
>> template? Coz' I was thinking if the PALS_B12 is an average volume of twelve
>> MR structrual volumes.So I can generate the flatten patch of this template
>> directly by Freesurfer without the need of having the info of the ID# and
>> case numbers. 
>> 
>> I am appreciate for any suggestions. :)
>> 
>>   
>>> I'm probably misinterpreting your intent, so please clarify your goal.
>>>     
>>>> Cheers,
>>>> jackie
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Am 29.08.2007 15:12 Uhr schrieb "Donna Dierker" unter
>>>> <donna at brainvis.wustl.edu>:
>>>> 
>>>>   
>>>>       
>>>>> Hi Jackie,
>>>>> 
>>>>> See inline replies below.
>>>>> 
>>>>> Donna
>>>>> 
>>>>> On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote:
>>>>>     
>>>>>         
>>>>>> Dear list,
>>>>>> 
>>>>>> I got a question about the selection of target space (mapping volumes
>>>>>> onto
>>>>>> surface). My attemp is to map the functional zstat.nii of FSL onto N27
>>>>>> template by using caret. I found different target spaces that I can
>>>>>> choose
>>>>>> from in the 'atlas surface selection' window,
>>>>>>   
>>>>>>       
>>>>>>           
>>>>> I hope you have a good reason for selecting Colin as the target surface,
>>>>> rather than PALS_B12.
>>>>>     
>>>>>         
>>>>>> in my case--- the zstat of individual in not yet normalized to any space,
>>>>>> but the group zstat is already normalized to MNI 305,by FLIRT. I am
>>>>>> wondering which target space and altas shall I choose, if I wanna
>>>>>> normalze
>>>>>> the zstat from FSL onto N27?
>>>>>>   
>>>>>>       
>>>>>>           
>>>>> We don't have a version of Colin that was normalized using FLIRT (linear
>>>>> affine), but we do have versions of colin in SPM99 and SPM2 space.  (See
>>>>> http://brainvis.wustl.edu/help/pals_volume_normalization for an
>>>>> explanation of how methods and spaces relate in our terminology.)  You
>>>>> could use one of these for your group results, but I'd really recommend
>>>>> using the PALS_B12 FLIRT surface as your mapping target for those group
>>>>> results.
>>>>> 
>>>>> For your non-normalized individual results, you really can't use any of
>>>>> our atlas targets -- colin or PALS_B12.  If you want to map the native
>>>>> individual results, you'll need to segment his/her structural volume and
>>>>> map to the individual's surface.
>>>>>     
>>>>>         
>>>>>> Is there any difference between mapping the individual zstat and the
>>>>>> group
>>>>>> zstat from FSL onto N27?
>>>>>>       
>>>>>>           
>>>>> Absolutely:  Mapping individual results to colin -- even normalized
>>>>> results -- is a bad idea.  Even mapping normalized individual results to
>>>>> PALS_B12 surface isn't a great idea.  Mapping individual results to its
>>>>> own surface reconstruction is a good idea.
>>>>> 
>>>>> Mapping group results to colin is no longer recommended, because of the
>>>>> limitations inherent in a single subject target.  Colin has strange
>>>>> anatomy in some places that cause undesirable mapping results in some
>>>>> areas (e.g., left posterior STS and IPL).
>>>>> 
>>>>> Mapping group results to PALS_B12 is the recommended option.
>>>>> 
>>>>> If you're interested in seeing how the individual's results differ from
>>>>> the group's, then I can think of two ways to accomplish this, but please
>>>>> be advised that I'm not experienced in these kind of analyses, so I
>>>>> don't know if a reviewer would be happy with them:
>>>>> 
>>>>> * Normalize your individual to the same target used for your group
>>>>> results.  Compute the difference in volume-land.  Map the difference
>>>>> volume to the PALS_B12 FLIRT surface.  Consider using the MCW BrainFish
>>>>> algorithm.
>>>>> 
>>>>> * Normalize your individual to the same target used for your group
>>>>> results; reconstruct your individual's surface; map the individual zstat
>>>>> to the individual's surface; and register it to PALS_B12.  Map the group
>>>>> zstat to the PALS_B12 FLIRT surface.  Use Attributes: Metric:
>>>>> Mathematical Operations to subtract one from the other (or
>>>>> caret_command's new metric math, if you have the latest and greatest
>>>>> command line utility).
>>>>> 
>>>>> Either way, you're guaranteed to get lots of clusters of differences;
>>>>> however, I'm not sure how you'd establish significance criteria.  Any of
>>>>> the 12 Buckner subjects that contributed to PALS_B12 will have such
>>>>> clusters where its individual surface differs from the PALS_B12 group
>>>>> target (i.e., normal anatomical variability is pretty high in humans).
>>>>>     
>>>>>         
>>>>>> (is there a availble N27 altas that is FLIRTed into
>>>>>> MNI305 ? )
>>>>>>   
>>>>>>       
>>>>>>           
>>>>> No.  You may have a good reason for using Colin, but I'd like to know
>>>>> what it is.
>>>>>     
>>>>>         
>>>>>> Thanks much for the help!
>>>>>> 
>>>>>> Cheers,
>>>>>> jackie
>>>>>>       
>>>>>>           
> 
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