[caret-users] padding buglets and initial flat weirdness

[Donna Dierker]

Caret-users,

A short while back, Roland Marcus Rutschmann posted about partial hem 
flattening trouble.  It took a while to resolve the issues, and most 
messages traded were (mercifully) off-list.

Here is a recap for the benefit of future troubleshooters entering 
keywords into search engines:

* Caret was extending the last slice, instead of second to last slice; 
John has fixed this buglet.  For details, see:

http://brainmap.wustl.edu/pub/donna/ARCHIVE/BAD_LAST_SLICE/bad_last_slice.html 

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* Caret was using the raw surface for painting CUT.FACE (not all of the 
padding was painted red); John has fixed this buglet.

* The initial flat map still looks weird, but this isn't a problem.  See 
DVE's message below.

Donna

-------- Original Message --------
Subject: 	Re: Initial flat map issues
Date: 	Sat, 1 Dec 2007 15:11:40 -0600 (CST)
From: 	donna at brainvis.wustl.edu
To: 	David Van Essen <vanessen at brainvis.wustl.edu>
CC: 	Roland Marcus Rutschmann 
<roland.rutschmann at psychologie.uni-regensburg.de>, John Harwell 
<john at brainvis.wustl.edu>, Donna Dierker <donna at brainvis.wustl.edu>, 
David Van Essen <vanessen at brainvis.wustl.edu>

	


Just one inline reply near the end of DVE's reply.

> Roland et al.,
>
> A few additional comments.
>
> 1) I agree that you shouldn't need to remove the big marginal tiles
> in order to get a clean flat map.
>
> 2) As Donna noted, the marginal tiles should now be a problem ONLY if
> the 'north pole' that is used as the projection-point for the initial
> flattening lies over a non-red (non-cut-face node).
>
> If that were to occur in a different case, the quick fix would be to
> rotate the sphere slightly, apply the current view, and then proceed
> with flattening.
>
> If it were a common occurrence, then the problem can be fixed more
> generically by padding for additional slices, so that a higher
> fraction of the final spherical surface is occupied by red.  However,
> I don't think this is worth doing until we know that the need is real.
>
> 3) Regarding whether to cut or not, I agree that the uncut map looks
> 'nicer'.  On the other hand, it definitely has greater compression of
> the occipital pole, so you have to decide where your tradeoffs lie.
>
> 4) In this regard, it would be helpful to know what types of analyses
> your are doing and how you are comparing results across individuals.
> Is there a fundamental reason why you are flattening only the
> occipital lobe instead of full-hemisphere segmentation?
>
> I am particularly curious as to whether you envision registering your
> individual hemisphere datasets to our PALS atlas.  This can be done
> at present, but the process is tedious.  I have an outline of a plan
> to make partial hemisphere registration faster, easier and more
> reliable, but it hasn't gotten onto mine or John's front burner.  Is
> this something that would be of interest to you?

Meanwhile, here is a script that worked for a monkey occipital lobe:

http://brainvis.wustl.edu/pub/donna/RISHI/PARTIAL_HEM_REG/
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> David
>
>
> On Nov 30, 2007, at 1:57 PM, Donna Dierker wrote:
>
>> Good point: If you make no cuts (and I agree you don't need to --
>> either the calcarine or north pole rectangulars), then Caret will
>> name the topo for you.
>>
>> On 11/30/2007 01:55 PM, John Harwell wrote:
>>>
>>>
>>> On Nov 30, 2007, at 12:39 PM, Roland Marcus Rutschmann wrote:
>>>
>>>> On Thursday 29 November 2007 22:58, John Harwell wrote:
>>>>> Roland,
>>>>
>>>> Hi again,
>>>>
>>>>> We have fixed the problem with the padding of the partial
>>>>> hemisphere's cut face.
>>>>
>>>> just some first results before I leave for the weekend.
>>>>
>>>> I tried your new version on my previous segmentation with and
>>>> without cropping
>>>> the last (most anterior) slice. I have no crossovers all over the
>>>> place.
>>>> Actually less crossovers without cropping the last slice. (see
>>>> cropped and
>>>> uncropped jpegs).
>>>>
>>>> After cutting the large rectangulars away the morphed flat looks
>>>> good to me. I
>>>> tried with and without applying a cut to the calcarine. The one
>>>> without cut
>>>> looks better to me. What do you think. Would I save such an
>>>> "uncut" flat
>>>> surface as "open" or "cut" in the topology file save dialogue?
>>>>
>>>
>>> It may not be necessary to remove the "large rectangulars" as the
>>> multi-resolution morphing may take care of them.
>>>
>>> My vote is to save the topology as "CUT" as Caret automatically
>>> assigns cut topology to flat surfaces.
>>>
>>> John
>>>
>