User:Jadrian Miles/Thesis proposal feedback/dhl notes - Revision history

Jadrian Miles at 02:42, 20 October 2010

2010-10-20T02:42:33Z

← Older revision		Revision as of 02:42, 20 October 2010
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	make a safer statement ("could not be")		make a safer statement ("could not be")

	peter: will you review kiselev macro+micro approaches. spaghetti		peter: will you review kiselev macro+micro approaches (Jadrian note: this is published as "Gibbs Tracking", MRM 2008). spaghetti
	plate. spin-glass. (not sure that the spin-glass is curve-oriented		plate. spin-glass. (not sure that the spin-glass is curve-oriented
	-- isn't it voxel-oriented?) Peter, I think, is arguing that these		-- isn't it voxel-oriented?) Peter, I think, is arguing that these

Jadrian Miles at 18:53, 12 October 2010

2010-10-12T18:53:24Z

← Older revision		Revision as of 18:53, 12 October 2010
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	4:28 pubs		4:28 pubs

	Win's paper isn't ``in review'' any more, sadly. But maybe he forgot		Win's paper isn't "in review" any more, sadly. But maybe he forgot
	to tell you :-) [I did just check on the pubs page, and it is listed		to tell you :-) [I did just check on the pubs page, and it is listed
	as ``in review'' not ``in press'' at this point, fyi.		as "in review" not "in press" at this point, fyi.

	4:29 MRI protocol development		4:29 MRI protocol development
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	very nice convolution animations :-)		very nice convolution animations :-)

	not clear that boundaries are ``the most important'' places --		not clear that boundaries are "the most important" places --
	important, yes, but be careful about black-and-white statements		important, yes, but be careful about black-and-white statements

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	algorithm?		algorithm?

	peter: regularization clever; ``there are quite a number of pathways		peter: regularization clever; "there are quite a number of pathways
	that connect to the outside.'' [I would have phrased the gray-to-gray		that connect to the outside." [I would have phrased the gray-to-gray
	constraint as either gray to gray or gray to exit]		constraint as either gray to gray or gray to exit]

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	this may be one of the ongoing challenges)		this may be one of the ongoing challenges)

	jfh: where is the incentive to avoid too many (100K) ``clusters''? I		jfh: where is the incentive to avoid too many (100K) "clusters"? I
	think this comes back to the probabilistic formulation.		think this comes back to the probabilistic formulation.

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	jfh: modify thesis statement. currently involves proving a negative.		jfh: modify thesis statement. currently involves proving a negative.
	make a safer statement (``could not be'')		make a safer statement ("could not be")

	peter: will you review kiselev macro+micro approaches. spaghetti		peter: will you review kiselev macro+micro approaches. spaghetti
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	-- isn't it voxel-oriented?) Peter, I think, is arguing that these		-- isn't it voxel-oriented?) Peter, I think, is arguing that these
	methods are still micro combined with macro. Maybe you should say		methods are still micro combined with macro. Maybe you should say
	``fasciculus + microstructure'' or even something that has more		"fasciculus + microstructure" or even something that has more
	anatomical description of the macro and micro parts as well.		anatomical description of the macro and micro parts as well.

Jadrian Miles at 18:50, 12 October 2010

2010-10-12T18:50:58Z

← Older revision		Revision as of 18:50, 12 October 2010
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	4:07 research agenda		4:07 research agenda

	you are having more ``uh''s and ``um''s than I think of you doing.		you are having more "uh"s and "um"s than I think of you doing.
	I'm not sure how you can best reduce that, but maybe being more		I'm not sure how you can best reduce that, but maybe being more
	cognizant about it will help		cognizant about it will help

Jadrian Miles: New page: 4:05 start as before, nice story 4:07 basser pointing 4:07 research agenda you are having more ``uh''s and ``um''s than I think of you doing. I'm not sure how you can best reduce that,...

2010-10-12T18:50:26Z

New page: 4:05 start as before, nice story 4:07 basser pointing 4:07 research agenda you are having more ``uh''s and ``um''s than I think of you doing. I'm not sure how you can best reduce that,...

New page

4:05 start

as before, nice story

4:07 basser pointing

4:07 research agenda

you are having more ``uh''s and ``um''s than I think of you doing.
I'm not sure how you can best reduce that, but maybe being more
cognizant about it will help

4:09 brain anatomy

cute shrinking of sushi into disected corona

4:11

4:12 WM macrostructure

I think the image was the arcuate fasciculus? [but apparently not]

4:14 diffusino MRI

4:16 diffusion-based tissue modeling

nice distinguishing of micro and macro here

Chad's question was more about clustering voxels than about clustering
curves. You might want to follow up about that with him, because I
think you guys were imagining different topics.

4:20 research agenda

4:20 thesis statement

that's a mouthful!

jfh: what is unambiguous?

I would say that the solution will be better, but not necessarily
unambiguous

4:24 talk roadmap

4:25 research context

computer scientists could also be repalced by applied mathematicians
or other fields -- your wording could be inferred to mean only
computer scientists

4:26 collabs

4:27 pipeline

the negative space of your pipeline is really interesting looking :-)

4:28 pubs

Win's paper isn't ``in review'' any more, sadly. But maybe he forgot
to tell you :-) [I did just check on the pubs page, and it is listed
as ``in review'' not ``in press'' at this point, fyi.

4:29 MRI protocol development

4:30 curve clustering

4:32 bundle modeling

4:32 roadmap

you should count to yourself when you ask for questions. You are only
giving a few seconds -- not enough for almost anyone to ask a
question. Subjective presentor time is much longer than clock
time...

4:33 research agenda

4:35 anatomical priors

you mention in the doc isertion of WM into GM happens orthogonal to
the surface?

4:38 iterative adjustment

wow, they look identical! :-)

very cute animations -- many made me smile along the way

4:39 piecewise priors

very nice convolution animations :-)

not clear that boundaries are ``the most important'' places --
important, yes, but be careful about black-and-white statements

4:43 microstructural validation

Are you sure that Ricean is the right distribution for axon diameters?
I know that's true for magnitude MR image data, but seems like a
strange distribution for axon diameters.

jfh: distribution questions and smoothing questions

4:46 ex-vivo&histology

4:46 research agenda

the red caps and the red parts of the sides of your example fascicle
geometry model is a little confusing.

4:48 initializing the combined model

(why are your slide titles blurry? -- everything else looks crisp)

4:48 talk roadmap

jfh: convergence

charniak: why do you get more out of the images after using the
current methods?

(nice answer)

4:52 roadmap

4:54 initialization

your undivide-and-conquer in geometry is nifty -- very CS like.

charniak: is that greedy, and if so does it make any difference. Ie,
does it matter what order you join things?

4:58 system energy

how will you weight the different parts of the system energy? Product
is strange -- shouldn't they be summed? I think that there is a
probabilistic derivation that you might be able to use to derive
this. My guess is that that will either lead to a product of
everything including over the clusters, or a set of sums, including
over the different micro-structural elements are.

5:02 timeline

nice echoing of your architecture diagram in your timeline

question: health privacy

ben: how much variation? Can you identify someone from their scan?

chad: what optimization algorithm? is it a standard optimization
algorithm?

peter: regularization clever; ``there are quite a number of pathways
that connect to the outside.'' [I would have phrased the gray-to-gray
constraint as either gray to gray or gray to exit]

jfh: worries that your bundles may be too different from anatomists

jfh: validation -- how do we know it's any good? slice afterwards?

(I stepped out, so didn't note things while I was gone)

peter: jittery boundaries were being discussed when I cam back in

ben: how do you convert image differences (between simulated DWI's and
actual) to parameter changes? (this is a deep and good question --
this may be one of the ongoing challenges)

jfh: where is the incentive to avoid too many (100K) ``clusters''? I
think this comes back to the probabilistic formulation.

chad: unambiguous. I think you probably need to weaken that word...
It's an attention-grabber (not in a great way)

chad: re thesis statement, worried about overfitting, parsimony, etc.
Probabilistic! Three questions, which I'm afraid I didn't manage to
get.

jfh: modify thesis statement. currently involves proving a negative.
make a safer statement (``could not be'')

peter: will you review kiselev macro+micro approaches. spaghetti
plate. spin-glass. (not sure that the spin-glass is curve-oriented
-- isn't it voxel-oriented?) Peter, I think, is arguing that these
methods are still micro combined with macro. Maybe you should say
``fasciculus + microstructure'' or even something that has more
anatomical description of the macro and micro parts as well.

peter: how about a reduced computational phantom that you can try
solving for? Even something that stays stable for data created from
the model itself.

peter: can check the robustness of solution with a computational
phantom where you can add noise.

jfh: bothered that scheme isn't idempotent. ie,
brain->images->model->images->model2 -- model should very close to
model2, shouldn't it?

chad: suggests presentation could have been inverted. too much
high-level stuff too early. may have been selling a little too hard
and not giving the detail enough. jfh suggests that a figure showing
the micro and macro together, perhaps in 2D to visually show how they
would go back and forth.

peter: more demonstration of synthetic data

ben/jfh: recovery from excessive challenges may involve a different
thesis statement (ie, if the yellow parts are gone, the thesis may no
longer be sufficiently large)

peter: not sure how the whole thing will fit together. worried about
putting it into practice and testing it out.

What are the effects on your proposal now to address your issues.

More publications may help with that.

Be prepared for more time -- this work may take longer than you are
predicting.