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BRAINSia / MiniPig

This is a private repository to manage the scripts and documentation for the MiniPig HD Project
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Questions for Neuroscience Methods Paper #5

Closed Schubisu closed 7 years ago

Schubisu commented 9 years ago

Hi Hans and all, As you know, we're currently working on writing a methods paper for the special about animal models in HD for Neuroscience Methods. I want to describe the process of atlas creation that we currently work on with the pigs, but I'm not even sure if I've yet fully understood the process myself. Could you have a look at the flowchart below and tell me if I'm on the right track? (This is still very basic)

atlas_creation_flowchart

hjmjohnson commented 9 years ago

This is not quite correct.

There is no Inter Subject Registration between the pigs in your study.

There are multiple atlases that need to be created somehow. After multiple atlases are created, we will no longer use the Domestic Pig atlas.

For segmentation, all the atlases will be warped to each individual subject in the native subject space. Then MALF will be run in individual native anatomical space.

reginakim commented 9 years ago

Hi all,

I attached a brief description about what we think we should do. I thought it could be a quick draw of graph, but it turned out to be a list of text instead. Sorry about the mess hand-writing (I was in a hurry, haha. ) Well, let me know if there is anything unclear on my writing.

Best,

Regina

2015-06-02 14-39

Schubisu commented 9 years ago

Thanks for your replies, that makes perfect sense. I'll try putting the steps in a nice flow chart (currently just playing around with yEd, labels, nodes and groups not consistent yet), do you think it would be possible to place a first single atlas (eg M268) into the chart?

I think we'll be able to send you a first draft of the methods paper next week, if you have the time, maybe you have some suggestions, especially on what to cite concerning the used algorithms etc.

atlas_creation_flowchart02

hjmjohnson commented 9 years ago

This diagram looks much more correct.

Hans

Hans J. Johnson hans.j.johnson@gmail.com

On Jun 3, 2015, at 8:05 AM, Schubisu notifications@github.com wrote:

Thanks for your replies, that makes perfect sense. I'll try putting the steps in a nice flow chart (currently just playing around with yEd, labels, nodes and groups not consistent yet), do you think it would be possible to place a first single atlas (eg M268) into the chart?

I think we'll be able to send you a first draft of the methods paper next week, if you have the time, maybe you have some suggestions, especially on what to cite concerning the used algorithms etc.

https://cloud.githubusercontent.com/assets/3865452/7960571/dfcda7e0-0a01-11e5-8caa-768c4ff4d257.png — Reply to this email directly or view it on GitHub https://github.com/BRAINSia/MiniPig/issues/5#issuecomment-108395446.

Schubisu commented 9 years ago

atlas_creation_table_02

Hi Hans and Regina, I've tried to implement your suggestions to the atlas-creation-process image and this is what I ended up with. I've separated the domestic pig atlas on the left, because it brings inconsistency with not having T1/T2. In the 'Deformed Atlas' collumn, I've merged left hemisphere of deformed ghost image with right hemisphere of minipig T1/T2. Is this somewhere close to what you had in mind? Best, Robin

hjmjohnson commented 9 years ago

This is much easier to understand. A much better figure.

reginakim commented 9 years ago

I like the figure!

Schubisu commented 9 years ago

Thanks for your prompt feedback!