Here is the pecking order (believe in this order):

Landmark page (http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html)
Cheat sheet
Tutorial

On 11/30/2006 09:00 AM, Mateus Joffily wrote:
Hi,

In the 'Caret5 Tutorial', during the spherical registration procedure, it is instructed to use the 'Human to Human' standard parameters (in Surface: Deformation: Run Spherical Surface Deformation: Spherical Parameters: Set Parameters). However, in "Erin's cheat sheet", it is instructed to read params from: Def Map File: 'TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map'.

If I am using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' atlas, which procedure should I follow?

Thanks,
Mateus

Donna Dierker wrote:

I did remove the port numbers from the list, which seemed to have no ill effect on my end. Perhaps it resolved the problem on your end.

On 11/29/2006 03:15 AM, Mateus Joffily wrote:

Hi Donna,

I don't know what happened, but now all the links work.

Thanks,
Mateus

Donna Dierker wrote:

Mateus,

Yes -- that's the right archive.

I don't understand why you're getting the time out errors; I can't replicate the problem on my end.

What happens when you try this link (i.e., same, except port number omitted):

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499

On 11/28/2006 01:03 PM, Mateus Joffily wrote:

Hi Donna,

I don't know if I am the only one experiencing this problem, but I am also unable to access the location: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I still get a 'time out error'.

However, I can access the SuMS database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?

Thanks,
Mateus


Donna Dierker wrote:

On 11/28/2006 11:48 AM, Mateus Joffily wrote:

Hi,

I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are:

1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use?



The answer to both 1) and 2) is use the PALS_B12 LR combo registration target dataset:

http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset your registration parameters. See this page and "Erin's cheat sheet" (linked from the page below) for more details:

http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do. There are separate landmark datasets for the left and right, but they differ very little, and using the LR combo enables you to do cross-hem or inter-hem analyses. The way we look at it, there's very little down side to using the combo dataset, but a lot of up side to doing so. So we routinely use the LR combo now.

We stopped using colin as a registration target a couple of years ago, but some documentation may still refer to it.


Thanks,
Mateus
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

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