On Thu, Nov 15, 2012 at 11:34 AM, Beatriz Paniagua <bpaniagua@gmail.com> wrote:

Hi Steve,

It looks good! Please, go ahead and add the data to the sample data module.
Is going to be any other work required on our side?

Regards,

BEA

On Thu, Nov 15, 2012 at 10:36 AM, Lucia Cevidanes <luciacev@umich.edu>
wrote:

Thanks so very much, Steve!

Bea is back to Chapel Hill today and the workshop yesterday was
very helpful with good feedback from attendees. I am still in Cleveland
and just presented to the bigger group a summary of our workshop from
yesterday.

I had seen that bug you mention in Slicer before because Bea worked with
a student on a version of our proposed CMF registration module for Slcer
and after it applied the transform when I loaded the registered images
in another software it did not seem to save the transform as it shifted
the images.

I had thought that this was also because the original images had
different origins, and when we used a another tool to correct all images
origin to 0,0,0, then it worked.

It is great news to hear you are also working on your side for this!!!!

I look very much forward to meeting you at the NAMIC project week in
January.

Thanks again,
Lucia

On Thu, Nov 15, 2012 at 9:33 AM, Steve Pieper <pieper@ibility.net> wrote:

Hi Beatriz -

Hope all is going well in Cleaveland!

The data you sent looks great to me - I was able to load it up and
work with it easily. I made the attached image as an example.

I saved the corresponding scene data in our new 'medical reality
bundle' (mrb) format and posted it here:

http://boggs.bwh.harvard.edu/tmp/DentalCBCT-pre-post.mrb

This file can be opened with slicer version 4.2 or above[1]. If this
looks good to you, we could add this to the sample data module.

Thanks again for sharing the data!

-Steve

[1] There is a small bug in version 4.2 such that the transform
hierarchies are not restored when loading a scene - this is fixed in
the latest nightly builds and will be included in the 4.2.1 patch
release coming out next week. http://na-mic.org/Bug/view.php?id=2725

On Wed, Nov 14, 2012 at 11:21 AM, Beatriz Paniagua <bpaniagua@gmail.com>
wrote:

Hi Steve,

We put together an unregistered adult that needed Orthognatic surgery
longitudinal CBCT for you guys to upload to Slicer4 as sample data. The
dataset has GS and labels for hard tissue for both pre- and
post-surgery
CBCT. Download the data here
(http://www.na-mic.org/Wiki/images/0/03/DentalCBCT_Slicer4.zip). We
thought
this is a perfect dataset since if can be used for building 3D surfaces
out
of segmentations, rigid registration, etc.
Let me know if this is data we can get started with.

If I understand correctly I will have to eventually to create this
Slicer4
self test module for demonstrating purposes. I will read the
documentation
you were sending yesterday and I will try to put together such a
module. You
will probably hear back from me soon with questions!!

Best regards from Cleveland,
BEATRIZ

On Tue, Nov 13, 2012 at 1:47 PM, Sonia Pujol <spujol@bwh.harvard.edu>
wrote:

Hi Beatriz,

I agree with Steve, thank you very much for your willingness to share
datasets.

This is priceless both for teaching and testing purpose.

Best Regards.

Sonia

On 11/13/12 12:10 PM, Steve Pieper wrote:

Hi Bea -

Excellent idea! Yes, one or more sample datasets would be great. It
might be nice to have a longitudinal series of the same subject
showing response to disease and/or treatment. Or maybe a normal vs.
diseased comparison? Recently we have been putting this data in the
NA-MIC community on midas [1]. You could request access to upload
there or you could send me a link to some data and I could add it.

Looking ahead, what we have been doing lately is creating self test
modules [2] so that we can confirm that the sample data can be loaded
and processed as expected (as part of the nightly testing and as part
of a self test of the installed package). Also, since these are
slicer modules, the self test can also have a button that downloads
the data and sets up slicer to work with the data. This has turned
out to be very convenient for giving demonstrations, since the first
step is simply 'press the button' rather than 'find the web site,
download the zip file, unpack the data, browse to the directory...'.
We can look into this once we have some good sample data to work
with.

Best of luck with the workshop,
Steve

[1] http://slicer.kitware.com/midas3/community/23
[2]

http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Developers/Tutorials/SelfTestModule

On Tue, Nov 13, 2012 at 11:44 AM, Beatriz Paniagua
<bpaniagua@gmail.com>
wrote:

Hi Steve (and Sonia)

How are you both, I hope this email finds you well.
I am currently visiting Lucia at UofM to finish loose ends and
coordinate
our JCEG workshop tomorrow
(http://www.na-mic.org/Wiki/index.php/CMF_Workshop_Cleveland_2012).
While
preparing our presentations we realized that the new Slicer4
function
download sample data doesn't have a CBCT dental dataset. We think it
would
be really good to add such a dataset to the sample data since we are
slowly
introducing Slicer4 into the Dental Community. We would be happy to
share a
de-identified dataset for this purpose.

Let us know what you think.
Regards,

BEATRIZ

--
Sonia Pujol, Ph.D.
Director of Training, National Alliance for Medical Image Computing
Surgical Planning Laboratory, Harvard Medical School
Radiology, ASBI L1-050, Brigham and Women's Hospital
75 Francis St, Boston, MA 02115