----- Forwarded message from William Sellers <[email protected]> -----
Date: Wed, 30 Jan 2013 03:55:47 -0500
From: William Sellers <[email protected]>
Reply-To: William Sellers <[email protected]>
Subject: Re: ? Programs
To: [email protected]
Dear Alannah,
It sounds like your want to isosurface from reasonably clean data. Osirix is
the best thing out there for doing that for free - it is Mac only though which
may be a problem (but it is so good, it is worth buying a cheap mac just for
this). Your non-mac free options are things like ImageJ but you need to install
several add-ons to get it to read DICOM files and I don't know how reliable it
is with big files. Avizo and Amira are the standard commercial offerings and
you can also use Matlab with the right toolboxes. If you want to code things up
yourself then you can use VTK - it's not too hard if you use its python
wrappers. The real difficulty is not the isosurfacing, it's reading the DICOM
files from your CT scanner. It's a very broad standard and Osirix is the only
program I've used that has reliably read all the versions I have thrown at it.
If your CT scanner software can output a more portable format like TIFF image
stacks then you have a lot more options but then you ne!
ed to remember to note down the image parameters because things like slice
separation will get lost. I notice that Photoshop can now read DICOM files -
you might be able to use that to automate image conversion.
Once you have your mesh and are measuring landmarks I'd be interested to know
what software you use. Meshlab will do this but I've never found it very
convenient and if you want a point in the middle of a triangle, I'm not sure
that it can measure its location. Most landmarks can be obtained from triangle
vertices on a dense mesh though.
Cheers
Bill
On 30 Jan 2013, at 05:47, [email protected] wrote:
>
> ----- Forwarded message from Alannah Pearson
> <[email protected]> -----
>
> Date: Mon, 28 Jan 2013 01:54:35 -0500
> From: Alannah Pearson <[email protected]>
> Reply-To: Alannah Pearson <[email protected]>
> Subject: RE: ? Programs
> To: [email protected]
>
> Hi Bill,
>
> Thanks for the suggestions. I am using CT scans which I ultimately was
> wanting to use and gather landmarks from. I am very new to this whole thing
> (literally only a few months) and at this point I'm just checking out what my
> options are. I've just started my PhD program. Ultimately, I want to use the
> scans in place of the actual specimen, so I need it to be fairly good
> quality. I will try the few trial options you have listed. I have Meshlab
> installed but I need an intermediary program that will convert my image stack
> into a smooth mesh. I understand there are a lot of options out there, at
> this point I'm trying to get a "visual" idea of what I am planning on doing,
> so loosely going through a practice process at the moment.
>
> It's nice to get a good idea of what I need and what the best options are.
>
> Thank you again,
>
> Alannah
>
----- End forwarded message -----
