Dear Morphmet community,
Couple weeks prior to his sudden demise, I suggested Dennis to consider moving
the morphmet at some point to a modern forum platform that support markups,
code formatting and inline images.
You can check out https://discourse.slicer.org to see one in action. The main
b
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the flyer for the application link and necessary documents. Application=
deadline is May 1st
Please help us spread this notice.
Thanks,
M
A. Murat Maga, PhD
Assistant Professor
Division of Craniofacial Med.
Dept. of Pediatrics
University of Washington
&
Member
Center for D
ure, which
will allow things like drawing free hands 3D open and closed curves, 3D angles,
distances etc.
https://www.dropbox.com/s/ap67lmxo0xh77h0/OpenCurve.mkv?dl=0
Meanwhile, inputs are welcomed (please email me directly).
M
A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medic
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=?utf-8?B?MTtDWTRQUjA4TUIyNzU4OzIzOnpsNmxSWFRzTW9WZjN4MlFJSi9GKzVrY0hE?=
=?utf-8?B?cHY1eGF6MXJraWw0OFhkRGYrYllPUEM4WTFLNXNjVEoyYkJ5bXlkVE9xT0Fp?=
=?utf-8?B?VVg4RXF2YThqTWwxM0ttc2JndFQyd3NqZFJKM09Rb3pma1FlY0ZBaFd3dVR
tter suited for people starting=
with 3D morphometrics. An announcement will be made for course registratio=
n and logistics in the next few weeks.
Feel free to pass this message people outside of morphmet.
A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of P
om non-vertebrates.
It will be great if the datasets can be accompanied with some annotated
landmarks. Our data dropbox is located at
https://faculty.washington.edu/maga/data_dropbox/
If you encounter problems uploading your data (too big, etc), please contact me
off the listserv and we wil
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eomagick, etc.), p=
lease provide us with a description of the format so that we can research w=
ays of converting them into an open format correctly and publish the workfl=
ow.
Feel free to forward this note to interested parties who may not be on morp=
hmet and thank you very much for your help
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We need to clarify a few things:
You already have 400 cases that you know the ancestry and sex, and you want to
use this database to infer ancestry of two skulls, for which you already know
the sex. All 400 cases, as well as your two unknown, specimens have associated
landmark data that were la
Dear all,
I just learned that our resource allocation request on the NSF's XSEDE HPC
infrastructure to create a science gateway for 3D quantitative phenotyping is
approved. When implemented, this will be a cloud platform where registered
users can upload their imaging datasets and use the provid
I would suggest microCT for things that small especially, if you can get access
to one or have the specimens ship to an imaging facility.
Resolution (and detail) will be far superior, and the amount of work you will
do to convert the voxel data to surface models is going to be far less than
stit
Patrick,
You can calculate Procrustes distance between any two configuration using the
procdist() function of the shapes package.
https://www.rdocumentation.org/packages/shapes/versions/1.2.3/topics/procdist
M
From: lv xiao [mailto:lxia...@gmail.com]
Sent: Saturday, January 06, 2018 5:37 PM
To
Skip,
As a work around you can subset your own data. All the values you will need to
do your own PCA scatter plot is in the
pseudoxy.PCA$pcscores.
That way, you get to do choose the coloring scheme and symbols.
From: Phillip Skipwith [mailto:pskipw...@gmail.com]
Sent: Friday, January 5, 2018 2:
framework, not EDA tools like PCA to answer this.
M
From: Anderson Feijo [mailto:andefe...@gmail.com]
Sent: Monday, January 1, 2018 11:02 PM
To: Murat Maga
Cc: MORPHMET
Subject: Re: [MORPHMET] Doubt Scaling photos
Dear Murat,
Thank you very much for your email and time for explore my dataset. To
Dear Anderson,
It has nothing to do with the scale of your data (or least not directly).
As you can see, you actually performed those two digitization attempts
differently. It is maybe 1-2 pixels off, but in a very consistent way (greens
are from one scale, red is the other scale, and cross is
In my experience rgl tends to be slow with meshes with high number of vertices.
You may want to do your data collection outside of R using programs optimized
for handling high-resolution meshes, such as MeshLab or 3D Slicer, save your
coordinates as a text file and import them into R.
M
From:
Hi folks,
I had a chance to compile my published CT imaging, landmark and genotype data
from last couple years into a project called 'Genetics of Craniofacial Shape in
Mus' at the Open Science Framework. Project is publicly available at
https://osf.io/w4wvg/
The bulk of the data comes from a m
Your values in csv are non-sensical.
I am not aware of a single function that will read the pts files, but you can
loop over the list of files and use read.table to read any ascii format. So
something like this would work for your case
pts.files=dir(patt='pts')
temp=read.table(file=pts.files[1]
Just to comment.
While it is worthwhile to investigate these issues, in my experience same sizes
are limited not because investigators are NOT willing to measure more
specimens, but there are no additional specimens to include in the analysis,
especially for studies based on natural populations
I want to chime in on Mike's comment about density of landmarking changing the
effect size. Nicolas Navarro and I did something similar in context of
quantitative genetics of mandible shape and came to a similar conclusion using
2D, 3D and 3D semi-landmarks sets on same dataset.
Navarro N, Maga
particularly interested in knowing other imaging
repos that cannot be imported into Slicer with the methods described in these
tutorials. I will try to respond as soon as I can.
Hope this helps some.
M
From: Murat Maga [mailto:m...@uw.edu]
Sent: Wednesday, February 22, 2017 2:19 PM
To: morphmet
Just a reminder. Survey ends March 8th.
Thanks for those who participated.
From: Murat Maga [mailto:m...@uw.edu]
Sent: Wednesday, February 22, 2017 2:19 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Survey for 3D imaging and morphometrics workshop
Dear members,
If you are working (or
Dear members,
If you are working (or planning to work) with 3D volumetric imaging datasets
(such CT, or MR) and doing morphometric analyses on them, please consider
taking this short survey (6 brief questions) I put together. Should only take
2 minutes. Survey will be open till March 8th 11PM,
Is there a way to correctly scale font size in MorphoJ on high resolution
display?
It doesn’t seem to honor the windows’ inherent font scaling, and the default
fonts are too small. I have to use the magnifying glass and it gets tedious
very quickly.
M
--
MORPHMET may be accessed via its webpa
Alexa,
I believe Slicer reads tif files as a vector (RGB) image. You need to use
“convert vector to scalar” module to convert it a grayscale volume. Next, you
need to use the “editor” module to create a labelmap (binary) image that will
be the basis for the isosurfacing operation to make a 3D mo
You can also try the markup tool in 3D Slicer (http://download.slicer.org) to
collect landmarks. While it doesn't have the extensive mesh editing
capabilities of MeshLab, it does have a pretty decent UI for annotation and
measurements.
It only read stl/ply AFAIK.
M
_
Roggero
Il 06/12/2016 01.06, Murat Maga ha scritto:
Dear Luci,
The very short answer is, it depends on your application (scanning hundreds of
same thing or a multi-user facility in which users will want to scan rocks,
biological specimens, engine parts). The major companies I am familiar with
Dear Luci,
The very short answer is, it depends on your application (scanning hundreds of
same thing or a multi-user facility in which users will want to scan rocks,
biological specimens, engine parts). The major companies I am familiar with are
Bruker (Skyscan), Scanco and GE. Expect to pay an
MorphoJ handles missing landmarks, but I don't think it has a function to
estimate them. SO without an estimation of your landmark position, your options
are either to drop the sample from the analysis (if you want to retain full set
of landmarks) or to remove the landmark from your analysis (to
I am not sure what you mean Meshlab opens, but not displays it. Do you actually
see information about your model in meshlab? If you see information about your
model, it opened it. Perhaps faces are inverted. I have seen proprietary
software (such as 3DMD) not exporting ply/stl properly from thei
Yes, copy all your meshes to a folder, and pass the path to it to placePatch. I
thought I used binary stls as well, but I might be mistaken.
Make sure the Z dimname (or sample name) in the p.k.n array matches the
filenames (minus .ply) since I think I that’s what it uses to match the LM
array to
Actually, on the same topic I would also like to announce our new paper in G3.
Navarro N and Maga AM. 2016. Does 3D Phenotyping Yield Substantial Insights in
the Genetics of the Mouse Mandible Shape?
Available early online at
http://www.g3journal.org/content/early/2016/02/22/g3.115.024372.abstrac
Hi all,
Apologies if you received this e-mail twice. Last time it bounced back to me
saying I am not subscribed to the list. Weird.
I want to bring our recent contribution on template based landmarking to
your attention. It is an open article available at
http://www.frontiersinzoology.com/c
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