RE: [MORPHMET] Morphmet in the Future

2019-07-01 Thread Murat Maga
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

RE: [MORPHMET] Help with surface scans

2019-04-23 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-forefront-prvs: 00179089FD x-forefront-antispam-report:

RE: [MORPHMET] Question about MorphoJ/Landmarking

2019-03-27 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-forefront-prvs: 0989A7979C x-forefront-antispam-report:

[MORPHMET] 3D Morphometrics summer workshop application is online

2019-03-18 Thread Murat Maga
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 Development

[MORPHMET] Real-time 3D mesh deformations with SLicerMorph

2019-03-15 Thread Murat Maga
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 Medicine UW

RE: [MORPHMET] Centroid size

2019-02-28 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-exchange-diagnostics: =?utf-8?B?MTtDWTRQUjA4TUIyNzU4OzIzOnpsNmxSWFRzTW9WZjN4MlFJSi9GKzVrY0hE?= =?utf-8?B?cHY1eGF6MXJraWw0OFhkRGYrYllPUEM4WTFLNXNjVEoyYkJ5bXlkVE9xT0Fp?=

[MORPHMET] SlicerMorph pre-release demo and testing

2019-02-27 Thread Murat Maga
d 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 Pediatrics &

[MORPHMET] data donation request

2018-12-19 Thread Murat Maga
tebrates. 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 will look for

Re: [MORPHMET] Centroid size correlation with size

2018-11-18 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:(265313219721884); x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test:

RE: [MORPHMET] Re: semilandmarks in biology

2018-11-11 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:(788757137089)(269456686620040)(70486880232457)(225004751977468)(278428928389397)(171593684265217)(163750095850)(85827821059158)(111039206520245)(211936372134217);

[MORPHMET] Looking for users of microCT other than Skyscan and Scanco

2018-10-19 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:(27855698271034)(76922548005417)(21748063052155)(28532068793085)(190501279198761)(227612066756510); x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test:

RE: [MORPHMET] Problem to export data from Landmak editor to MorphoJ

2018-10-10 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:; x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test:

[MORPHMET] Data donation request

2018-09-04 Thread Murat Maga
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! M A. Murat

RE: [MORPHMET] Trouble with 2-D morphomeric analysis in geomorph

2018-08-02 Thread Murat Maga
x-uw-ex-currentlocation-365-recipient: Outside x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:(85827821059158)(100405760836317); x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test:

RE: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread Murat Maga
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

[MORPHMET] 3D Quantitative Phenotyping Gateway (3DQPG): A Community Resource for Quantitative Phenotyping of Biological Structure

2018-03-15 Thread Murat Maga
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

RE: [MORPHMET] Portable scanner for 3D models

2018-02-13 Thread Murat Maga
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

RE: [MORPHMET] DA value calculation

2018-01-07 Thread Murat Maga
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

RE: [MORPHMET] Issues with subsetting nts array with classifiers and plotTangentSpace visualization

2018-01-05 Thread Murat Maga
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

RE: [MORPHMET] Doubt Scaling photos

2017-12-29 Thread Murat Maga
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

RE: [MORPHMET] Issue with digit.fixed on 3D mesh geomorph

2017-12-20 Thread Murat Maga
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

[MORPHMET] Public high-resolution CT scans and genotype data

2017-09-29 Thread Murat Maga
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

RE: [MORPHMET] Question on Morpho

2017-07-14 Thread Murat Maga
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')

RE: [MORPHMET] Re: number of landmarks and sample size

2017-06-02 Thread Murat Maga
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

RE: [MORPHMET] number of landmarks and sample size

2017-05-31 Thread Murat Maga
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,

[MORPHMET] RE: Survey for 3D imaging and morphometrics workshop

2017-04-12 Thread Murat Maga
be 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

[MORPHMET] REMINDER: Survey for 3D imaging and morphometrics workshop

2017-02-28 Thread Murat Maga
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

[MORPHMET] Survey for 3D imaging and morphometrics workshop

2017-02-22 Thread Murat Maga
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

[MORPHMET] MorphoJ and hidpi screen on windows 10

2017-02-07 Thread Murat Maga
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

RE: [MORPHMET] Help with .tif files

2017-02-03 Thread Murat Maga
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

Re: [MORPHMET] Re: plotting landmarks on Morpheus?

2016-12-24 Thread Murat Maga
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

Re: [MORPHMET] RE: micro-CT suggestions

2016-12-06 Thread Murat Maga
d on insects. Many thanks for any information, Angela 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 speci

[MORPHMET] RE: micro-CT suggestions

2016-12-05 Thread Murat Maga
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

RE: [MORPHMET] Re: Problem with missing data using MorphoJ

2016-11-13 Thread Murat Maga
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

RE: [MORPHMET] problems opening ply files

2016-11-01 Thread Murat Maga
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

RE: [MORPHMET] placePatch in Morpho (R)

2016-03-10 Thread Murat Maga
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

RE: [MORPHMET] Multivariate Analysis of Genotype-Phenotype Association

2016-02-26 Thread Murat Maga
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

[MORPHMET] template based automated landmarking

2015-12-08 Thread Murat Maga
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