Winter 2020 3D Morphometrics Workshop at FHL

Lectures, labs and all documents associated with 3D Morphometrics workshop at FHL (Winter 2020)

Computer and software instructions for the 3D Morphometrics Workshop

Computer specs: Please bring a laptop with these suggested specs:

• A quad-core CPU from last couple years (i7 or i5 is preferred).
• 1920x1080 or higher screen resolution.
• 8GB or higher RAM (memory)
• 100-200GB available storage space (for software and data). Please note that solid state drives (SSD) both SATA and non-volatile memory express (NVMe) are preferred over spinning hard-drive disks (HDD) due their high sequential read/write performance (usually 10X or more faster than HDDs).
• A discrete (not an integrated one) GPU with minimum of 2GB of RAM with the latest GPU driver installed.
• A three-buttoned mouse.

Your laptop should be running windows 10 (windows 7 has issues and is not supported anymore), or Mac OS 10.11 (El Capitan) or later. A recent version of a common Linux distribution (like Ubuntu or CentOS) is also fine. Please note that segmentation is a memory intensive operation. It is suggested, you have 6-10X more memory than your full dataset size (i.e., if you are working on a 1024x1024x1024 dataset, you will need about 10GB RAM to work on in in Slicer). You can always reduce your dataset to match your hardware capacity.

Required software and data

You should have these software install these on your laptops before coming to workshop.

1. We will use a customized version of 3D Slicer with all the tools we need pre-loaded. Please download it for your OS from http://download.slicermorph.org and follow the instructions in the pdf file.
2. Download and install git from https://git-scm.com/downloads
3. Download and install R 3.6.2 from https://cran.r-project.org/
4. Download and install Rstudio Desktop from https://www.rstudio.com/products/rstudio/download/
5. Docker Desktop (for Mac and Windows) https://www.docker.com/products/docker-desktop (If you have windows 10 Home, or an older Mac, you will need to install Docker Toolbox. Please read the instructions at https://docs.docker.com/toolbox/toolbox_install_windows/.
6. Follow the instructions to download the docker image and example datasets. We strongly encourage you to complete these steps prior to arriving to FHL.

Additional software: We will not use them for the workshop specifically, but you might find them useful for specific tasks:

1. Drishti (mac and windows only); https://github.com/nci/drishti/releases
2. Convert3d (command line tools for image conversion) https://sourceforge.net/projects/c3d/
3. Dcm2niix (DICOM to nifti conversion) https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
4. Fiji https://fiji.sc/

Accounts: Please create accounts on these websites prior to workshop

• MorphoSource: https://morphosource.org
• GitHub https://github.com
• Slicer Forum, https://discourse.slicer.org (alternatively you can use your github or google accounts to signup)
• Please sign up for the SlicerMorph announcement to keep up-to-date with SlicerMorph project and extension updates http://mailman11.u.washington.edu/mailman/listinfo/slicermorph-announcements

Important Websites:

• Sample Data to be used in labs: https://app.box.com/s/p356vlvglk2t6phv0t3soj82xw21xwch
• SlicerMorph project website: https://SlicerMorph.github.io
• Workshop lectures and labs https://github.com/SlicerMorph/W_2020. Please review the Self-Paced Prelab contents either on Sunday afternoon when you arrive at FHL, or prior to trip
• Link to the file dropbox to upload your lightning talks (or any other data) https://faculty.washington.edu/maga/data_dropbox/

Funding acknowledgement

Development of SlicerMorph and the intense workshops are generously funded by National Science Foundation Advances in Bioinformatics collobrative research grants to Murat Maga (ABI-1759883), Adam Summers (ABI-1759637) and Doug Boyer (ABI-1759839).