Manual Install Instructions
User Manual:
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Page Count: 4
INSTALLATION INSTRUCTIONS
(These steps won’t be necessary when SlicerMorph becomes part of the Slicer’s extension catalogue)
1. We assume a recent nightly of the 3D Slicer is installed on your computer.
2. Clone SlicerMorph repository (https://github.com/SlicerMorph/SlicerMorph) to your local drive.
3. Make a SlicerTemp folder. This folder needs to be created in a place writeable by Slicer (e.g., your temp folder
in your OS or your desktop).
FIRST TIME SETUP IN SLICER for SLICERMORPH
EDIT->APPLICATION SETTING (EDIT->PREFERENCES on Mac and Linux)
1. Modules tab:
• Modify the temporary directory setting to point out to SlicerTemp folder you create above.
• Add the SlicerMorph subfolder from cloned repository (e.g.,
C:\Users\Murat\Documents\Slicer_Morphometrics\UIDevelopment\SlicerMorph) to the additional Module
Path field
• Similarly, add SlicerMorph\MorphoSourcery to the additional Module Path field
• If you don’t see GPA or MorphoSourcery in the list of the modules in the next step #4, it is likely that your
module path is incorrect. Make sure you navigate to SlicerMorph folder.
2. Cache
• Create a folder called RemoteIO under the SlicerTemp and specify as the cache location (will be necessary to
recover sample data downloaded from internet).
3. Volume Rendering
• If you have a dedicated GPU (like a Nvidia Geforce or Quadro card), set the Default rendering method to GPU
Raycasting and quality to Normal, and specify the RAM amount on your GPU. If you are using a laptop with
both an integrated GPU (like i7 processors from Intel) and a discrete onboard graphics card (e.g., Dell Precision
laptops), there are additional steps necessary to make sure Slicer OpenGL operations run on the discrete GPU.
Follow the instructions on the forum https://discourse.slicer.org/t/can-i-choose-which-gpu-to-use/3149/5.
These are not critical for the demo today, but your 3D rendering speed may not be ideal.
There is one optional customization to be done. For that you need to close and re-open Slicer, which will update the
module listing with GPA and other additional modules.
4. Modules
• Go back to modules menu and customize the icons on the toolbar: By dragging and dropping these modules into
the Favorites: Sample Data, MorphoSourcery, and GPA. Since we currently don’t have application icons, you
may want to rearrange the order so that it is a bit more clear to you which is which.
GETTING STARTED WITH SlicerMorph
Getting Data:
SlicerMorph -> MorphoSourcery: To be able to use MorphoSource, you need to be registered with the repository.
Please obtain a personal username and password from the M/S prior to the demo. MorphoSourcery uses Slicer’s built-in
web-browser infrastructure, and M/S can be navigated exactly in the same way through Slicer as if in a desktop browser.
Save a few sample datasets of your choosing into your cart, so that you can directly download them to the Slicer through
MorphoSourcery. We suggest working with 3D models (ply/stl etc) initially, before moving onto volume datasets
(DICOM/TIFFs etc)… 3D models are usually smaller, and are faster to download. Currently there is no mechanism to set
the voxel spacing correctly for image stacks. We rely on the user to set voxel spacing through the Volume module and
the M/S metadata.
As you navigate the samples, you have an option to just download the dataset as a zip file or download and have Slicer
unpack the zipfile and load it directly into the existing scene. Both have its ups and downs. Regardless of the option you
choose, downloaded sample data will be available in the SlicerTemp folder you specified in step #1.
File->Download SampleData: To obtain sample datasets provided with SM, switch to SampleData module and scroll
down to find SlicerMorph tab. Currently there are 5 datasets associated with SlicerMorph project. These datasets
become available only after successful addition of SlicerMorph module to Slicer: Two pairs of sample datasets (Mouse
and gorilla skulls). Each pair consists of a landmark only dataset and a reference mesh/landmark pair that will be used
for 3D visualization. The fifth dataset is sample microCT image sequence output from a popular scanner
(Bruker/Skyscan) that is provided to showcase the direct import tool we have in SM. Download them all. They will be
located in the SlicerTemp folder, unzip each dataset into their own folders.
Utilities:
SlicerMorph->SkyscanReconImport: This particular module imports a reconstructed image stack from Bruker/Skyscan
microCT into Slicer with correct orientation and voxel spacing. It uses the log file (*_rec.log) found in the reconstruction
folder to obtain the right settings. To test the module, a sample output from Bruker is provided in the SampleData.
Uncompress the zip contents, and navigate to the P0_2_Rec.log file in that folder.
SlicerMorph->ReadLandmarkFile: This utility imports IDAV Landmark Editor’s landmark file into the existing scene as a
markup (one file at a time). You can use Slicer’s default Save function to save the imported file in fiducial file format
(fcsv) that can be used with SlicerMorph. Please note that we had very few samples to test this tool. If you encounter
issues, please provide us with some sample data.
GPA MODULE
