freesurfer / samseg

This repository contains the code for the SAMSEG.

An open-source software suite for processing human brain MRI

Introduction

FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.

FreeSurfer provides full processing streams for structural and functional MRI and includes tools for linear and nonlinear registration, cortical and subcortical segmentation, cortical surface reconstruction, statistical analysis of group morphometry, diffusion MRI, PET analysis, and much more. It is also the structural MRI analysis software of choice for the Human Connectome Project.

For expansive documentation on using and understanding FreeSurfer tools, please visit the FS Wiki.

Developer

Please review the contribution guidelines and visit our build guide for step-by-step instructions on configuring and building the source code.

Support

If you've encountered an issue or have a question about using FreeSurfer, follow these steps to get help:

1. Search the archives: It is highly likely that someone else has run into the same problem before you. The fastest way to get answers is to search the archives of our mailing list.

2. Ask a question: Subscribe to the mailing list and start a discussion!

If you've found a bug in the software, feel free to open an issue or submit a patch after reviewing our CONTRIBUTING.md documentation.

License

Terms and conditions for use, reproduction, distribution and contribution are found in LICENSE.txt.

samseg's Issues

How do I train samseg with my own data

In practical application, the segmentation effectiveness of a single MRI structure is not consistently robust in certain areas. Therefore, I intend to train a new probabilistic model tailored to my own data.
Thanks.

how to use the mesh created by samseg?

I put --save-mesh at samseg command, and finally samseg created a mesh file. but it can not be used in freeview as rh.pial (recon-all). So, how to use the mesh files created by samseg?

Optimsing SAMSEG

Hello!
I am a masters student trying to optmise SAMSEG to detect WMH in stroke. I was wondering if it would be possible to add stroke images (with manually segmented WMH) to optimise the hyperparameters for modelling spatial location and shape of lesions. If so, I am struggling to find how to adapt the code to add images from or dataset for optimisation proposes, as I am new to coding.
Kind regards,
Adrija.

is there any statistical concern on removing the gaussian probability from timepoint model

hello dr cerri, first of all, thank you for your great work in samseg. i noticed you are removing the gaussian probability from timepoint model in the longitudinal fitmodel. is there any specific statistical concern.

Does Samseg use the GPU?

Dear Developers,

without cuda drivers, samseg issues a warning at the beginning that the GPU will not be used. This warning disappears after the cuda drivers are installed but the execution time was the same as before and "watch nvidia-smi" does not show any GPU usage at all.
Does the current version use the GPU at all? If not, do you have a GPU compiled version available or could you provide a short guide how to compile samseg with GPU support?

Thanks a lot!

Kind regards,
Lukas