Parallel processing toolbox designed to create individual brain atlases using FREESURFER. It relies on Nipype and Python multiprocessing library to parallelize jobs.
This could outpout files either to Nifti file format or convert it to analyze (uint8) file format. Last can be use as input into Cartool to perform EEG source reconstruction and Region of interest computation.
To install the toolbox, clone this repository:
git clone https://github.com/Functional-Brain-Mapping-Laboratory/Labelling_utility.git
Then go to the repository main folder and install dependencies:
cd Labelling_utility
pip install -r requirements.txt
If you plan to use a local freesurfer installation, please refer to the freesurfer wiki to learn how to setup and install Freesurfer
The toolbox could be run either using your local FREESURFER installation, either using a docker image. The latest allows you to run the tooblox on OSX and WINDOWS systems.
To locally run the utility, simply go to the repository folder, open a terminal and type:
python -m labelling
If you want to run the processing using the provided docker image, you can use the docker_gui interface:
python docker_gui.py
Gorgolewski, Krzysztof J. ; Esteban, Oscar ; Burns, Christopher ; Ziegler, Erik ; Pinsard, Basile ; Madison, Cindee ; Waskom, Michael ; Ellis, David Gage ; Clark, Dav ; Dayan, Michael ; Manhães-Savio, Alexandre ; Notter, Michael Philipp ; Johnson, Hans ; Dewey, Blake E ; Halchenko, Yaroslav O. ; Hamalainen, Carlo ; Keshavan, Anisha ; Clark, Daniel ; Huntenburg, Julia M. ; Hanke, Michael ; Nichols, B. Nolan ; Wassermann , Demian ; Eshaghi, Arman ; Markiewicz, Christopher ; Varoquaux, Gael ; Acland, Benjamin ; Forbes, Jessica ; Rokem, Ariel ; Kong, Xiang-Zhen ; Gramfort, Alexandre ; Kleesiek, Jens ; Schaefer, Alexander ; Sikka, Sharad ; Perez-Guevara, Martin Felipe ; Glatard, Tristan ; Iqbal, Shariq ; Liu, Siqi ; Welch, David ; Sharp, Paul ; Warner, Joshua ; Kastman, Erik ; Lampe, Leonie ; Perkins, L. Nathan ; Craddock, R. Cameron ; Küttner, René ; Bielievtsov, Dmytro ; Geisler, Daniel ; Gerhard, Stephan ; Liem, Franziskus ; Linkersdörfer, Janosch ; Margulies, Daniel S. ; Andberg, Sami Kristian ; Stadler, Jörg ; Steele, Christopher John ; Broderick, William ; Cooper, Gavin ; Floren, Andrew ; Huang, Lijie ; Gonzalez, Ivan ; McNamee, Daniel ; Papadopoulos Orfanos, Dimitri ; Pellman, John ; Triplett, William ; Ghosh, Satrajit (2016). Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.12.0-rc1. Zenodo. 10.5281/zenodo.50186
Cortical reconstruction and volumetric segmentation was performed with the Freesurfer image analysis suite, which is documented and freely available for download online (http://surfer.nmr.mgh.harvard.edu/).
DKT40 classifier atlas: FreeSurfer atlas (.gcs) from 40 of the Mindboggle-101 participants (2012)
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest, Desikan et al., (2006). NeuroImage, 31(3):968-80.
"The organization of the human cerebral cortex estimated by intrinsic functional connectivity" https://www.physiology.org/doi/full/10.1152/jn.00338.2011
"Local-Global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI" https://academic.oup.com/cercor/article/28/9/3095/3978804