Macapype
0.7.1
Github
Site
Installation
Dependancies
External software dependancies
Python packages dependancies
Creating environment with all packages
Install macapype package
from github
Using git
Using pip
from pypi
From conda
Testing the install
Container install
Dockerfile
Docker image
Note on Singularity
Quick test
Download datasets
Testing depending on the installation
Testing from Singularity image
Testing from docker image
Testing from python package install
From pip install
From github install
Testing the macaque and baboon datasets
Testing different pipelines and options
Launching a processing
Commands
Expected input data
Command line parameters
mandatory parameters
exclusive parameters
optional parameters
more optional parameters
Command line examples
Derivatives
Introduction
Data Preparation
Brain extraction
Brain segmentation
Optional Post brain segmentation
Parameters
Adding -params
Advanced parameters settings
Individual Parameters
Adding -indiv
Advanced parameters settings
Useful tips (before processing)
How to orient the axis labels your images ?
How to tilt the orientation of your images ?
Nudging the image with FSLEyes
In FSLEyes
Apply the nudge transfo to the Orig image
rename everything back as intended in BIDS
How to compute cropping parameters ?
Page
Installation
Container install
Quick test
Launching a processing
Derivatives
Parameters
Individual Parameters
Useful tips (before processing)
Installation
Container install
Quick test
Launching a processing
Derivatives
Parameters
Individual Parameters
Useful tips (before processing)
Index