ConFixel
is companion converter software for ModelArray for converting data back and forth from the HDF5 file format.
ConFixel
software includes three converters: ConFixel
for fixel-wise data (.mif
), ConVoxel
for voxel-wise data (NIfTI) and ConCIFTI
for CIFTI-2 dscalar files. Each converter converts between the original image format and the HDF5 file format (.h5
) that ModelArray uses.
Below lists the commands in each converter. After installation, these commands can be directly called in a terminal console.
ConFixel
converter for fixel-wise data (MRtrix image format.mif
):.mif
-->.h5
: commandconfixel
.h5
-->.mif
: commandfixelstats_write
ConVoxel
converter for voxel-wise data (NIfTI):- NIfTI -->
.h5
: commandconvoxel
.h5
--> NIfTI: commandvolumestats_write
- NIfTI -->
ConCIFTI
converter for greyordinate-wise data (CIFTI-2):- CIFTI-2 -->
.h5
: commandconcifti
.h5
--> CIFTI-2: commandciftistats_write
- CIFTI-2 -->
When converting fixel-wise data's format (.mif
), converter ConFixel
uses function mrconvert
from MRtrix, so please make sure MRtrix has been installed. If it's not installed yet, please refer to MRtrix's webpage for how to install it. Type mrview
in the terminal to check whether MRtrix installation is successful.
If your input data is voxel-wise data or CIFTI (greyordinate-wise) data, you can skip this step.
Before installing ConFixel software, you may want to create a conda environment - see here for more. If you installed MRtrix in a conda environment, you can directly install ConFixel software in that environment.
You can install ConFixel
software from GitHub:
git clone https://github.com/PennLINC/ConFixel.git
cd ConFixel
pip install . # for end user
# you may remove the original source code if you are an end user:
cd ..
rm -r ConFixel
If you are a developer, and if there is any update in the source code locally, you may update the installation with:
# Supporse you're in root directory of ConFixel source code:
pip install -e . # for developer to update
We provide walkthrough for how to use ConFixel
for fixel-wise data, and walkthrough for ConVoxel
for voxel-wise data.
As ConFixel
software is usually used together with ModelArray, we also provide a combined walkthrough of ConFixel + ModelArray with example fixel-wise data.
You can also refer to --help
for additional information:
confixel --help
You can replace confixel
with other commands in ConFixel.