Software dedicated to create ROIs in fMRI data
User guide: https://fmroi-docs.readthedocs.io
fMROI is a free software designed to create regions of interest (ROI) in functional magnetic resonance imaging (fMRI). However, it is not limited to fMRI, and can be used with structural images, diffusion maps (DTI), or even with atlases such as FreeSurfer aparc-aseg and Julich atlas. Before running fMROI, ensure that you have installed the dependency packages.
- MATLAB 2018a (or earlier)
- Image Processing Toolbox - MATLAB
- SPM - Statistical Parametric Mapping
Download the fMROI source code and add the root folder (./fMROI) to the Matlab path.
Project web page:
https://github.com/proactionlab/fmroi
To launch fMROI you just need to type fmroi in the Matlab comman window.
To load an image, the users have three alternatives:
- by clicking on File>Open Menu, to open a nifti file (functional, structural, DTI, etc.);
- by clicking on the menu File>Load ROI to open a binary nifti file and automatically use it as ROI;
- clicking on File>Load Template to open one of the templates installed in fMROI.
After loading the image, users can create and manipulate ROls in the tabs at the bottom of the control panel.
To create an ROI, the user must click on the Gen ROI tab, select the method from the popup menu, adjust the parameters and when ready, click on the Gen ROI button.
After this procedure the generated ROI will appear in the ROI Table tab, as well as an image will appear in the list of loaded images (roi_under-construction.nii).
To save the ROls, the user must select the Bin Mask checkbox to save each ROI as an independent mask, or Atlas+LUT to save all the ROls in the same image and click on the Save button at the bottom of the ROI Table tab.
GNU GENERAL PUBLIC LICENSE Free Software
Want to contribute? Great! Send an email to Andre Peres [email protected].
Default argument names used by roi algoritms:
- srcvol - source volume, a 3D matrix in RAS with the image information.
- curpos - cursor current position, it is a 3D vector with the cursor position in RAS.
- minthrs - handles.slider_minthrs: minimum threshold, srcvol values below the minthrs receive zero;
- maxthrs - handles.slider_maxthrs: maximum threshold, srcvol values higher than maxthrs receive zero;