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Software dedicated to create ROIs in fMRI data

License: GNU General Public License v3.0

MATLAB 100.00%

fmroi's Introduction

fMROI

User-Friendly ROI Creation and Neuroimage Visualization Software

User guide: https://fmroi.readthedocs.io

Description

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.

Getting Started

Dependencies

MATLAB 2018a (or earlier)
Image Processing Toolbox - MATLAB
SPM - Statistical Parametric Mapping

Installing

Download the fMROI source code and add the root folder (./fMROI) to the Matlab path.

Project web page:
https://github.com/peresasc/fmroi

Quick Guide

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.

License

GNU GENERAL PUBLIC LICENSE Free Software

Development

Want to contribute? Great! Contact Andre Peres at [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;

Maintained by members and collaborators of Proaction Lab
FPCE, University of Coimbra
Rua do Colégio Novo - 3001-802
Coimbra, Portugal
https://proactionlab.fpce.uc.pt

fmroi's People

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morteza-mahdiani

fmroi's Issues

Update drawingmask "select ROI" dropdown menu after clearing the ROI Table

If render color is selected when the 3D check is off can't render image anymore

Change 'Help' items functionality!

I was thinking about the UI/UX of the fMROI and saw that "Help" and "View" are not user-friendly! We can think about a new frame for showing "About" contents and a link button to the documentation for forwarding to the "Documentation webpage"! As you see here when the about section is visible you can't go to the control panel while you go to the "View" section of the main "Menu" bar at the top of the GUI!

create the logo panel

Findmax method

When creating an ROI with some methods, the findmax button could create a confusion.
For instance, when using the regiongrowing method, the cross location changes but not to the accurate maximum on that region, since it might not be the proper method to do so.
Maybe that button should only be available when convenient for the ROI algorithm.

Input file format!

I have loaded a nifti file and the software notified me that fmroi can't load 4d files and it is possible to load the first dimension of the data! I accepted and was then faced with a heavy load and too many lags for the loaded data! I don't know if this is a kind of bug or not but just let me know about the inputs more to explain in the documentation also!

Visible off not working in the rendering axis.

When we tick off the image view checkbox, the selected image should be invisible in all 4 axes, however it is not happening in the rendering axis.

Imshow error when starting

There's an error when trying to run fmroi from the command line. It is related to showing the quick guide as a image, the error says there's no field corresponding to 'Interpolation' and 'Bilinear'.

create_flowchart

Create a flowchart of all the fMROI functions. It will allow seeing how the functions call each other hierarchically.

Create the documententation

Implement the menu Config>Display resolution callback function

Displacement in the logic chain

When we create a logic chain conjunction (AND) between a sphere and a cluster, if the cluster is in the first row and the sphere is in the second, then the output image is displaced by one or two voxels. However, if the sphere is in the first row the output is okay.

@peresasc

Warning: The JavaFrame figure property will be removed in a future release.

During fMROI opening:

Warning: The JavaFrame figure property will be removed in a future release. For more information see UI Alternatives for
MATLAB Apps on mathworks.com.

In findjobj (line 191)
In removeeditborder (line 20)
In create_panel_mainctrl (line 206)
In fmroi (line 199)

BUG - confusion with left and right sides of the brain

In the last versions, when we create a logic operation with ROIS there is a bug, and it switches the right and left sides.

Warning of JavaFrame property

When opening fmroi I get the following:

Warning: figure JavaFrame property will be obsoleted in a future release. For more information see the JavaFrame resource on the MathWorks web site.

I get this line for every function inside fmroi, however it still works.

Move "Display resolution" from "Config" menu to "View" menu.

create the wellcome panel

bug mousemove

The mousemove function is picking positions outside the axes. The last version before github is working well.

when saving ROIs the cursor is not being deleted so it stays forever in the windows.

Change names in the interface

1 - Change the name "slices alpha" to " slices opacity"; and "ROI alpha" to "render opacity";
2 - Change the tab "Configs" to "Settings";

Update in import ROI algorithms

The current version of menuconfig_improifun_callback.m asks for selecting the method file and automatically imports the GUI and caller files. However, a better approach is choosing a folder with all files or a .zip file with all the scripts.

Investigate possible sources of lagging during image refresh

The refresh of the images is slow especially when there are several images opened. Click and hold the left mouse button and move over the images and you will see that the red cross (image cursor) is far behind the mouse pointer.

Check the GPU in MAC OS!

I was looking through the activity of a MAC's GPU with M1 chipset and it doesn't use the GPU capability while I think in M1 the GPU has been considered as an internal system architecture! Needs to be considered if we are thinking about the usability of the software!

Check lines 52 to 57 from axesdrawing_buttondownfcn_callback.m

Error when Canceling 'load ROIs'!

In the menu from the file section when we select load ROIs and then cancel the loading we face with error while it is not similar for the open option!

Error while exiting the main frame!

With the recent updates, I have always faced errors when exiting the software.

Adding SPM to path automatically and Notify Errors?!

Whenever I am running the fmroi in a new device and forgot to add the SPM to the Matlab path I can't open the nifti files. The issue is that there is no notification or error message in the main GUI so you should see the command line in Matlab to understand this issue otherwise you think that it is working properly but can't see the results. (Maybe we can alternatively consider a textbox for notifying the errors)
@peresasc

GUI testing!

Make the GUI components invisible while there is no data loaded!

We also need to see if we can do this regarding the possibility of actions. I mean make each component visible when the purposed data or mask was loaded.
@peresasc