0. About

This is just a repository with some auxiliar functions. Main script iterates over a list of subjects plotting MRIs in the desired plane and coordinates. I created this in order to do some quality controls in my work, but I'm planning to keep improving it...

1. Installation and Dependencies

Python 3.8.

1.1. Dependencies

matplotlib==3.4.3
nibabel==3.2.1
nilearn==0.8.1
numpy==1.21.3
pandas==1.3.4
scikit-learn==1.0.1
scipy==1.7.1

1.2. Installation

Just pull the git repository and uncompress in your python-library folder. If you don't know where it is, check with:

import sys
for path in sys.path: print(path)

2. How to use

import MReye as mreye

All functions include documentation, check with help().

3. Running the main script

The main script takes the following positional arguments:

1: Starting directory.
2: Text file with subjects to be plotted.
3: The program expects that each subject has a sub-directory. It also expects that the subdirectory is the same name of the subject directory plus a sufix. If there is no sufix leave it blank ('').
4: Sequence to be plotted.
5: Plane--> x, y, z.
6: Coords --> List with coordinates to be passed to nilearn.
7: Output directory.

So, the program expects the following directory structure:

start_dir
|__subj1
   |__subj1_sufix
      |__flair_ax
         |__flair_ax.nii.gz

Example:

python -m MReye /media/start_directory ~/subjects_list.txt sufix t1_ax z [-30,-20,-10,0,10,20,30] ~/out_directory

Where subjects list is just a text file with the name of each subject.

4. License

This project is distributed under MIT license. Please, refer to license.txt for further information.