fMRI_fsl

Apply Full Analysis on FLANKER Dataset & Mapping brain regions using fsl and Unix commands.

To Download FLANKER dataset , Kindly click Here

Note that all tasks were part of the Health informatics course which was an fMRI based course in the 2nd semester of the 3rd year at Biomedical Engineering Department, Cairo University under the supervision of Dr.Meena Makary

Brief description:

1) QC-Task :

Check for MRI Artifacts and Motion correction for all 26 Subjects.

Click for steps 😄

2) Preprocessing-Task :

Apply Skull stripping / Feat time corrections / ETC to manually preprocess your subject data.

Click for steps 😄

`Filtered image`
`Skull striped image`

3) GLM-Task :

Manually apply General Linear Model on your data.

Click for steps 😄

Example	GLM Design	Z-stat
`Sub-1`

4) Neuroanatomy-Task :

Examine brain region cortical&sub-cortical with Harvard-Oxford brain strctural atlas.

Click for steps 😄

Region	Example	Image
`Cortical`	Frontal Medial Cortex
`Sub-cortical`	Right Thalamus

5) Scripting 1st Level Analysis :

Automatically perform 1st level analysis on all 26 FLANKER dataset subjects using Unix commands.

Click for steps OR Watch this Tutorial 📺

Credit for the Script: andrewjahn 🙌

6) Higher Level Analysis:

perform 2nd&3rd Level Analysis on the FLANKER dataset to obtain the segnificant clusters.

Click for steps 😄

A) 2nd Level Analysis

`Design matrix for 2nd level analysis`

B) 3rd Level Analysis

`Design matrix for 3rd level analysis`

Significant clusters in cope3

`Region`	`screenshot`
1) 52% inasular cortex & 29% Frontal Orbital Cortex
2) 66% Lateral Occipital Cortex, inferior division & 10% Occipital Pole
3) 81% Paracingulate Gyrus & 7% Cingulate Gyrus,anterior division
4) 22% Precentral Gyrus & 12% Inferior Frontal Gyrus, pars opercularis
5) 79% Lateral Occipital Cortex, inferior division
6) 87% Lateral Occipital Cortex, inferior division
7) 49% Lateral Occipital Cortex, superior division