Understanding my MRI's

Consider this area my self-learning page, but I welcome you to learn with me and post comments.  At the bottom of the page, you will find an overview and definitions of MRI's.  I often have to refer back to these to understand the differences between the different scans. 

My 2/3/2016 MRI Images

Image Set 1 - AX FLAIR (2/3/16)

This is a collage of my AX FLAIR images where damage is visible. The yellow circles are where I believe I am seeing existing lesions. 

Image Set 2 - SAG FLAIR (2/3/16)

This is my SAG FLAIR scan. For this one, I added yellow arrows showing lesion damage.

Brain Anatomy

As I started having more problems with my MS, I became very curious about how the brain worked and which section of the brain controlled which area.  Unfortunately, high school anatomy class was long ago, so I've had to re-familiarize myself with some of this.

Food For Thought

I thought it would be interesting to start looking at some of my MRI images and aligning it to the Brain Anatomy picture above to see if I was recognizing correlations between my lesion locations and functions of the brains as outlined.  Who knows if I'm actually on to something here.  When I mentioned doing this comparison to the doctor that measured my cognitive abilities, she said there were just too many neurological connections so my observations probably would not be accurate.  With that said - take what you want from this and know that this is just me being nerdy.

So what does this mean for me.  Can I truly correlate my lesion load to the diagram?  Mostly YES. 

Area/Function along with *issues I am seeing day to day 

13 - Frontal Lobe (higher mental functions)
* Concentration
* Planning
* Judgement

12 - Cerebral Cortex (eye movement & orientation) 
* I don't think I've noticed anything with this area 

  3 - Motor Function Area (initiation of voluntary muscles)
* Walking is hard to get started, unsteady, balance is off

  9 - Sensory Area (sensation from muscles and skin)
* Tingling feet and hands

11 - Wernicke's Area (written and spoken language comprehension)
* Issues getting words out.  Saying wrong words 

  1 - Visual Area 
* Pan Uveitis (where it all began)


Simple Overview of MRI Process

  • The patient is placed into a magnetic scanner
  • A radio wave is sent into the scanner
  • That radio wave is turned off
  • The patient sends out or emits a signal
  • That signal is received and used to reconstruct a picture
All protons have a magnetic spin, but they spin haphazardly.  To discipline the protons, we use a big magnet from the outside (i.e. - the MRI machine). Once we are put into an MRI scanner, our protons align themselves in the external magnetic field, like a compass needle in the magnetic field of the earth. The protons are now disciplined (or spinning in line with each other).

Understanding MRI Terms (Technical / Not So Technical) 

The Scans

  • T1 - is the spin-lattice relaxation time which relates to the recovery of the magnetization along z direction after RF pulse. The time it takes tissue to recover from an RF pulse so you can give another pulse and still get signal. 
  • T2 - is the spin-spin relaxation time which relates to the decay of magnetization in transverse plane after RF pulse. The time the signal lasts after giving an RF pulse.
  • FLAIR (FLuid Attenuated Inversion Recovery) - is an inversion-recovery pulse sequence used to nullify the signal from fluids. For example, it can be used in brain imaging to suppress cerebrospinal fluid (CSF) so as to bring out periventricular hyperintense lesions, such as multiple sclerosis (MS) plaques. An adjusted T2 that can suppress the signal from the Cerebrospinal fluid or CSF. This technique is more sensitive for multiple sclerosis lesions and for lesions closed to the ventricles.

The Planes

  • AX (axial) - a plane, slice or section made by cutting the body or part of it at right angles to the long axis. If the body or part is upright, the cut would be parallel to the horizon. B or Bo - a conventional symbol for the constant magnetic field produced by the large magnet in the MR scannerImages taken from front to back side to side, at right angles to the nose (image a).
  • SAG (sagittal) - a plane, slice or section of the body cutting from front to back through the saggital suture of the skull, and continued down through the body in the same direction, dividing it into two parts, then turning one half to view it from its cut surfaceImages taken from front to back, parallel to the nose (image b).
  • COR (coronal) - a plane, slice or section made by cutting across the body from side to side and therefore parallel to the coronal suture of the skull. Images taken from side to side, parallel to the nose (image c).


  • Contrast - substance used to improve the visibility of internal body structures in magnetic resonance imaging (MRI).[1] The most commonly used compounds for contrast enhancement are gadolinium-based. Such MRI contrast agents shorten the relaxation times of atoms within body tissues following oral or intravenous administration. 

Hematopoietic stem cell transplant, HSCT, Multiple Sclerosis, MS, Myelin, Inflammation, Clinica Ruiz, Northwestern University, Chicago, Mexico, Israel, CTCI, Italy Careggi, Russia, Maximov, Avonex, Betaseron, Copaxone , Novantrone , Tysabri, Gilenya ,Tecfidera, DIAD, MRI, EDSS