Tuesday, 25 June 2013

I am my Brain

These T1 weighted images show off my beautiful brain in 1.2mm voxels, and in all three orthographic orientations. I have made the most space for what I think is my best side, which is the saggital view. I think the midline saggital view really gives a beautiful perspective of the anatomy. Depicting the brains gyrification reaching right down toward, and around, the corpus callosum. Also these images show one of the many benefits of volunteering for MRI research. Besides gaining your own data (and being able to practise your own image analysis skills), you do get a sort of free health check as some imaging centers employ radiographers that examine your structural scans for abnormalities and contact your GP is there is cause for concern.

As a near 22 year old, left handed writer, right handed guitarist, left-eye dominant male, I believe this image is of typical anatomy. Which resolves a non-existent, retrospective concern for my health.

I was participating in a pilot of a pain study, so this structural scan preceded the resting state and task based functional scans (BOLD+ASL), where an electrode intermittently stimulated my right foot. It was my first time exposed to the GE-EPI sequence environment. As forewarned, it was very loud. However it was enjoyable because it was awesome to think that 'right now my brain is being digitized'. Every 1.5 seconds a whole volume of my brain was being created in an attempt to represent the physiological reactions to the various stimuli I was being exposed to over time.

Enjoy looking at my brain, this 1.4 kg mass represents me, which is amazing. Take or damage any part of it and you have potentially removed any aspect of my human nature that will be especially tricky to regain. My abilities to recognise you, remember my first memory, to use speech, to walk, to laugh, to cry. There is no part of me that is ethereal, everlasting, greater than or impervious to my biology. This is where my thinking takes place, where I (unconsciously) instruct other parts of my body to just carry on. Carry on breathing, pumping, digesting. Carry on doing these things so I can carry on thinking, doing, loving, observing and enjoying the brief sneeze of time that I have been granted by the parents that bore me, who used their respective 1.4 kg's to procreate (Let's assume thought was used!).

To get these images from the scanner to you readers

After downloading the DICOM files from the scanner itself to my unix terminal. I used the command 'tar xjf', which essentially uncompresses the files and creates a folder containing numerous files that need to be converted into nifti format in order to be read by programs such as FSLview and SPM etc.

To convert all of the dicom files to nifti I used the 'dcm2nii' command:

       : dcm2nii -o . -i n -p n 0005/*

This function conveniently also provided cropped, oriented and cropped & oriented '.nii.gz' images in its output that have 'c', 'o', and 'co' prefixes respectively.

From this point the images can be viewed in FSL, however in order for them to be visible in SPM you have to apply the gunzip command to remove the '.gz' extension

      : gunzip *.gz

Here you are left with plenty of tar.bz2 files and the DICOM file folder, which I tend to delete from this point to clean up my folder (as long as the images open correctly and look okay otherwise you may need these compressed versions for subsequent conversion!).

        rm -r 0005/
        rm *.bz2

After opening the 'co' images in FSLview and finding the most aesthetically pleasing slices, one can use the tools_>single view button.

To bring up a large view of a single orthographic orientation. Use the switch view button and you can happily cycle through the 3 orientations and save screenshots in .pneg format using the snapshot button (right of the switch view button).