Brain is simply fascinating.
I'm keeping this repository for those who are afraid to start neuroscience or something else because it seems dark, comprehensive, and complex, even though it interests them a lot. I'm at the same point, and let's see how far we can go with self-discipline.
Note that: Computational neuroscience is a theoretical field, with need of lots of experimental studies to go further after reaching some level of knowledge. Therefore, in this repository we will be covering most of theoretical background of these studies with lack of experience. (Edit: with commiting myself to neuroscience I also found a chance to get lab experience in two different biomedical department) I personally desire to create a significant value in the field of computational cognitive neuroscience, and as other things it requires quite much work... Sometimes it might feel scary, but the knowledge we gain in the path somehow keeps us from being unmotivated.
As can easily be seen, before starting this text (in one of the hot summer months of 2022), I had no previous experience in neuroscience. However, exploring the brain, understanding cognitive processes, and attempting to solve some of the questions that intrigued me in this field had been on my mind for a long time. To prepare for this, I tried to develop myself in areas that could be considered related to my field of study during my time at university.
As a long-term goal, I aimed to be part of brain research projects that use artificial intelligence as a tool, by combining it with computer science and gaining a clear understanding of the problems in neuroscience. While I believed that deep learning and new technologies would play a significant role in the discovery of the brain, I also rolled up my sleeves to learn traditional methods. I woke up every day with a different excitement to learn new things, as there were many unknowns I wanted to unravel, and I enjoyed this challenge.
At the end of the journey, I am now continuing my master's degree in Biomedical Engineering, on cardiovascular diseases (we cannot escape some realities; the reasons are a subject for another place and time, summer 2023). However, on this page, you can find what I was interested in during nearly one year of neuroscience studies.
In this repository, you will find the resources I have found up-to-date, what I am reading, what I plan to read and what I have learned in a certain order.
- Cognitive Neuroscience: The Biology of the Mind {2019}
(Edit: -> After some research, I jumped on this book because it is much more up-to-date, easy to read, and recommended.) - Principles of Cognitive Neuroscience {2012}
(Note: It's also easy to read, it simplifies very complex topics. Good book. I didn't read it all, I skipped over it.) - Neuroscience 6th Edition {2018}
(Note: Pretty hard to read, best to go with the main course. Best medicine for its patient.) - Analyzing Neural Time Series Data Theory and Practice {2014} (Mike X Cohen)
(Note: I started this book for learning signal processing from scratch for EEG data. His writing style is really enjoyable.)
Courses to comprehend what is happening.
- Philosophy and the Sciences: Introduction to the Philosophy of Cognitive Sciences
- Understanding the Brain: The Neurobiology of Everyday Life
- Medical Neuroscience (Course is given by Leonard E. White, Ph.D. who is also one of the writers of Neuroscience 6th Edition.)
- Neuroscience time series analyses (free - youtube)
- Neuroscience time series analyses (paid - more resources and from scratch matlab codes/data)
ADNI - https://adni.loni.usc.edu -> Awesome initiative. MRI/PET, clinical, genetic biospecimen data for Alzheimer's and some other diseases.
OASIS - http://www.oasis-brains.org -> 5 different imaging dataset
- Philosophy of Cognitive Sciences
- Cognitive Neuroscience The Biology of the Mind
- Analyzing Neural Time Series Data Theory and Practice
I couldn't handle every part to take notes because of study circumstances. However, in future, if I'll take, I'll definitely publish.
If you take the time to read it, you will notice that, although I enjoyed the process, it has been quite a rollercoaster ride for me. Sometimes, there are childishly excited peaks, sometimes pieces of information written as if I were an expert doctor, and other times, you may come across empty and inexplicable things that no one will ever understand why they are there.
I completed the course "Philosophy and the Sciences: Introduction to the Philosophy of Cognitive Sciences". It's relatively short and superficial course. They cover the main concepts of brain evolutionary theory and consciousness. After explaining the fundamentals of ideas, they mostly provide external resources for further information.
I started course "Medical Neuroscience". Dr. White is pretty nice teacher, in first week he starts with the long introduction of the course. He recommends Neuroscience 6th book for further information. (It seems really hard to read for me, but anyway, we are in the path.)
I continued my research to find convenient resources for myself to start cognitive neuroscience. I will be updating Resources with my progress.
I will not be able to share some links due to copyrights, but I will be writing some of the notes I took in the Notes section.
In the second part of week one, he starts "Neuroanatomy". Frankly, I feel pretty awkward watching this course. We haven't been studying anything biological since we started university, and the language barrier with medical terms puts an extra burden on it. Still, I can say that I understand 60-70% of what is being said, Dr. White explains the topics really well. I completed the week one with lots of questions.
I must say that the course "Medical Neuroscience" is started as one of the most difficult course I have ever taken. However, this difficulty does not reduce my interest, on the contrary, I am even more curious. I research the parts that I think I need to research and leave the rest because some topics are too deep and need to be looked at again later.
I read "Principles of Cognitive Neuroscience" until page 40s. Then read "Neuroscience 6th" only 5 pages (it took me 2.5 hours to read 5 pages???). I realized that I need to work Neuroscience calmly and without ruining the order. The discipline of neuroscience gives me a much more settled feeling than programming.
I skipped over "Principles of Cognitive Neuroscience" and started to "Cognitive Neuroscience: The Biology of the Mind". Well, I won't continue to skip. I did this because the second book is much more up-to-date and recommended. I read the holy book "Neuroscience" 10 pages with lots of dictionary checking, searching for unknown biological and medical terms. I understand "patience" is the key...
Off-day for cognitive neuroscience.
I spoke with my professor at the university, who has a PhD in neuroscience. He gave some advice, and I talked to so many people at university today. Couldn't find the time to work.
I continue the book Cognitive Neuroscience: The Biology of the Mind. Their explanations of the topics are clear, and they provide several experiments and stories to make it more deducible.
I learned about the nervous systems. It recalled knowledge that I already have at high school. It is really strange feeling tho. When I was in high school, I was thinking and grumbling like "all of these informations are useless and we will never use". Of course, there are some stuff I see the first time. However, some of the new information were like I have always wondered, but have never made research about it. This chapter (Structure and Function of the Nervous System) is quite satisfying and full of useful information to fill spaces in the mind. I guess this chapter is one of the most technical one, and I think I will be even more enjoyed in other chapters.
Off-days for cognitive neuroscience. I am working on 3 different research projects, so I needed to be focused on others. Worked on signal processing and eye-tracking.
I started watching and completed first week of course "Understanding the Brain: The Neurobiology of Everyday Life". It is lightweight version of Medical Neuroscience and Cognitive Neuroscience book. Actually, in this case I repeated same topics for 3 or 4 times from different resources without realising. Anyway, in my opinion it is important to repeat these main vocabulary of neurobiology and cognition to take it in the long-term memory and you can use the same order which is 1) watching course "Medical Neuroscience", 2) reading book and stuff about Cognitive Neuroscience, 3) watching course "Understanding the Brain: The Neurobiology of Everyday Life". I started feel the knowledge, but also see I still have quuiite looong way to go.
I started signal processing for neuroscience, Mike X Cohen's book "Analyzing Neural Time Series Data Theory and Practice" and videos. I am still making literature review for eye-tracking for programming. In 1990, How do we read algorithms? A case study. proposed the analysis of data collected from eye movement to investigate the cognitive process of programmers, based on theories that linked eye fixation to comprehension to understand how programmers read and understand algorithms. I do my research about extraction features of comprehension state from eye-tracking outputs.
Today was the first productive day of my new program. I realised that I cannot keep up with the lots of new knowledge and research projects without restrict plan, so I made one.
I continued through medical neuroscience course. I finished the part of Cerebral Cortex, Brainstem and Blood Supply, and it was really hard to keep up with. I spent a fair amount of time understanding the locations of the arteries and the brain regions they supply, however, quiz was really hard to pass. I read the part of CNS, and Blood Supply and the Brain from Cognitive Neuroscience book. I watched the next videos of Mike X Cohen's and I start feel to really really enjoy this process. Even though it is painful, I can feel that I learn actual science. I read Mike Cohen's book on signal processing and analysis and repeated what he explained in the videos.
Well, in this period, I studied like an actual nerd. I also read the book "atomic habits" recently, so I got some tips to organize my study routine and its effectiveness...
Here below is the my current daily routine which I think its quite nice to practice topics over and over again and progress in a solid way.
( You can feel the knowledge in your veins )
- [5AM - 6AM] -> Reading casual totally normal human book
- [6.15AM - 7.30AM] -> Watching Medical Neuroscience or The Neurobiology of Everyday Life course videos
- [8AM - 9.30AM] -> Reading/studying Cognitive Neuroscience book
- [10AM - 11.30AM] -> Watching neural signal processing and analysis videos
- [12 - 1PM] -> Reading/studying neural signal processing book
- [2PM - 5PM] -> Flexible duties (job/other research projects etc.)
- [6PM - 7PM] -> Reading/studying neural signal processing book
I realized that all materials I study are supporting each other. Neuroanatomy is the most hard topic for me right now, and it definitely requires lots of repetition on same topics to memorize exact location of each nerves, brain regions and functions of whole complex structures. Thus, I think this study plan is quite effective.
In some days, I just could not find any power to study one more hour signal processing from book as last study task. However, it's still okay, we're fine. I am still breathing.
I decreased the amount of study, and went to university to socialize and catch up. Anyways, I completed 3rd week of Medical Neuroscience and 3rd week of Neurobiology. I am also at middle of the static spectral analysis on Mike Cohen's course.
About Medical Neuroscience: As I mentioned before, it is one of the most comprehensive online course I have ever taken. I learn a lot, I forget a lot, however, it is still quite useful and significant to comprehend how medical side of neuroscience think. This course provides numerous insights about neuroscience.
About Neurobiology: It cannot be considered as comprehensive if we consider medical neuroscience course load. It includes light-weighted and non-medical aspects of neurobiology.
It's time to give a break for neuroscience.
Neurobiology course week 4 is done and I am close to complete 4th week of medical neuroscience. I started reading Neural Signal Analysis systematically. I also learnt some about the neurodegenerative diseases from cognitive neuroscience book.
The more I learn about the brain, the more I want to continue. I still have the passion it seems. There are enormous amount of interesting facts and fields to study.
Neuroscience week 4 is also done. I learnt about Synaptic Transmission and Synaptic Plasticity, however, it is quite hard to figure out. I continued the neurodegenerative diseases from cog. neurosci. book. I am at the Methods to Perturb Neural Function. I feel like I am not studying enough, but here we are.
Anyways, I think it is important to not break rhythm of study.
I studied Sensory Systems. I did some visitings, and I am about to start project in Tactile Research Laboratory at Boğaziçi University.
Well, anatomy of neural systems makes me a little bit sad. I cannot manage sparing enough time for practicing and memorizing, and there are loottts of things to memorize. I finished the 5th week of Medical Neuroscience. I am pretty sure that I will watch these videos 2-3 times again and again next year, because when I use the feynman technique, I mostly figure out how much I do not understand :)
For now, my main purpose is to get a familiarity with the deep neuroscience topics, and I think it is quite useful while reading academic papers even though I cannot memorize most of the topics, at least it makes sense.
I completed hearing and vestibular system & gaze in Neurobiology course and started Movement and Motor Control at Medical Neuroscience. I am trying to develop note taking skills, however, it is still quite hard to keep up with.
Reading cognitive neuroscience book provides more insights page by page. The genetic manipulations on animals, invasive and non-invasive methods to stimulate animal and human brain are clearly explained. I am trying to keep up with my program, however, it seems I will first complete everything in neurobiology course before moving forward in medical neuroscience. It is because following lots of courses at the same time is mentally burden for me right now.
More readings at library. The things I learn about are quite fascinating and this situation gives me a feeling that "I need to learn more", so I think I'm at the right point.
I helped the design of the experimental setup of our research for spinal cord injuries at Vivarium where is part of the Boğaziçi University Center for Life Sciences and Technologies. We did pilot experiments to solve early mistakes, and handling rats was time consuming.
I also finished 6th and 7th week of the course Understanding the Brain: The Neurobiology of Everyday Life.
Resting to not be burnout.
I completed rest of the course Understanding the Brain: The Neurobiology of Everyday Life. I'll continue with the Medical Neuroscience with taking notes. Serious things will happen...
Cleaned everything until 7th week in Medical Neuroscience course, and I started 8th week rather than 7th, because I need insights of motor control and activity for my internship topics at BOUN.
Cognitive Neuroscience textbook is also quite enjoyable to read. I am about middle of the 4th chapter which explains the hemispheric specialization. The corpus callosum experiments are interesting and amazing. At 1940, some clinical surgeries are made to seizure disorder patients with taking too much risk because of the lack of technological tools and knowledge. To everyone’s relief, the surgery was a great success, and ships are sailed to new harbor with its results.
I did nothing about my coursework because I attended the International Conference on Computer Science and Engineering to present my paper about offensive language detection.
Completed week 8 at Medical Neuroscience coursework. I sent my financial-aid request to AI for Medicine Specialization courses at Coursera (I need to learn medical imaging)...
I am also peer counselor at computer eng. department at my university, so I started to provide information to 1st year students.
I cannot take serious notes for neuroscience in current situation because my focus time is limited. I plan that I will recap everything with taking notes when I start my PhD.
11 days, non-stop, just read the papers related with MR imaging studies of posterior fossa and fibroids. Finally, I determined the topic for my graduation thesis. I will work on the diagnosis and prognosis of posterior fossa which is a brain tumor in children under supervision of Dr. Bilgin Keserci.
The context of medical neuroscience course is quite deep and "medical", but I think it's really worth it. Even just remembering the keywords or the parts from brain, provides more insight and curiosity.
It has been almost 4 months of diary. Nothing in life goes as expected or unchanged. (Passion in neuroscience still here though) The side effects are always affect my study habit, and I cannot focus most of the time. But there's a power in me that allows me to do something worthwhile, or perhaps a possibility to create value.
In this year, by studying more about the neuroanatomy, neuroimaging and cognitive science, I will be in the next stage of my dream that being able to help patients with neurodegenerative diseases.
In posterior fossa diagnosis task, we got ideas to propose new perspective of analysis by understanding the missing parts of the literature.
In this period, I was still constantly reading posterior fossa and fibroid papers and implementing codes of the brain data to understanding what we have and what we can do with it.
I will discuss the details of pf in the paper I'll write, so this diary is not convenient to use in that purpose.
Posterior fossa is a serious disease among children. The most common posterior fossa tumors in children are medulloblastoma, astrocytoma and ependymoma. Atypical rhabdoid teratoid tumors and brain stem gliomas are relatively rare. As the posterior fossa is a limited space, the tumors presenting in this region cause symptoms early on and require prompt treatment to avoid potential morbidity and mortality. Early detection and diagnosis of these tumors and prompt neurosurgical consultation is crucial in the optimum management of pediatric infratentorial brain tumors {cite}. That's why we are trying to diagnose accurately with AI to go beyond human ability.
With the start of the school days, I had to put the theoretical neuroscience work behind relatively. In theory there is time to do everything, but in reality there are too many factors to spoil it.
I cannot find time to actively study neuroscience, but I continue to study brain tumors in children both technically and clinically at the research level. I read lots of medical research papers besides my 6 quite busy computer science lectures and projects. Medical Neuroscience courses must be finished in 2 months so I'll figure out how...
We are still on the right track, so I cannot say anything goes wrong. In this peroid of time, I had the opportunity to further understand how much there is a need for people who can combine clinical/medical and technical knowledge. These two are in need of each other, but there is a serious gap between them. You can see this constantly, both in published articles and in other works.
I haven't been here for a long time...
Recently, I am working on early detection of Alzheimer's disease from MR images, besides trying to artificially augment the brain images via Variational Autoencoders and other methods. It's pretty irritating as I am dealing with dimensions for hours.
Also, still continue to write a paper related with posterior fossa tumors.
I have come to the end of the Medical Neuroscience course, which has the most comprehensive content I have ever taken. It took me over 5 months to complete.
Some highlights from the course:
- You can expect standard college level neuroscience course. Dr. White follows the companion book that he is also one of the writers (Neuroscience 6th Edition). Most of the online courses are superficial and do not provide in-depth knowledge. You will be surprised by the range of this course.
- There are lots of guide and tools that you can utilize with your study flow. He underlies the specific book chapters that explain the issues in more detailed before each class.
- You will learn quite interesting facts about the life itself such as how we can deceive our brain to perceive the world in a different way.
- It is quite difficult to complete the exams. Final clinical exam cases were quite challenging to find out which problems in the brain might arise from the problems seen in the patient.
I also got access to ADNI (Alzheimer's Disease Neuroimaging Initiative) data. Currently, we are creating task specific data set from large amount of shared data. I will be doing my graduation thesis from here it seems. We have 3D MRI and PET data with per 6 months for 3 years visits for many patients. You can check details of the ADNI dataset from Open Source Brain Datasets.
While working with brain images, there are several must preprocessing steps such as skull stripping and normalization. However, I couldn't use preprocessing libraries in the way I intended, so still have some issues here.
Also each of my compulsory computer science lessons have a quite comprehensive projects to do, so neuroscience will be suspended until I have to work for my Neural Engineering exams.
In this long interval, I've done 4 different term projects, and neural engineering homework. Also I destroyed my final exams :)
My previous neuroscience studies quite helped in the Neural Engineering course, which is normally a biomedical engineering course in YTU. I am one of the highest in overall results, and it was quite satisfactory and joyful to see that I am able to explain and comfortably use what I have learned while coming this far.
Average and Grade -> 91/100, AA(A+)
As a new development, I have solved the problem with FreeSurfer that will help me while preprocessing the 3D MRI data in my graduation project which is about Alzheimer's Disease.
Currently, my external focus is studying math and statistical learning to understand theory of signals, images and machine learning to be able to create reasonable computational models in my PhD. From this day forth, i will focus on more math, psychology and cognitive task modeling.
I've been trying to build my graduation project with solid foundations for a while. Deep learning studies on Alzheimer's disease have increased considerably. However, in the current situation, the results of most studies do not mean much, since most of them are doing these studies with weak understanding in deep learning.
Pre-processing of brain images takes time, especially skull-stripping. I enjoy what I'm doing though. The fact that the code I wrote is quite organized compared to the past gives a strange pleasure. I'll publish everything with my graduation paper.
I'm also trying to wrap up the paper on the posterior fossa as well, where we discuss a few questions that seem quite simple but are worth examining. We're close to light at the end of the bridge.
I am trying to manage and complete the writing of 3 journal papers in an artistic way. We're at (almost) the end of it all, but many new things noticed while writing the context make it difficult to conclude papers. Even though it is sometimes quite confusing and tiring that the subjects I work on and write papers on are different from each other, the feeling they bring to me is invaluable. At the end of the day, I think the pleasure I get will make us resistant to longer journeys.
Also, stuck with the Alzheimer's Disease training phase. I've coded and completed entire pre-processes, however, during the training phase I'm getting much lower results than I expected - also quite lower from the literature. I feel the desperation deeply, but at least I am well aware that this is how it works. So keep working.
A lot of things happened in these days, including the devastating earthquake. Therefore, the life could not proceed as expected.
I spent my almost entire time into the paper that we wrote for pediatric brain tumors. We went into a lot of depth, and frankly, it is a work that makes me feel very comfortable with. The amount of knowledge and the perspective we propose, is quite close to the top level papers, and we do indeed plan to submit the article to Q1 journal, which is really hard to be accepted as an undergraduate student.
I finalized my part in pediatric brain tumors study. It was unexpectedly long, concentrated and time-consuming, but I learned lots of thing on the pathway.
For example: QUALITY always takes time. You need to be very meticulous and work on what you have in detail. You will need to read your chapters over and over again and rewrite most of it from scratch. More importantly, you should also make sure that the information you provide is reliable and measurable.
Recently, I work on counterfactual explanations for machine learning, which I deeply read the most important papers. I came up with an amazing idea in order to use these fact base explanations with pediatric brain tumors. It actually can be used for every single classification task, where we may need local explanations for machine decisions. So, it seems like we will be delving into this topic a bit more and doing further work on explainability in medical research.
This is my last entry for now, on this journey.
During this period, I studied a lot about medical stuff (especially neuroscience), in addition to my technical responsibilities at the university and labs. I even managed to submit 2 medical papers to a Q1 journal and improved my knowledge of "how to research".
Unfortunately, many of my plans didn't work out, as always. I couldn't go for a neuroscience internship in the Netherlands (which got cancelled for ridiculous reasons). Plus, my current situation doesn't allow me to pursue a master's or PhD in neuroscience abroad, even though I'm well-qualified as an undergraduate to study almost anywhere for further education and research.
So, I've decided to continue my medical work on heart diseases under the supervision of Assoc. Prof. İlkay Öksüz, while pursuing a master's degree in Biomedical Engineering at Istanbul Technical University.
Sometimes, life doesn't provide the ideal circumstances for us to achieve what we want. Our ideas about things are constantly changing, and I believe we should take chances if we think they might be right because how can we know what's right anyways? Our brain simply deceives us and makes us live the way it wants. Everything is connected.
In conclusion, life is also a living organism and our decisions are significant in shaping our world. The simplest and biggest questions may be 'Why?' and 'How?' and learning constantly is the key to figure out.