FreeSurfer - automated tools for reconstruction of the brain’s cortical surface



FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FreeSurferWiki Software registration, download, and documentation is found on the FreeSurfer Wiki.
Mailing List Archive General support and questions list for FreeSurfer.

FreeSurfer is brought to you by the Athinoula A. Martinos Center for Biomedical Imaging. Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute and is part of the National Alliance for Medical Image Computing (NA-MIC) funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Thanks to Ron Kikinis, Steve Pieper and NA-MIC (NIH Roadmap for Medical Research Grant U54 EB005149) for providing engineering advice and support for testing and open sourcing of FreeSurfer.


More of "my crazy sister" - The Scribble Pad

The Scribble Pad


So, yesterday I posted a rant about the situation w. my family/nutjob sister...you may have seen it, you may not have, but I took it down because it was white trash crazy even for me.

I have spent the past 2 days phone tagging with family, I am emotionally exhausted.

Here is where the dust has settled:

-My sister is agreeing to leave and she is staying with this guy for the time being.
-My mother has agreed to continue the loan but only if she controls the fat of it, and gives my sister money exclusively for school (she is now saying the money is for schooling), and a car is totally out of the question. And, the loan will go to repay my mother's bank account.
-A temporary restraining order has been initiated.

I have been speaking with my brother a lot, which I think is for the best, as I am a fool. I am constantly easily manipulated. If my sister needs something she can feign decent behavior for short periods, normal respectful behavior, she can say the right things at the right times to make people believe it won't happen again // she is remorseful. My sane sister and my brother are resistant to these lies but for some reason I always end up falling for them, which again is probably because I am a ridiculous social retard.

I feel depleted and stressed and horrible, and I am so tired of feeling this way. I am tired of this, years and years of it.

When I was 26 years old, I still lived at home, with my crazy sister. Toward the end of summer my sister went from her usual state of disorganized chaos to a whirlwind of insanity and abuse. I still do not know what the trigger for it was exactly, perhaps it is because she really is mentally ill and randomly had an episode. Either way, the net effect of this was her basically existing as a ball of fury and rage, destroying things, attacking people, attacking me physically for no reason at any hour of the day. I remember laying in my bed at night shaking; I remember being blitzed with stress at all hours. Shortly after this I moved out... this period was so totally unpleasant , I felt changed by it. I worried for my mother, worried for them all, but I had to get the FUCK out of that nuthouse. What kept me there was the concern for my mother... I was the one who discovered her bad behavior and stopped it, I was the one who intervened if she threatened her, I was the one who discovered the theft and prevented it... my presence was a sort of limiting factor for her, she knew she could not go THAT far or else the authorities would be called. It was my responsibility to keep things under control, from escalating into terminal and unrecoverable.

But I remember then, being just totally destroyed by this situation, physically nervous system wise, I had no choice but to leave, because it was completely sick and abnormal and unhealthy and I quit.

That fall my sister began taking medication, and became more functional.
That fall, I became severely depressed, surely a direct result of the blitzing paralyzing stress plastering me every hour of the day. When stress that intense happens to me, I always have a mood fail after a few weeks or months, even when the stress gets better/goes away. I remember finding it ironic. Here I was laying in a bed crying, in pain all the time, immobile unable to dress or shower, and there she was functioning better.

I moved out shortly after this, when I got better. So done, so totally.

Of course she stopped taking medicine, stopped working, stopped everything functional and decent and normal, and regressed into the usual. Ultimately she thinks there is nothing wrong with her, and I'm tired of trying to figure out what is wrong and how to fix it or keep things stable-ish.

I am overwhelmed mentally by stress and worry now, and all evidence throughout my entire life leads me to believe the way I feel now is suggestive of an endeocrinological/nervous system state which leads to mental decompensation. The mental chaos, symptomatic of psychogenic stress, leading to stress hormones, will always destroy me after weeks and months of it. No exceptions. I am old enough and wise enough now to know anything that makes me feel this way needs to be terminated ASAP. Standing in a fire won't save the house or stop it... it will just kill me. I will be consumed and turned to ash.

There is a lot different now than in the past in terms of my health and resilience, but I refuse to put myself at risk to ever feel as badly as I did then if I can help it. I know how I feel now is the gateway to that. This is pure stress, and my brain was made to break.

I'm tired of this. I can't do anything, and as was the case then, I need to stop getting involved. I've no power to fix anything, just as good of a chance of making it worse... I'm sorry if my mother abrogates responsibility for her own life and happiness, I'm sorry my sister is parasitic and cancerous, but it really isn't my responsibility and I don't have the magic ability to fix these things. It's like, the sanest inmate of the asylum trying to help the others. A joke.


User Interfaces as a Force of Entropy - DESIGNING *for humans: Display and Control Design

User Interfaces as a Force of Entropy

The Big Picture
Increasing improvements in user interface design are a natural result of the physical laws of the universe. To understand the underlying meaning of that statement, and its potential consequences, it is necessary to enumerate a sequence of logical assumptions (which I will attempt to summarize, but are no replacement for a fuller reading of the sources cited below):
1. The universe is driven by physical forces, including entropy Рthe dispersal of energy from localized concentrations towards generalized equilibrium. The clich̩ example of entropy is the spread of heat from a cup of coffee to the surrounding room. The heat spreads from the local area (the coffee cup) to dissipate equally within the room.
2. The origination and evolution of all systems in the universe from stars, to rocks and eventually life, has been driven by entropy. Moreover, over the history of the universe systems have developed that have been progressively more effective at increasing entropy (i.e. distributing energy). Astrophysicist Eric Chaisson has applied the measure of energy rate density – the flow of energy per unit timer per unit mass – as a common metric that can be used to compare the relative energy emissions of everything from stars, to plants, to people, to cities. His chart of energy rate densities from an upcoming publication, illustrates the emergence of higher energy density systems over time. While stars are incredibly powerful, they are also incredibly massive and pound-for-pound do not emit the relative energy of plants and animals (incidentally, “Gya” is shorthand for giga years, as in billions of years ago).
Chaisson Timeline
3. A key contributor to the entropy contributions of living organisms is the complexity of their behaviors – for example, digestion, mobility and cognition. Across species, mammals have higher energy rate densities than reptiles, which are higher than fish, and so on. The more highly evolved the animal, the higher the energy gradient (birds being the interesting anomaly to this pattern due to the high energy demands of executing flight in three dimensional space.)
4. Technology originated and evolved with life, to the point where man-made technologies have even higher energy rate densities than the humans that created them. Kevin Kelly illustrates this (using data drawn from Chaisson), in his recent book, What Technology Wants. As Kelley illustrates below, computer chips, with their extremely high ratio of heat output to mass, have energy gradients that are among the highest of any system in the history of the universe. In other words, the evolution of systems has followed a path of progressively higher entropy output, starting from large scale inanimate systems (stars, planets) to smaller scale living systems (plants, people) and presently to even smaller scale technological systems.
Kelley Energy Curve

Interfaces as Entropy Enablers

If you’re still with me, you may be thinking that this is all interesting, but how does it relate to user interface design? We can consider the implications at a couple of levels.
Superficially, user interfaces are the mechanisms by which we control computer chips, how we interact with these powerful entropy engines. At the least, this should lead one to appreciate that we’re dealing with powerful stuff even if we have grown accustomed to them because of their ubiquity. Chaisson even suggests that more transistors may have been produced than any other product in cumulative human history. From a historical perspective, the activity of designing interfaces which control interactions with these chips could be considered as fundamental a human activity as laying the bricks to build cities.
At a deeper level, we can consider the computer chip as a product and force of evolution and entropy. Like humans (and from humans), chips evolved as a progressively powerful entropy-generating system. But from an evolutionary context, why do chips appear to be a successful system? In evolution many systems or groups don’t not successfully proliferate – for examples the Neanderthals did not spread out or survive very long, compared to Homo Sapiens. In the case of humans, spoken language led to the rapid advancement and growth of the human population 50,000 years ago. Similarly, I posit that graphical user interfaces have accelerated the propagation of the computer chip. Early on, interacting with computer chips was difficult, requiring specialized knowledge and skills. Over recent decades, the refinement and proliferation of the graphical user interface allowed an explosion in the number of people who could interact with computer chips across a range of contexts, activities and platforms.
In other words, user interfaces have enabled a rapid increase in the number and uses of computer chips, directly impacting the rate of energy dispersal. There is a logical and perhaps inevitable sequence to this as the graphical user interface connected the language of the humans to the language of the computer. Taking this a step further, we can consider graphical user interfaces as an adaptive trait of computer systems that led to their successful proliferation, with humans as the carriers.

The Future of Interfaces

User interfaces increase entropy. To an interface designer, this might be taken as encouraging, discouraging, or both. To be discouraged is pointless as entropy is fundamental and inevitable. I see it as encouraging that those aspects of interface design that we should strive for as a profession - accessibility, ease of use, effectiveness, and efficiency – are characteristics that will continue to lead to the evolution and expansion of technologies.
What does this mean for the future of interface design? I would expect a continued expansion of chips with greater power, smaller scale and concomitant higher energy gradients. Similarly I expect interfaces that allow us to keep up with this growth in technology by effectively controlling more power and complexity. At some point in the future, we will reach a limit in what can be done by a user interface just as we will reach a physical limit in what can be done by a computer chip (i.e. the flattening of the Moore’s Law curve). What is the ultimate end state of the user interface and what can apply from entropy in the short-term to influence the design of interfaces? I will consider these possibilities in future discussions.


My sister is insane - The Scribble Pad

The Scribble Pad: My sister is insane.

I come from a lower middle class family. I've a mother, father, three siblings and myself. I am the eldest, my brother is second born, then there is my middle sister, and my youngest sister follows two years after her. Our ages right now are 29, 28, 27, and 25. (PS we are now old omg).

Well let me put it bluntly. My middle sister is pretty much insane.

No one really knows what exactly is wrong with her. I've tried to figure it out. Borderline PD? Bipolar D/O? Antisocial PD? Traumatic brain injury from being born cyanotic with a nuchal cord? Chronic dietary allergy leading to brain damage like psychosis and dementia? Was it the time she climbed the kitchen cupboard, pulling it forward, being showered with utensils sustaining a massive laceration to her forehead at 4 years old?
No, that's probably a symptom, not a cause. Even as a small child my sister was hyperactive and risk taking and irrational.

The few times she has seen a psychiatrist for her totally dysfunctional behavior and generally bankrupt way of conducting herself, she ended up with a diagnosis of bipolar disorder. Of course, pretty much anyone and anything will end up with a diagnosis of bipolar disorder these days (all that is required is admitting you are fucked up and have mood problems: I assure you, you will end up with a bipolar disorder diagnosis sooner or later.)

Crazy as fuck, totally irrational, immoral, aggressive, consistent pattern of violating peoples rights without guilt, paranoid, disconnected from reality to the point of being slightly psychotic ... a few words to describe her.

Here is an example of things she has done. This is a very very brief list.

-Stolen thousands and thousands of dollars from my mother and father, who are barely living above poverty, are in their mid 60s, and unemployed.

-Committed credit card fraud numerous times; opens lines of credit in other people's names, shows no remorse when caught. Will accuse my parents of "ruining her life" so it's fair that she continues to steal their credit.

-Years ago when my baby sister lived at home, she would steal her things, her money, her credit cards, pretty much anything she could find. My baby sister moved out shortly after. She avoid(ed) doing this to me because I would lock up all of my belongings making it difficult, although should I not lock up my belongings I would find them stolen.

-Stolen my parents car numerous times, ending up in numerous car accidents due to an inability to prioritize the responsibility of operating a major vehicle. The accidents are entirely her fault although she denies this (things that lead to an accident: putting on makeup while switching lanes; leaving the door wide open in the middle o the street; all of the accidents are caused by her not giving a shit about what is going on around her).

-She has not held a job in years. She has not held a job more than a few weeks in her entire life. She does not work now, and she is 27 years old.

-She is prone to extreme violence and rage, which can be unpredictable. The catalyst for a rage attack is usually being denied something she wants, or general frustrations things are not going her way. In the past when I lived at home my arms were pretty much constantly covered in nail marks and slashes. During rages she will become physically violent with the person and also their belongings, she enjoys breaking things in rages that belong to other people. The day I moved out she threw over all of my perfumes while screaming, for example. She has hit and bit my mother who is over 60 years old. One time, she pushed my mother into a wall causing profuse bleeidng from the head. I called the police and she spent the night in jail. The next year she would throw it in my face that I was a terrible person for calling the police on her. She never shows any guilt or remorse for her behavior, and when she does feel guilt it is very fleeting and superficial.
My sister will always conceptualize her behavior as logical, a valid response to an injustice. She does these things because we made her do them or we have violated or wronged her in some way. She has a gaping vast sense of entitlement.

If my sister is not going on rages, I will always tell my parents to check their credit cards because odds are she has opened a line of credit and is stealing form them (lack of rage = my sister is stealing from someone and is impulsively going on shopping binges/not working).

-She is prone to episodes of completely magical thinking and paranoia to the point of quasi-psychosis. she will have elaborate delusions of how various people are conspiring against her in school or work (for the few times she has been employed). She will eagerly share her delusions with me, telling me how this person said this to that person and they all think this and they are all against her ... the thoughts will be complex and detailed, but there is never any objective evidence for anything she thinks. If I try to tell her that it's possible she is mistaken about other people and their conspiracies against her, she becomes enraged I do not validate her opinions/perspectives. Basically whenever my sister is around any group of humans she quickly forms a delusion and a plot that they are all against her, to the point of total irrationality; it is more than a feeling of persecution or ostracisim (which is probably valid since she is a hostile nutcase)... she will literally form EXACT ACTIONS that people supposedly did or said that are entirely fabricated. She will misconstrue the slightest behavior as a validation of her delusions. ("When she looked at me like that, I knew she saw the website that they all have where they make fun of me and call me a prostitute; I know they are calling me a prostitute, and everyone in the school is aware of this rumor!!!")

-At times she will randomly accuse her professors or classmates of these wrongdoings, which usually leads to her dropping out of the classes or the school. She has been to many classes in many schools. She does have a 4 year degree but it took about 8 years to complete because of her pattern of dropping out of classes from her conflicts and irrational thinking and paranoia.

-A times she will demonstrate abject recklessness. She has engaged in prostitution, with strangers. She will meet random strangers go to their apartment to do drugs, although she does not have a drug abuse problem or alcoholism which makes the behavior even more bizarre.

Tonight, myself and my brother decided to go home to have dinner with my mother and father. This is an ordinary uneventful thing. My sister came home went on a screaming rage for no reason and began breaking things. So we left.

I beg my mother to toss her on the street and I warn her of stories observed as a nurse, of elderly who live with adult children and are abused and prisoners to their whims. My mother is incapable of seeing my sister as anything other than a small child who needs her. It is very sad because my mother has bent over backwards to help my sister, and my sister continues to abuse her and use her, physically and emotionally.

Pretty much no one in my family will deal with her. My baby sister has cut her off completely. My brother talks with her but keeps a firm distance. Like a true loser/sucker I communicate with her still sometimes and try to be friendly with her, in spite of her behaviors. ... but even I keep a good distance and won't be too close for too long.

She has no friends and no relationships, which is mostly because of her paranoid hostile thinking. She is incapable of being approachable or friendly to anyone.

This is actually a very short list, a general snapshot of what a nut she is.

As stated, there have been times she has seen a psychiatrist and the diagnosis given was bipolar disorder. She has tried lithium, which noticeably helped with aggression and impulsivity. Subjectively the lithium therapy made her much easier to be around because it seemed to suppress her rage and violence and impulsive insane thinking. She no longer takes it and refuses to take it because she does not think she needs it. In her words, she stopped taking it because "it made her sleep too much and she couldn't stay up late to study for school."
WHen she stopped the lithium she was calmer at first but she will always devolve into chronic insanity... random irrational extreme behaviors, and anger and aggression and paranoia.

I doubt she has bipolar disorder, as she never has depression, and when I questioned her about depression (sharing my experiences) she looks at me like I am an alien. Depression is completely antithetical to my sister's personality and the closest she can get to depression is a feeling of defeat when her desires are not granted. I have tried to probe to see if there have been periods of depression and she says she can't relate at all. Furthermore her insane behavior certainly does flare up and get worse, and calm down/get better, but it is always there which again argues against bipolar disorder.

From my perspective its' almost as if she has brain damage. Dealing with her feels like dealing with a demented patient, her brain clearly does not work properly... but yet, she is not properly mentally ill. She's not schizophrenic, not psychotic, she can go to school and pass classes sometimes... but interacting with her makes you very aware that you are dealing with someone who has a brain that is completely FUBAR. She can't help it, and that is obvious. Speaking with her, the responses do not follow as they should. It's hard to describe what this is like, but interacting with her more than a short while makes you quite aware her brain is not operating normally.

An interesting observation I noted is that my sister has a very rapid basal blink rate, and when she is going off her rocker her eyes will flutter so rapidly, appearing distinctly abnormal. I made this observation years ago, as it was so obvious to me as being not normal/a sign. Upon further research I discovered blink rate is controlled by dopamine signalling, and blink rate is elevated in hyperdopaminergic states like drug abuse, mania, or psychosis. Right away this offers a clue that there is clearly an organic abnormality, as I have never observed a normal person blink this often (I'm sure it does happen but in day to day life no one seems to have this rapid blink rate I have observed in her).

The ironic thing is I observed my own blink rate will shift based on my mood and energy; I too seem vulnerable to this sign, as periods of heightened energy and manic-like conditions which have occurred in the past were associated with very rapid blinking. Before it occurred to me I had first noticed it in her, and how abnormal it looked, and how such a sign was out of conscious control and must be entirely organic.

It was noted by the psychiatrist her WBCs was suggestive of an allergy, she has always suffered nasal congestion / sinus problems, so I wonder if she is prone to like a wheat or dairy allergy which is causing brain degeneration. My paternal grandmother was schizophrenic, some forms of this disease are believed to relate to allergic responses causing brain damage... of course that is hypothetical.

Other interesting observation is that of the four children my parents have had, my brother and youngest sister seem entirely mentally stable, no signs of depression, no signs of abnormal thinking. Myself and my sister clearly have a vulnerability to some kind of mood or mental disorder, although the manifestation is very different (my primary issue has always been depression, my sister is generally disorganized/rageful/impulsive and her behavior/thought processes are not consistent or sound, she is just "crazy" for lack of better term.)
My brother and sane sister have brown eyes and no acne, whereas myself and my sister have green based eyes and noted history of acne.

The most interesting part is my crazy sister is negative for PCOS and has a normal reproductive/endocrine system whereas my sane sister has had very bad PCOS (similar to myself) but in spite of this my sane sister has never had an acne problem.
I say this is interesting because PCOS is considered one of those diseases that will *Cause* mental problems like depression, however my sane sister is entirely stable in spite of her history of PCOS, meanwhile my crazy sister has no PCOS has regular menses and normal endocrine system in this capacity (even donating HER EGGS repeatedly which IMO is a criminal behavior given how defective she is...)

My mentally insane grandmother was slavic and had light eyes, so I wonder if the eye color merely represents the presence of genes affecting the nervous system that otherwise cause insanity? Fairly coincidental...

Acne is noted to cluster with mood problems, so I guess that isn't a surprise either. THe interesting thing about the acne in my sister's case is this: my sister has always had crystal clear skin in her teen years; the acne did not start until her late teens and early 20s. This is also when my sister notably became mentally unstable. In my sister's early teen years she was relatively normal, relatively agreeable, although always prone to anger and more impulsive. There was a clear shift in her around the time she started college, and this clustered with the development of significant acne. I wonder if the acne is (was) a symptom of some body abnormality also affecting her brain.

I don't know if this would be classified as a rant, or a vent, or free flow thoughts. All I know is tonight I tried to have dinner with my parents and family and I was not able to because , oh that's right, my almost 28 year old sister is a mental invalid and she is incapable of normal behavior and no one knows why, but the entire family just accepts that is the way it is.

No one is perfect and certainly many people in my family have significant flaws. I have significant flaws. But dealing with my sister is like dealing with a wild animal that happens to look like a human. It is not like any other experience relating to any other normal human, and I consider her more like my brain damaged/impaired patients than a normal person.

I used to try to help her when I was young, then I realized there is no way to fix a person who is unfixable. Right now, the family sort of operate like "that is how it is, she is to be endured".

The most infuriating thing is there really isn't a name for this. She could be a psychopath, she could be "borderline", it could be brain damage, who knows. I sure don't.

I worry terribly for my mother and father as they age and have less and less resources to cope with her behavior. I have seen similar things happen to other elderly people. Right now their stance is to give in to her at all times to placate her and avoid rage. That is a finite solution because they cannot afford to support a grown adult with endless needs, in old age.

Right. So, that's that.