Scientists Plant False Memories, Basically Tell Us How To Do What We Already Knew From Watching Movies



In a study further illustrating why the public doesn't trust scientists with messing around with their brains, a neuroscience group from MIT were able to not only plant false memories, but also reactivate these memories at a later time and in a specific context. Using optogenetics - the stimulation of cells genetically altered to be especially sensitive to light - the researchers were able to generate fear-conditioned memories in mice when the mice entered a previously explored location known to be safe. In other words, the investigators were doing what psychologists do best - messing with people's minds.

However, besides its clear use for evil and obvious appeal to government and corporate leaders with a god complex, the experiment is a good example of the power of optogenetics, and makes significant headway in the search for the elusive engram - the neural signature of memories believed to be encoded primarily in the hippocampus, and particularly in the dentate gyrus and subfield CA1. Now, if they could find out how to erase those memories, that would be money. "Are you talking about that one time in second grade where you drank so much orange soda you peed your pants and I had to come pick you up from school, snookums?" Mom - GET OUT OF MY ROOM!

Kudos to Steve Ramirez and the Tonegawa lab, who are the kindest, bravest, warmest, most wonderful human beings I've ever known in my life.


Press Release
Science Paper

FMRI Workshop: University of Rochester



For those of you attending the University of Rochester, and who are intrigued, enticed, and otherwise titillated by neuroimaging methods like FMRI, I will be hosting a workshop in basic FMRI methods next week beginning Monday, July 22nd, at 2:00pm. It will be held in room 269 of Meliora Hall, on the Riverside Campus.


What to bring: A laptop with AFNI installed on it; a positive attitude; water bottle; extra socks; and a quasi-religious faith in the ability of FMRI to unlock the mysteries of life and and therewith dehisce those suppurating elements of ecstasy and trauma of our lives: The boredom, the glory, and the horror.

Tips are accepted and gratefully appreciated.

Rochester! I am Coming for You!

Go for the eyes, Boo, go for the eyes!

The next three weeks will be spent in durance ecstatic at the medical center in Rochester, New York, working in a primate neurophysiology lab with Ben Hayden and his lab which has generously agreed to host me during my stay. Which is a good thing, because if they didn't host me, I would likely spend all of my time gorging myself on ribs at Dinosaur Bar-B-Que in a vain attempt to forget all of my sorrows. Like my daddy always said: You won't find the answer at the bottom of a basket of ribs. Unless, of course, the question is about the basket.

In any case, I look forward to working with them, bouncing around some ideas, working with the monkeys, attending Eastman School oratorios, noshing at Dinosaur Bar-B-Que, hosting an FMRI workshop, hitting the famous Rochester roads every morning and taking a swipe at that elusive 100-mile week, finishing Absalom, Absalom!, listening to Bill Evans CDs, and avoiding the herpes B virus. Pray for me.

In case any of you reading this will be in the Bloomington area, I recommend checking out the Weiss-Kaplan-Newman trio at 8pm this Tuesday (July 16th). They will be playing, among other works, Shostakovich's horrifying piano trio no. 2 in e minor - a piece which never fails to set my vile blood on fire.



Template Spreadsheet for FMRI Results



Organizing FMRI results is hard work. Perhaps that explains why the vast majority of the world's population doesn't do it, and wouldn't do it even if they knew how. Nevertheless, for a harmless drudge such as yourself, organization and interpretation of results is a daily necessity, and the more streamlined you can make it the better for you and your adviser overlord who unfortunately will not be able to fund your summer research but will be ordering that custom-made Bentley imported from England. Keep at it, and one day you'll be the one importing cars and being swarmed at conferences by more science-worshiping nerdlings than you can shake a stick at.

To help you out with this, there is a short Excel spreadsheet template that you can find here which will automatically plot a barchart of your results and calculate both main effects and interactions. This is especially useful for plotting and calculating double dissociations, which is one of the most attractive, sultry, sexy results found in the literature. According to most people, anyway. Me? I'm more of a simple-effects kind of guy. Ladies?

Hit the video in case you aren't completely sure how Excel works, and need a brief refresher. Or, if you're just curious what kind of shirt I'm wearing today.


A Reader Writes: Basic FMRI Questions

Mine's bigger

I recently received an email with some relatively basic questions about FMRI, and both the question and answers might apply to some of you. Admittedly, I am not 100% sure about the weighting of the regressors for the ANOVA, but I think it's pretty close. Whatever, man; I'm union.

Some of the words have been changed to protect the identity of the author.


Dear Andrew,
 
Thanks for your message. My background is in medicine and I am trying  to do fmri research!
I will be grateful for your help: 
 
1. How do you interpret the results of the higher and first level fsl analysis - I am used to p values and Confidence intervals - are fMRI results read in a similar way?
 
2. Importantly- I have a series of subjects and we are interested to look at effect of [a manipulation] on their response to [cat images] over one year, we have four time points one before the operation and three after. These time points are roughly 4 months apart.
 
Our Idea was to see how the response to [cat images] changes over time- with each subject serving as their own control- How do I analyse that? We have some missing time points as well- subjects did not come for all the time points!
 
Regards,
 
Simon Legree
 
 
Hi Simon,
Congratulations on your foray into FMRI research; I wish you the best of luck, and I hope you find it enjoyable and rewarding!
In response to your questions:
1. FMRI results also use p-values and confidence intervals, but these are calculated at every single voxel in the brain. For example, if you are looking at the average BOLD response to [cat images] at each voxel, a parameter will be estimated at that voxel, along with a particular p-value and confidence interval. What you'll notice in the FSL GUI is a cluster thresholding which will only display a specified number of spatially contiguous voxels all passing the same p-threshold.
One crucial difference between first and higher-level analyses in FSL (and any FMRI analysis, really) is the degrees of freedom. At the first-level, the degrees of freedom is specified as the number of time points minus the number of regressors; at the second-level (or higher level) the degrees of freedom is specified as the number of time points that went into that higher-level analysis - which is usually the number of subjects included in the analysis. Unless you are doing a case study, you usually will not be dealing with the degrees of freedom at the individual level. (However, see documentation on mixed-effect analyses like AFNI's 3dMEMA, which will take individual variance and degrees of freedom into account.)
2. For an analysis with each patient serving as their own control, you would probably want to do a paired t-test or repeated-measures ANOVA for each subject. For the paired t-test, you would need to weight each cluster of regressors so that they sum to +1 and -1, respectively; in your case, +1*Before, -0.33*After1, -0.33*After2, -0.33*After3. However, if you hypothesize that there is a linear response over time, you might want to do an ANOVA and weight the timepoints linearly; e.g., for a decreasing response over time, +0.66*Before, +0.33*After1, -0.33*After2, -0.66*After3. There are a number of different ways you could do this. As for the subjects with missing time points, you would need to take that into account when weighting your regressors; I also recommend doing a sanity check by doing the analysis both with the timepoint-less subjects and with them. If there is a huge discrepancy between the two analyses, it might suggest that there is something else correlated with missing time points.


Hope this helps!
-Andy

Establishing Casaulity Between Prediction Errors and Learning

You've just submitted a big grant, and you anxiously await the verdict on your proposal, which is due any day now. Finally, you get an email with the results of your proposal. Sweat drips from your brow and onto your hands and onto your pantlegs and soaks through your clothing until you look like some alien creature excavated from a marsh. You read the first line - and then read it again. You can't believe what you just saw - you got the grant!

Never in a million years did you think this would happen. The proposal was crap, you thought; and everyone else you sent it to for review thought it was crap, too. You can just imagine their faces now as they are barely able to restrain their choked-back venom while they congratulate you on getting the big grant while they have to go another year without funding and force their graduate students to work part-time at Kilroy's for the summer and get hit on by sleazy patrons with slicked-back ponytails and names like Tony and Butch and save money by moving into that rundown, cockroaches-on-your-miniwheats-infested, two-bedroom apartment downtown with five roommates and sewage backup problems on the regular.

This scenario illustrates a key component of reinforcement learning known as prediction error: Organisms tend to associate outcomes with particular actions - sometimes randomly, at first - and over time come to form a cause-effect relationship between actions and results. Computational modeling and neuroimaging has implicated dopamine (DA) as a critical neurotransmitter responsible for making these associations, as shown in a landmark study by Schultz and colleagues back in 1997. When you have no prediction about what is going to happen, but a reward - or punishment - appears out of the blue, DA tracks this occurrence by increasing firing, usually originating from clusters of DA neurons in midbrain areas in the ventral tegmental area (VTA). Over time, these outcomes can become associated with particular stimuli or particular actions, and DA firing drifts to the onset of the stimulus or action. Other types of predictions and violations you may be familiar with include certain forms of humor, items failing to drop from the vending machine, and the Houdini.

Figure 1 reproduced from Schutlz et al (1997). Note that when a reward is predicted but no reward occurs, DA firing drops precipitously.

In spite of a large body of empirical results, most reinforcement learning experiments have difficulty establishing a causal link between DA firing and the learning process, often due to relatively poor temporal resolution. However, a recent study in Nature Neuroscience by Steinberg et al (2013) used a form of neuronal activation known as optogenetics to stimulate neurons with pulses of light during critical time periods of learning. One aspect of learning, known as blocking, presented an opportunity to use the superior temporal resolution of optogenetics to test the role of DA in reinforcement learning.

To illustrate the concept of blocking, imagine that you are a rat. Life isn't terribly interesting, but you get to run around inside a box, run on a wheel, and push a lever to get pellets. One day you hear a tone, and a pellet falls down a nearby chute; and it turns out to be the juiciest, moistest, tastiest pellet you've ever had in your life since you were born about seven weeks ago. The same thing happens again and again, with the same tone and the same super-pellet delivered into your cage. Then, at some point, right after you hear the tone you begin to see light flashed into your cage. The pellet is still delivered; all that has changed is now you have a tone and a light, instead of just the tone. At this point, you begin to get all hot and excited whenever you hear the tone; however, the light isn't really doing it for you, and about the light you couldn't really care less. Your learning toward the light has been blocked; everything is present to learn an association between the light and the uber-pellet, but since you've already been highly trained on the association between the tone and the pellet, the light doesn't add any predictive power to the situation.

What Steinberg and colleagues did was to optogenetically stimulate DA neurons whenever rats were presented with the blocked stimulus; in the example above, the light stimulus. This induced a prediction error that was then associated with the blocked object - and rats later presented with the blocked object exhibited similar learning behavior to that stimulus as they did to the primary reinforcer - in the example above, the tone stimulus - lending direct support to the theory that DA serves as a prediction error signal, rather than a salience or surprise signal. Followup experiments showed that optogenetic stimulation of DA neurons could also interfere with the extinction process, when stimuli are no longer associated with a reward, but still manipulated to precede a prediction error. Taken together, these results are a solid contribution to reinforcement learning theory, and have prompted the FDA to recommend more dopamine as part of a healthy diet.

And now, what you've all been waiting for - a gunfight scene from Django Unchained.



How to Fake Data and Make Tons of Money, Part 2: CreateNIFTI.m

After you've been working in science long enough, you may start to discover that the results that you get aren't necessarily the ones that you want. This discrepancy is an abomination, and clearly must be eliminated. One way to do this - at least with FMRI data - is to manually read in a dataset, and overwrite existing values with new ones.

While you can overwrite values in any dataset, I find it helpful to first create a blank dataset that has the same dimensions and orientation as the other data that you are working with. For example, by creating a copy of an existing image and then switching all the values in that dataset to zero. Starting from the ANALYZE files (i.e., .img/.hdr), you will need to convert them to NIFTI before you can use the script; I use AFNI's 3dcopy and then 3dAFNItoNIFTI to do this.

Once you have copied your file, you can zero out the values by using the script createBlankNIFTI.m and then fill in new values using createNIFTI.m. I'm sure these can both be combined somehow in the future, but there isn't a terribly high demand for this capability yet, so I'll leave it as is.



AFNI Command: 3dUnifize

Are you disgusted with the way your T1-weighted images look? Trying to reduce the intensity imbalance in your anatomical? When your friends tell you that your structural looks "fine", do you find yourself not really believing them? If so, then 3dUnifize can help. Simply supply a prefix for the output dataset and the name of your anatomical image, and thirty seconds later you have a relatively balanced T1 image.

To be honest, probably very few, if any, people will use this program. However, it does draw attention to the ability to look up and check on intensity values of your images, as this can be a useful diagnostic tool in some cases. Once you've loaded up the AFNI GUI click on the Overlay tab and look at the values to the right of the ULay (Underlay) and OLay (Overlay) labels. These will provide the intensity of the image, whether in arbitrary units - for example, if you had a raw T1- or T2-weighted image loaded - or statistical values, such as when you overlay a t-map.

Also, due to a recent purge in the lab, I am now officially moved in to a new office. More exciting details about my life, plus an obnoxiously loud computer fan, can be found in the following video.


Electrically Shocking Your Brain Enhances Cognition, Somehow

For those of us wishing to improve our cognitive abilities without having to deal with a concomitant host of unpleasant hobgoblins, including patience, perseverance, industry, toil, thrift, caloric restriction, abdominal exercises, and master cleansing, science has once again come to the rescue. In place of the boredom and the loneliness and the indignity of solitary study, we can instead improve our minds by zapping localized patches of cerebral cortex with small electrical currents, which to me seems conceptually similar to sticking a fork in an electrical socket. This technique is known as transcranial magnetic stimulation, or TMS.

There is a TMS facility at my university, although I have only observed it done to others. From what I could tell, the real payoff occurred when the experimenter was able to position the TMS coils just right so that when the unit was turned on, the subject's finger moved a couple of centimeters, as though jerked by an invisible string. I didn't fully appreciate its significance at the time, although I later learned how it could be used to establish which regions were necessary to carry out specific processes, and how disruption of activity in one area of the brain could either up- or down-regulate functions in other areas.

However, far from being only used to disrupt neural communication, several experiments have shown that TMS can be used to enhance neural functioning, and, by extension, possibly improve skill acquisition and memory retention. Although TMS is designed to depolarize neurons and induce neural firing, different frequencies of TMS can lead to markedly different results; and even within the same frequency, different results can be induced from applying the same frequency to different regions and during different tasks. For example, a 5 Hz TMS pulse over the dorsolateral prefrontal cortex disrupts performance in a delayed match-to-sample task, while the same frequency applied to the midline parietal cortex increased performance.

One theoretical framework for how TMS can improve performance is that of addition-by-subtraction, in which cognitive functioning is enhanced through disruption of competing cognitive processes. For example - and to use extremely simplified cortical representations - let's say that a participant is shown a series of emotional and fearful men's and women's faces and is asked to categorize each face as male or female. TMS is then used to disrupt the emotional part of the brain (again, extremely simplified example), which prevents the processing of extraneous, competing emotional information to interfere with the task. The participant thus becomes faster and more efficient at categorizing the face by gender.

An excellent review of these techniques and other issues related to TMS can be found in the new issue of Neuroimage in an article by Luber & Lisanby, found here. Obviously, it is only a small series of steps before we install public TMS facilities that look like huge futuristic salon hairdryers which can be used for an array of cognitive enhancing techniques, such as mathematical reasoning, crossword puzzle solving, and remembering your girlfriend's birthday.

Creating NIFTI Images from Scratch: CreateNIFTI.m

There may come a time, for whatever reason, where you want to create your own NIFTI image with your own values at each voxel. After all, those processed t-maps and beta maps tend to become a nuisance once in a while, and it feels far better to simply create your own.

First, you need to create a text file with the voxel coordinates and the value at that coordinate. For my script, for example, there are four columns: The first column is the value, and the next three columns are the x-, y-, and z-coordinates for that value. (Note that these are the native coordinates of the image, and not MNI or Talairach coordinates; if you want to use normalized coordinates, open up the image in a viewer, navigate to those normalized coordinates, and write down the corresponding native coordinates.) A sample text file might look something like this:


4 50 40 30 %Insert value of 4 at coordinates 50, 40, 30
5 50 40 31
7 50 40 32
10 50 40 33
500 50 40 35


Once you have saved the text file, you can either use an existing image or create a blank template image using a program like "nifti_tool -create_im ". Then, use the following script with both the image and the text file as arguments (making sure to pass them as strings):

function createNIFTI(imageFile, textFile)


hdr = spm_vol(imageFile);
img = spm_read_vols(hdr);

fid = fopen(textFile);
nrows = numel(cell2mat(textscan(fid,'%1c%*[^\n]')));
fclose(fid);

fid = 0;



for i = 1:nrows
    if fid == 0
        fid = fopen(textFile);
    end
   
    Z = fscanf(fid, '%g', 4);
   
    img(Z(2), Z(3), Z(4)) = Z(1);
    spm_write_vol(hdr, img);
end


This can then be modified to suit your evil purposes.

Tutorial video coming soon; in the meantime, I have some business to attend to, which involves going back home and having fun and laughing with my friends. Just hang tight.