Friday, June 28, 2013

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.

Thursday, June 27, 2013

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.

Wednesday, June 26, 2013

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.

Saturday, June 15, 2013

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]')));

fid = 0;

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

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.

Friday, June 7, 2013

An Empirical Look at the Peer-Review Process

"Everybody talks about the weather," Mark Twain once famously declared, "But nobody ever does anything about it." He then ate a knife to show the seriousness of his statement.

The same sentiment applies to reviewers in academia. Young researchers are frequently traumatized by their first exposure to the peer-review process, in which a paper is scrutinized and criticized by one's colleagues, ostensibly to judge whether the paper is acceptable for publication and to suggest improvements. However, as every one of us scientists intuitively understands, in reality it serves as nothing more than a vicious catharsis for the shattered dreams and failed career and (probably) frustrated sex life of the reviewer, unable to distinguish between his personal neuroses and legitimate criticism, by ruthlessly excoriating an otherwise brilliant exposition of scientific reasoning and experimental methodology. This trauma is then propagated along to other reviews in a never-ending cycle of misery and despond, with the abused becoming the abusers. Conrad summed up this mentality in his book The Secret Agent, in which he characterized a particularly violent group of terrorists plotting against a repressive government as not necessarily opposed to tyranny per se; they were merely unhappy that they were not the ones doing the tyrannizing.

The whole review process has been thoroughly criticized by many, but one of the first systematic exposés of peer-review was done back in the 1980s by two young researchers. To better understand their motivations, let's turn the clock back a few decades to the United States of the '80's: Top Gun, one of the supreme achievements of world cinema, had just been released in theaters to universal acclaim; cocaine flowed like crack through the streets of America; and the nation was beginning to feel its oats after successfully invading and destroying the hated island of Grenada. Life was so good, you could taste it in your spit.

However, even in the midst of all this success and prosperity, problems with the peer-review process still loomed large in the minds of the public. This is where our two young heroes, a couple of spitfire hoydens named Peters & Ceci, entered the picture, intent on producing concrete evidence of systematic bias among reviewer. Although subsequently tortured and murdered for their heresy by the peer-review mafia, their publication still circled clandestinely among groups dedicated to changing how the review process works.

Before their ghastly deaths, Peters & Ceci had taken papers previously accepted for publication and changed a few trivial details on the manuscript - for example, changing the author affiliation from a prestigious university, such as Yale, to a less prestigious-sounding, totally fictitious institution, such as the Nelson Center for the Study of Bodacious Ta-Ta's. Everything else, including materials and methods, remained exactly the same. After resubmitting these manuscripts, surprisingly few were reaccepted; in fact, out of the nine journals sampled, only one accepted the same papers it had accepted earlier! Keep in mind that these were all papers that had been accepted at respectable journals; virtually nothing had been changed, except for trivial details that had no bearing on the quality of the reported results. Reviewer comments were focused on methodological details ("Analysis of variance was improperly used in a post-hoc fashion"), writing style ("The theoretical focus of the introduction could be tightened up considerably"), and even, incredibly, features of the individual authors ("Just where can I meet this Nelson fellow?").

On the face of it, these results may seem to be cause for suffering and despair, as we find ourselves at the mercy of only one more facet of an openly hostile universe. One may well ask whether anything can be done, or whether it would instead make more sense to curse God, and die.

I offer a few suggestions. First, make sure that you are at a prestigious university; and if you are not, begin to associate with people who are at prestigious universities. Offer to make them authors on your paper, even if they haven't done anything. Ingratiate yourself with well-known figures in your field, even going so far as to openly debase yourself by performing menial tasks for them, or by humiliating yourself by offering to eat one of their used tissues. By stripping away any vestige of self-respect, you will increase your chances of their agreeing to be a co-author on your paper, as long as they don't have to do any work and never have to see you again. This, in turn, will increase your chances at publication.

The word sycophant has had negative connotations, long associated with spineless, weak, craven poltroons who would not hesitate to pawn their souls for the most trivial of earthly gains. Our job is to make it a positive word, associated with success, advancement, and - above all - publication.


Ceci and Peters laid on the grimy floor of their cell, wasted, defeated, only a putrid dish of water sitting between them. Their eyes were hollow and sunken and their frames emaciated, their faces dirty and wizened, their hair wild and bedraggled. Ceci's eyes roved around the room and he gibbered in an incomprehensible argot, thin strands of drool running down his cheeks in viscous rivulets. They had not eaten in five days and they awaited the hour of their execution with neither apprehension nor resolve but exhaustion.

There was the sound of a key turning in the door and an enormous Swede entered the room, holding a maul in his right hand. He seemed to fill up the entire room with his frame and he had two little pig's eyes set into the sockets of his skull and a cheesy rictus pasted on his face like a doll's. When he moved he gave the impression of a boulder set into motion. He gestured with the maul for Peters to get up but Peters merely glared at him and would not move. The Swede seemed to expect this and he bent down and picked him up by the meatless bone of his arm and dragged him to his feet.

Peters spit in the face of the Swede but it seemed as though it was all part of his day for he did not blink or wince but merely smiled, his right hand raising up slowly and methodically and then snapping down like the lid of a box and the maul made a sound like hitting a pumpkin with a club. Peters' eyes bulged as he collapsed to the floor like his bones had turned to jelly and the blood began to stream out of his ears.

The Swede bent down to look at him and watched as the capillaries in his eyes began to break up. Ceci's eyes darted zigzag across the room, his mouth open and his lower jaw flapping up and down uncontrollably. The Swede looked over at him and smiled.

*   *   *

The next day their lifeless bodies were dumped in a shallow arroyo along with everyone else who had dared to challenge the might of the peer-review process. For the next two days the air was filled with the whine of flies and the wolves and buzzards wallowed in the carrion, and when the feast was over there was nothing left save for their bleached skulls and the bones of their briskets curving in upon themselves like grotesque half-closed traps.


Link to the paper can be found here.

Thanks once again to Keith Bartley, who is quickly becoming an Andy's Brain Blog VIP. VIP status includes a free year-long subscription to the blog, shampoo samples, Nutella aroma therapy, and a summer vacation to North Dakota, including a tour of the legendary sugarbeet processing plants, a pitchfork steak fondue, and tickets to the one-hour acting monologue Bully! The Teddy Roosevelt Story.

Wednesday, June 5, 2013

Overview of

For those of you without access to a Unix-based platform, or whether you are just having a difficult time correctly installing your Python libraries, may not be an option for generating templates of AFNI processing scripts. In that case, you can still use, the command called upon by the GUI. Building an script from scratch is not all that difficult, but it can be time-consuming, and I recommend using one of the templates already provided on the AFNI website before creating your own.

The simplest use of is to use the -ask_me option, which, although limited and not supported anymore, can be useful for creating processing templates that you can then alter. -ask_me will then go through a series of basic questions, such as where your functional data and timing files are located. You can also specify options specific to 3dDeconvolve, such as the basis function for each regressor.

While this will generate a basic template script, however, it is a relatively limited one. For more advanced purposes, I recommend copying one of the examples provided in the help of, pasting it into a tcsh script, altering it as you need, and then executing it. For example, the following piece of code will search for datasets in the sb23 directory, make a copy of the anatomical dataset and move it to that directory, remove the first 3 volumes of each run, and align each EPI dataset to the last acquired volume (usually, the volume acquired closest to the anatomical run). An individual label is provided for each timing file (make sure that they line up in the order that they are input), and each is convolved with a boxcar function for a duration of 30 seconds. Three separate contrasts are carried out, with different weights for each calculated beta (see the lines under "regress_opts_3dD").

       -subj_id sb23.blk                             \
                        -dsets sb23/epi_r??+orig.HEAD                      \
                        -copy_anat sb23/sb23_mpra+orig                     \
                        -tcat_remove_first_trs 3                           \
                        -volreg_align_to last                              \
                        -regress_stim_times sb23/stim_files/blk_times.*.1D \
                        -regress_stim_labels tneg tpos tneu eneg epos      \
                                             eneu fneg fpos fneu           \
                        -regress_basis 'BLOCK(30,1)'                       \
                        -regress_opts_3dD                                  \
                            -gltsym 'SYM: +eneg -fneg'                     \
                            -glt_label 1 eneg_vs_fneg                      \
                            -gltsym 'SYM: 0.5*fneg 0.5*fpos -1.0*fneu'     \
                            -glt_label 2 face_contrast                     \
                            -gltsym 'SYM: tpos epos fpos -tneg -eneg -fneg'\
                            -glt_label 3 pos_vs_neg                        \
                        -regress_est_blur_epits                            \

Aside from that, make sure to read the help output of thoroughly. Most likely, one of the examples given will relate to what you want, and it is most efficient to copy that example and make the necessary changes. Also remember that will only generate a script, which contains all of the individual lines needed to run each step - e.g., slice-timing correction through 3dTshift, regression through 3dDeconvolve, and all of the rest. If you need to make any further alterations, you can simply open up the script with your favorite editor and tweak it.

Overview of the -ask_me option in This is for little kids, and grandmas.

More advanced video showing you how to copying other people's work and pass it off as your own.

Thanks to Harshawardhan Deshpande, who is called by his enemies, both out of fear and respect, "El Muchacho".