Tuesday:
Today we had our first fMRI fundamentals talk. Dr. Hirsch taught it, and it was really interesting. We learned about some brain theories and how the fMRI works. I am going to try and explain the whole lecture in another post.
After the talk, about half of the summer students and I went back to the area where I normally sit. (there are two areas in the lab, the main area and the back area. I sit in the main area because that's where Spiro is, but there is more room in the back so a lot of summer students work there.) I started working more on choosing my stimuli, which, at a certain point, became a group activity. After a while, we all went back to doing our own things. By the end of the day, I narrowed my stimuli down to about 80 pieces and started to shorten them to 10-15 second long clips.
Choosing the stimuli was tough. As I mentioned in a previous entry, I cannot assign emotions to the pieces that I use: they must be chosen by a population similar to my subjects. However, in choosing the pieces to put into the pre-study, I have to choose pieces with relatively obvious and clear emotions. Out of the 110 pieces I started with, I felt that all of them had an easily defined emotion. I did my first filter through by deciding that each piece needed to have at contain at least one minute defined by a single emotion. This got rid of easily 20 songs.
Friday, July 9, 2010
Thursday, July 1, 2010
Monday
Now back to a semi-daily log:
Monday:
Today was a crazy day. Slight backstory, on Thursday I went to talk with dr. Hirsch about my study, but she was super busy. She said she we could talk friday, but I wasn't coming in on friday, so we planned to talk today. Almost all day her doors were closed. There was another summer student waiting to talk to her about his study, which is about the perception of pain as a person giving pain and as an observer. It was interesting and, luckily, only used a simulation of pain infliction using pictures. Had the pain not been simulated, the experiment would basically be the famous Milgram experiment, just with 2 people doing the shocking instead of 1. We talked a lot about his experiment, my experiment, and other stuff. Eventually dr. Hirsch came outside, told the other student that she was super busy but could meet with him for a few minutes and said nothing to me. At this point, I decided to go talk to the grad student in charge of summer students, Grace, about my study. When I went to talk to her, she basically told me that, because I am not required to do a study for a specific program, I can't run one. So for about an hour, I had nothing to do. Spiro wasn't there, so I couldn't get any new work from him, and I didn't want to work on my study if I wasn't going to be able to continue with it. Eventually, Grace came back and told me that I could, in fact, work on my study, but the students who are required to do a study get priority for things over me.
For the rest of the day, I did reading and stimulus-finding. (This was actually the day I changed from decision making to math.) What's really nice about the lab is that basically everyone is happy to help with whatever you want. I asked Spiro a ton of experimental design questions, and not only did he not mind me asking, he also knew the answers. Additionally, I was able to bounce a lot of my ideas off of other summer students; my final design was helped along a lot by Evelyn.
Based on today's developments, I think I will be a bit behind schedule for finishing running my pre-study by the end of this week, but I feel like it's not actually that big of a deal.
Monday:
Today was a crazy day. Slight backstory, on Thursday I went to talk with dr. Hirsch about my study, but she was super busy. She said she we could talk friday, but I wasn't coming in on friday, so we planned to talk today. Almost all day her doors were closed. There was another summer student waiting to talk to her about his study, which is about the perception of pain as a person giving pain and as an observer. It was interesting and, luckily, only used a simulation of pain infliction using pictures. Had the pain not been simulated, the experiment would basically be the famous Milgram experiment, just with 2 people doing the shocking instead of 1. We talked a lot about his experiment, my experiment, and other stuff. Eventually dr. Hirsch came outside, told the other student that she was super busy but could meet with him for a few minutes and said nothing to me. At this point, I decided to go talk to the grad student in charge of summer students, Grace, about my study. When I went to talk to her, she basically told me that, because I am not required to do a study for a specific program, I can't run one. So for about an hour, I had nothing to do. Spiro wasn't there, so I couldn't get any new work from him, and I didn't want to work on my study if I wasn't going to be able to continue with it. Eventually, Grace came back and told me that I could, in fact, work on my study, but the students who are required to do a study get priority for things over me.
For the rest of the day, I did reading and stimulus-finding. (This was actually the day I changed from decision making to math.) What's really nice about the lab is that basically everyone is happy to help with whatever you want. I asked Spiro a ton of experimental design questions, and not only did he not mind me asking, he also knew the answers. Additionally, I was able to bounce a lot of my ideas off of other summer students; my final design was helped along a lot by Evelyn.
Based on today's developments, I think I will be a bit behind schedule for finishing running my pre-study by the end of this week, but I feel like it's not actually that big of a deal.
Weeks 4 & 5
Weeks 4 & 5: Research
When I got to the lab on Monday, I started thinking about what I was going to work on for the rest of the summer. I really liked all the programming stuff I was doing, but I wanted to also do some research, and not just work on the results of Spiro's work. So I decided I wanted to run my own study, the problem was, I had no idea what I wanted to study! My timing plan for the week was to do general research for a few days and find a topic by Tuesday or Wednesday, and then have a project plan by Friday. I went through a RIDICULOUS amount of study ideas; everything from using music and American Sign Language to help autistic children to communicate, to researching handedness, to researching the effects of amount of music on advertising. By tuesday (surprisingly) I decided I was going to research the effect of musical emotion (the perceived emotion of a given piece) on decision making. (Quick side note: my ideal research project was to have something that I could do a behavioral study on this summer and look at other results in the lab so that I could go up to school in september, present my results to a lab, and then do the imaging part of the study at UR. This idea fit all those criteria.) The advertising idea was the precursor to the decision making idea. For the rest of the week, I worked on study planning.
The two biggest parts of this study are obviously the music and the decision, so right away I started compiling a playlist of emotional music. In most studies that deal with emotion, the 4 goto emotions are happy, sad, angry, and fearful. However, I had an idea that, for a decision making task, a more tense piece of music may rush the decision while a more relaxed piece would make the subject think more. So, instead of angry and fearful, I decided to use tense and peaceful.
In papers I have read about music emotion studies, the general consensus is that the emotion of the stimuli cannot be judged solely by the researcher, rather it must be judged by a population similar to the subjects the will be used in the experiment. This means that the first thing I have to do is run a pre-study with a whole bunch of musical stimuli.
While I prep and run the pre-study, I will plan the actual study. The decision to be made in the experiment was making everything difficult. I wanted a decision (could be high or low risk, doesn't matter) that had two option: the first looks like the better choice on the surface, but when you think about it, it is definitely the worse of the two. The other choice is the opposite: looks bad on the surface but after some thought, is actually pretty good. It is VERY difficult to find a decision like this. In fact, I found it nearly impossible. After a few days of research, I gave up on the decision and instead focused on task performance; specifically math. The experiment now studies the effect of emotional arousal level on simple math performance. Earlier in the summer, I read a thesis that discussed the effects of musical arousal (in terms of tempo, volume, and likeablility) on task performance; specifically math and memory. I had a lot of issues with this study, but that doesn't really matter. What's important is that I am using her idea of musical arousal, but instead of defining it by volume or tempo, I am defining it by emotion (which include a whole new brain area).
I am running the study in a simple block design that is streamlined for good fMRI performance. The way the block design works is that I have music emotion blocks, problems set blocks, and rest blocks. Music emotion blocks are simply a piece of music with a given emotion that is about 1 minute long. Problem set blocks are just a set of arithmetic problems. The difficulty will be predetermined by a computer test I am writing. Each p-set will have about 150 problems in it (I think) because the task is to get as many problems as is possible done during the allotted time. A rest block is about 20 seconds long, and is just silence with a blank screen. Each trial is set up like so: a music emotion block and a p-set block are paired and run simultaneously (the piece of music plays while the subject answers problems). After the minute is up, there is a rest block. This is repeated 9 more times (for different conditions). Finally, the entire experiment is repeated to test for accuracy (that may not actually happen).
This is streamlined for fMRI because it has constant stimulus/rest blocks. In the scanner, a study must be designed in this way in order to actually see the activation. By inserting a rest period between each trial, it allows the brain to return to baseline (how the brain fires when nothing is happening). However, before I can run any of the experiment, I still need to run the pre-study.
When I got to the lab on Monday, I started thinking about what I was going to work on for the rest of the summer. I really liked all the programming stuff I was doing, but I wanted to also do some research, and not just work on the results of Spiro's work. So I decided I wanted to run my own study, the problem was, I had no idea what I wanted to study! My timing plan for the week was to do general research for a few days and find a topic by Tuesday or Wednesday, and then have a project plan by Friday. I went through a RIDICULOUS amount of study ideas; everything from using music and American Sign Language to help autistic children to communicate, to researching handedness, to researching the effects of amount of music on advertising. By tuesday (surprisingly) I decided I was going to research the effect of musical emotion (the perceived emotion of a given piece) on decision making. (Quick side note: my ideal research project was to have something that I could do a behavioral study on this summer and look at other results in the lab so that I could go up to school in september, present my results to a lab, and then do the imaging part of the study at UR. This idea fit all those criteria.) The advertising idea was the precursor to the decision making idea. For the rest of the week, I worked on study planning.
The two biggest parts of this study are obviously the music and the decision, so right away I started compiling a playlist of emotional music. In most studies that deal with emotion, the 4 goto emotions are happy, sad, angry, and fearful. However, I had an idea that, for a decision making task, a more tense piece of music may rush the decision while a more relaxed piece would make the subject think more. So, instead of angry and fearful, I decided to use tense and peaceful.
In papers I have read about music emotion studies, the general consensus is that the emotion of the stimuli cannot be judged solely by the researcher, rather it must be judged by a population similar to the subjects the will be used in the experiment. This means that the first thing I have to do is run a pre-study with a whole bunch of musical stimuli.
While I prep and run the pre-study, I will plan the actual study. The decision to be made in the experiment was making everything difficult. I wanted a decision (could be high or low risk, doesn't matter) that had two option: the first looks like the better choice on the surface, but when you think about it, it is definitely the worse of the two. The other choice is the opposite: looks bad on the surface but after some thought, is actually pretty good. It is VERY difficult to find a decision like this. In fact, I found it nearly impossible. After a few days of research, I gave up on the decision and instead focused on task performance; specifically math. The experiment now studies the effect of emotional arousal level on simple math performance. Earlier in the summer, I read a thesis that discussed the effects of musical arousal (in terms of tempo, volume, and likeablility) on task performance; specifically math and memory. I had a lot of issues with this study, but that doesn't really matter. What's important is that I am using her idea of musical arousal, but instead of defining it by volume or tempo, I am defining it by emotion (which include a whole new brain area).
I am running the study in a simple block design that is streamlined for good fMRI performance. The way the block design works is that I have music emotion blocks, problems set blocks, and rest blocks. Music emotion blocks are simply a piece of music with a given emotion that is about 1 minute long. Problem set blocks are just a set of arithmetic problems. The difficulty will be predetermined by a computer test I am writing. Each p-set will have about 150 problems in it (I think) because the task is to get as many problems as is possible done during the allotted time. A rest block is about 20 seconds long, and is just silence with a blank screen. Each trial is set up like so: a music emotion block and a p-set block are paired and run simultaneously (the piece of music plays while the subject answers problems). After the minute is up, there is a rest block. This is repeated 9 more times (for different conditions). Finally, the entire experiment is repeated to test for accuracy (that may not actually happen).
This is streamlined for fMRI because it has constant stimulus/rest blocks. In the scanner, a study must be designed in this way in order to actually see the activation. By inserting a rest period between each trial, it allows the brain to return to baseline (how the brain fires when nothing is happening). However, before I can run any of the experiment, I still need to run the pre-study.
Week 3 in Review
I know I haven't posted an entry in an extremely long time, so I am going to write a couple of long entries that sum up what I've been doing at the lab.
Week 3: Scripting
Last I posted, I explained what spiros script does, the work he is doing, and what I did on the script. During the rest of the week, I worked a lot more on scripting. There was a small problem with the script where any voxel with a value of zero (which was most of them) turned gray and made the image extremely hard to read. It was a simple fix, but it took forever to figure out!
On FSL there is an awesome tool called "atlases" (I may have already talked about them?) With an atlas, you can take any normalized brain image, click on any spot on the image, and the atlas will tell you what part of the brain you are looking at. While working on the node script, I thought it would be a really cool feature if there was an atlas for the nodes, so I started to look into how to make an atlas. Unfortunately, there are no online resources for creating atlases in fsl, and the users manual for the atlas tool has a note on the bottom that says: HINTS AND TIPS FOR ATLAS DEVELOPERS. And then the page ends. So, because I had not much better to do, I found where the atlas info was stored on the computer, and tried to figure out how to write one. A basic atlas consists of two files: a reference image and a data file. The reference image is a standard fsl file(.nii.gz) but the data file is written in XML, which I don't know and have basically no use for. So instead of learning xml, I just copied and pasted the contents of one file and filled in the blanks for my atlas. The way that the file works, is that on each line there are the x, y, and z coordinates of the brain area and then a title. The file then finds the coordinates on the reference image and determines how large the brain area is based on intensity values. Once I figured all this out, I was under the impression that I would have to manually open each of the 369 node images and define the center of each node for the data file. I tried that for about 8 images, and then decided that there must be an easier way. I came in the next day, and pieced together a few scripts that could find image centers to make an "atlas creator" script. I paired the atlas creator with the node script, and 20 minutes later (running the script took FOREVER) I had a personalized atlas that showed all of the nodes! The last step was to create an installer package that would create the necessary files and move them to their correct locations.
The next thing Spiro asked me to do was to see if I could somehow show the connection on each node, or make a 3D representation of the nodes and connections. I tried, but didn't get very far. One of the programs involved learning the C programming language, which I did over the weekend. However, when I got back to the lab on Monday, I decided I wanted to design my own study.
Week 3: Scripting
Last I posted, I explained what spiros script does, the work he is doing, and what I did on the script. During the rest of the week, I worked a lot more on scripting. There was a small problem with the script where any voxel with a value of zero (which was most of them) turned gray and made the image extremely hard to read. It was a simple fix, but it took forever to figure out!
On FSL there is an awesome tool called "atlases" (I may have already talked about them?) With an atlas, you can take any normalized brain image, click on any spot on the image, and the atlas will tell you what part of the brain you are looking at. While working on the node script, I thought it would be a really cool feature if there was an atlas for the nodes, so I started to look into how to make an atlas. Unfortunately, there are no online resources for creating atlases in fsl, and the users manual for the atlas tool has a note on the bottom that says: HINTS AND TIPS FOR ATLAS DEVELOPERS. And then the page ends. So, because I had not much better to do, I found where the atlas info was stored on the computer, and tried to figure out how to write one. A basic atlas consists of two files: a reference image and a data file. The reference image is a standard fsl file(.nii.gz) but the data file is written in XML, which I don't know and have basically no use for. So instead of learning xml, I just copied and pasted the contents of one file and filled in the blanks for my atlas. The way that the file works, is that on each line there are the x, y, and z coordinates of the brain area and then a title. The file then finds the coordinates on the reference image and determines how large the brain area is based on intensity values. Once I figured all this out, I was under the impression that I would have to manually open each of the 369 node images and define the center of each node for the data file. I tried that for about 8 images, and then decided that there must be an easier way. I came in the next day, and pieced together a few scripts that could find image centers to make an "atlas creator" script. I paired the atlas creator with the node script, and 20 minutes later (running the script took FOREVER) I had a personalized atlas that showed all of the nodes! The last step was to create an installer package that would create the necessary files and move them to their correct locations.
The next thing Spiro asked me to do was to see if I could somehow show the connection on each node, or make a 3D representation of the nodes and connections. I tried, but didn't get very far. One of the programs involved learning the C programming language, which I did over the weekend. However, when I got back to the lab on Monday, I decided I wanted to design my own study.
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