Day 33

          I got to work early and I added presenter's notes to the slide show. After the staff meeting, I had to fill out a survey of how my experiences were this summer. Afterwards, Halle and I walked over to the color science building to participate in an experiment. They had us look at 60 images and circles areas in the images that were important then number those circles by level of importance. It was a nice, simple activity for the morning. After the experiment I talked with Dr, Berns who is the head of the color science program about the program. He gave me a tour of facility. The equipment was pretty nice and the work was compelling. He also highly recommended the imaging program as an undergrad then going into color science for grad school.
          In the afternoon Elaine and I ran through the powerpoint again. It definitely got a lot better and I don't think that we will go over during the final presentation. I'm kind of looking forward to just presenting. Hopefully everything will go well for everyone.

Day 32

        Today felt long. I brought in some cupcakes this morning from a family party that we had over the weekend. Those made the morning slightly more exciting. Elaine and I went up to see Joe Pow this morning to check over our powerpoint. He warned about going over the 20 minutes which is my biggest concern at the moment. Hopefully we'll get through it all right on thursday.
       Elaine and I began to work on our poster that summarizes our research and the capabilities of the new NMR machine. It is about half way done and it is looking very professional. I am excited at the thought that it will be hung up in the lab that we have been working at all summer. I'll probably work on it some more tonight and we can show Dr. Hornak tomorrow morning.
      Lastly, Elaine and I also did the first run through of our presentation by ourselves today. We both have plenty of room for improvement in the area of clarity of our words. A lot of the theories that we are presenting are very delicate so it's important that our language is precise and accurate. Again, I'm hoping that this will work out for thursday.

Day 31

           Today was another slightly boring day because all Elaine and I had to work on was our powerpoint. We keep adding slides to explain concepts, variables, and theories we introduced previously. However these explanations are going to take some time so we've had to cut back on some other slides. All in all it's coming along. I think that everything in regards to changing NMR variables to create a better picture is going be kind of dry; but when we actually start showing NMR images, I think we'll pick up some attention.

Day 30

          Today we asked Joe about the theory part of our presentation. He was very helpful in clarifying the terms and concepts that we would be covering in our presentation. Elaine and I worked on clarifying these concepts. I got a really good idea of where our presentation is going thanks to the theory work Elaine and I put into it today.
         We showed Dr. Hornak our presentation for the first time at the end of the day. He gave us some really good suggestions about re-wording some areas and completely avoiding concepts with over-complicated explanations. Dr. Hornak also said that Elaine and I could make a poster presenting the work we have been doing over the summer and also showing off the capabilities of the new NMR machine. This task would be for next week if we have extra time after we have finalized our presentation.

Day 29

         Today we got some more images done for our powerpoint. Elaine brought in more plants that we needed to image with the optimal microscope. So I went right to work on those. Afterwards I put them in our powerpoint. This is a lengthy process because the microscope only has a broad enough view to image a small section of a plant stem. This problem translates into me carefully overlapping many images of the same plant to get the entire stem. In addition to that we also ran slice thickness scans on one of the plants. However the signal was so low in these images once we countered the automatic intensity scaling feature that these images were useless due to their darkness.
         We spent most of the day doing these things so we weren't able to do the theory part of our presentation. That is tomorrow's task...

Day 28

            This morning Elaine and I continued to work on our powerpoint. We're also trying to nail down the title for our presentation. It's a little harder than it may seem. We also created a list of everything that has to get done for our presentation.
            A student came by who was interested in the imaging science program so we got to tell her what we've been doing all summer. In addition Bethany paid for all of the interns to come to lunch with her. It was a lot of fun.
            In the afternoon Elaine and I merged what we had both been doing separately with the powerpoint. We're making progress. We're also going to retake some microscopic images as well as a few NMR images. This should give all the images we need; but we still have to spend a lot of time on the first part of our presentation in which we describe the science and theory behind MRI imaging.

Day 27

            Today was the undergraduate research symposium . In addition Dr. Hornak wasn't here so Elaine and I had free reigns for the day. We watched a couple presentations by the undergrads. They were actually pretty engaging. There was also a free catered Chinese lunch = good deal.
            In addition to that we got to go on the roof of the imaging science building. There was an experiment being set up. A plane would fly over the roof with a camera underneath and take notice of a bunch of crates that were evenly spaced. I don't actually know the point of this but we did get to help set up. Most of the interns also came back later when the plane was supposed to be flying over. After waiting an hour or so the plane still hadn't flown over so we just left. We later found out that the plane had actually flown over several times and none of us had noticed. I'm not upset though, the roof was awesome, plane or no plane. Good day.

Day 26

             Today Elaine and I spent a lot of time on very few things. We were working with the graphs for our variables for T1 and T2. We were working on creating a line of best fit for both of the graphs. In addition Dr. Hornak was showing us to  to make them look more visually up to par.
               In addition we also to the images for our slice thickness variable. This has turned into a lengthy process because instead of use converting the image to a jpeg, we also have to record signal averages and counteract the signal scaling feature within the program. So we're now ready to create a graph for those signal values and create a slide with the corresponding pictures.

Day 25

           Today was a day full of progress. Not only was there indeed an automatic scaling feature in the NMR program, but Dr. Hornak was also able to find a way to counteract it affects. So Elaine and I were able to change the scans we had taken the day before to represent their true intensities. This made the data comparable, and we were able to graph it. There is still some margin of error in the graphs so we did some of the images over again at the end of the day.
           All the interns got to go to the grill-out for undergraduates who conducted research over the summer.  That was pretty fun except it took them a while to serve all the people that had come.
           Elaine and I also spent some time on the powerpoint. I did comparison slides showing the cross-sectional image of a plant under a microscope and the corresponding NMR image of that plant. So good data and good results basically equaled a good day.

Day 24

           Elaine and I got right to work with the NMR machine so it didn't have time to break on us. The images I took with the older NMR  were not very good. I say this because if you change a certain variable on each image and write down the intensity if the same pixel on each image, those intensities should form a exponential decay or loss if you graph them. However, the results I got with the older NMR machine were pretty much gibberish. So we started re-taking those images to get the proper graphs. Unfortunately after spending the morning taking images and plotting the points, those graphs were also gibberish.
          Dr. Hornak deduced that there must be an automatic scaling feature to the program which makes comparing the intensities of various images to each other nearly impossible. So when we left at the end of the day, Dr. Hornak was working on trying to find someone who might know how to turn off this feature that we think exists.

Day 23

          I caught Elaine up to speed on everything she had missed last week. We both went right down to the NMR machine in the basement with Dr. Hornak. We were excited to use it since it had been down for a decent amount of time. So of course we repeatedly got a warning message after two minutes of use. This error translated into yet another day we couldn't use the NMR. On an up note is was fixed at the end of the day.
          Elaine and I didn't get much done because almost everything we need to do involves the NMR. So we worked through our powerpoint some more instead. Dr. Hornak also set a meeting for me to talk with Dr. Smith who is a polymer chemist. I'm thinking about majoring in polymer chemistry so it was interesting to hear about the equipment in his lab and some basic theories. His main message though was to get a solid foundation in undergraduate school (major in chemistry) then specialize in polymers. So despite not being able to use the NMR, a little learning still occurred.  

Day 22

              I got in early and began working on my blog. After the staff meeting, I spent some time organizing a powerpoint slide. I took a dozen NMR images of the same fish that were taken at various spot at sequential spots along its body. I then organized them so it showed the cross sectional images of the fish every millimeter starting at the the tail and going all the way up to the top of the head. I must say, it looked pretty neat.  
               Soon enough, we all left for the field trip. We went to Amiel's for lunch and got subs. The food was pretty good. Once we got to Xerox, we watched a video about how the company was expanding its products. A few of the researchers that were making the discoveries for these new expansions gave us presentation about their work. Some of their work was detecting lit cigarettes at gas stations, creating security features for documents (uv marks, gloss, etc) as well as personalized, instructional medical videos for patients. That was the most interesting part to me. We got a tour of the manufacturing facility for a $600,000 printer afterwards.
              When I got back to RIT, Joe said the NMR machine was back up and running again. So hopefully, Elaine and I can begin taking images on monday...

Day 21

            I came in early to convert the NMR images I took with Dr. Hornak the other day to jpegs. But when I went downstairs, all three of my labs were caution taped. I guess those rooms were due for cleaning because all the furniture was in the hallways. So I went upstairs and wrote my blog instead.
           After the staff meeting, I worked on two graphs that were supposed to tell me the T1 and T2 values for the sample I had imaged. In addition to that, I also tried to convert my images because the lab was open after and  hour or two. Only one of my graphs was conclusive the other was completely messed up. The old NMR machine is not producing the best data that can be used for graphs.
           Then I was having problems with converting the images. Turns out I was using the wrong version of IDL. But the second Dr. Hornak left, of course, there were problems again. I was a little frustrated, so I just stopped and went to the grill-out. That turned out to be a lot of fun despite the fact that several interns are gone on vacation. We managed to get a Frisbee stuck in a tree. Matt climbed the tree to try and get it out, but was unsuccessful.
           I talked to Dr. Hornak after lunch about the pictures. He figured out that the picture I was trying to convert had been corrupted somehow and that's why it wasn't working. After that I was finally able to convert all the pictures with no problems. Later in the afternoon, the engineer came to fix the NMR machine. He brought all kinds of equipment and was hooking it up and running tests and fixing current and other things I wasn't quite following. But I had to leave while he was still working so I'm looking forward to see how thing's are coming...

Day 20

         Today until the rest of the week Elaine is on vacation so it's been kind of quiet. I talked to Dr. Hornak after the staff meeting about Elaine and I's idea about the final presentation regarding optimizing NMR signal. He seemed to like it and he just encouraged me to do a section at the end with implications in which Elaine and I would cover things that could be imaged with an NMR tube and some of the pictures we have taken thus far (plant stems, fish, etc..).
         He told me ways to get the variables that would influence image quality. So now I have a rough outline of the things I need to do to get the right variables for the best image possible. I think we finally managed to pin down a project this time, so I'm pretty excited.
          In te afternoon Dr. Hornak and I went to the college of science to continue to work out the kinks with the older NMR machine. We ran into a few more problems. The main issue was that a line of high intensity signal kept appearing in some of the images that should not be there. However, we were able to take some good images that we can use to calculate some of the variables. My next task is converting those images to Jpeg and creating and excel graph with signal intensity and TR values.

Day 19

         Today Elaine and I managed to get a lot done. In the morning we began working on our powerpoint. Because the NMR machine is still down, we have abandoned the idea of creating a presentation that focuses on the dehydration of plants and the effects of certain liquids. So now we think we'll give a presentation on how to optimize NMR image quality by showing the effects of certain variables. Such variables include slice thickness, magnitude of the magnetic field, sample relaxation time, as well as a few more technical variables.
          We began working on our powerpoint. We wrote a few slides that had to do with the basic science principles behind NMR imaging. In the afternoon we went back over to the college of science to work on the parameters for the old NMR. After two hours Dr. Hornak was able to get it working pretty well. This was very uplifting to us.
          That was pretty much it for the day. It doesn't sound like a lot, but it felt like we made a lot of progress with our final presentation.

Day 18

        Elaine and I scheduled time to use the old NMR machine today. However Dr. Hornak sent us an email this morning that we had actually scheduled it on sunday. Those tend to be the effects of friday afternoons; thankfully there was still time left in the afternoon that we were able to reserve.
        As part of the staff meeting, Elaine and I took all the interns down to our lab and showed them what we have be doing the past few weeks. I think that went pretty well. As I was talking about our progress I realized that we have learned a ton in the past few weeks and have taken close to 100 images between the NMR and the microscope.
          After that we went up to Dr. Hornak's office. He was in a bit of a panic because we only have a few weeks left, our NMR machine is down, the old NMR is not looking too promising, and he wants us to still have a good time and learn in spite of that all. So he introduced us to a mini MRI machine that we could try to use. Our currently broken machine had a magnetic field of 11.6 tesla. This mini machine has a magnetic field of 5 x 10 ^ -5 tesla. As you can imagine, this is a huge difference that means there is much less signal and a lot of background "noise" (interference). Consequently this machine which is about one cubic foot is incredibly sensitive to metal. We spent the morning with a compass trying to figure out where there was the least pull from surrounding metal objects (these objects interfere with the signal). The best spot turned out to be the front lawn.
             We tryed to set up the machine in Dr. Hornak's office first, but the signal was very poor. We are not sure if it's going to work out; but one of the up sides is that we can fit sample in it with a 5 cm diameter which opens up many more doors than 4.5 mm.
            In the afternoon, we spent more time trying to set up the imaging program on the old NMR machine. We got an image that was very distorted compared to the other NMR. Dr. Hornak was able to center it and make it the right proportions. But then a gradient overload caused the system crash. So we might very well be back to square one...

Day 17

        Friday was a bit of a slow day. Elaine and I didn't do mch in the morning. We were scheduled to use the 12-year-old NMR machine in the college of science in the afternoon so we did print out the program parameters for the machine we have been using in order to copy them into the other system.
       We had our picnic, grill-out for lunch. Prati brought gnome bowling which is surprising harder than it would see. We also spent some quality time playing frisbee. 
       After lunch Dr. Hornak took Elaine and I to the older NMR machine. The normal probe for the machine does readings for spectroscopy. The one we've been using allows a person to use the machine for imaging purposes. This means that whenever we use the older machine we have uninstall the spectroscopy probe, install the imaging probe and put the other one back when we're done. This process requires us to disconnect about 10 cords, take out the probe from the bottom of the machine, insert a new one and reconnect the cords.
        We spent time trying to copy the imaging program, however this was not very successful. The program is a much older version on the other NMR so a lot of the parameters did not transfer properly. We spent a lot of time troubleshoting but were not very successful.