fMRIbrainvoyager 2文档格式.docx

1、How can go wrong: alter blood flow（drgus, hormonal states, age, gender）. Sometimes there are some neural activity differences in different conditions, perhaps there are some differences in neural responeses but it may not be measured by firm. One way that can happy is that it is not a bulk change or

2、 stable change. Since fmri show an average response of the time space.Voxel, 60,000 perhaps be an image. How to make a claim from a well make brain to mental thoughts of a man. the brain area for “love”. How to make inference mental operation. Brain activity and behaviour: Forward inference : determ

3、ine which brain region is associated with an isolated behaviour. Parametric study : Focal Reverse inference: use local brain activity to （determine which mental states are evoked by a complex behaviour） identify mental operation. No other brain area activated. Just for pain. Good especifition. Are y

4、ou lying? Mind reading is possible? Look differences between Multi-voxel classification: use distributed patterns of brain activity to predict which mental state is being experienced. Signal and noiseFourier transform: analyse signals, power spectrum （功率谱）。 Only changes that are quite slowly can be

5、detectable by the fmri, changes that quite rapidly ups and down can not detected by the fmri （not pass well）. Like every 3/4 seconds. Design experiments that were really changes slowly. 5mins faces, 5mins houses would be best, but that is not the whole story because of the noise. Because of the stuc

6、k between the hemodynamic （人的血液动力反应） response suggest the low frequency of the experiment or stimulus, while intrinsic noise（固有噪声）suggest the high frequency of the stimulus. So how to balance between these two. 20s would be a better choice. Block design. 20s-30s seconds. Frequency repretations. What

7、 is the noise? could be heart rate, breathing, brain areas/cortex communicated /connected with each other. Frequencies.Experimental design has low frequency. Smooth the data . we normally smooth 6mm. howe ver, there are other people who smooth data in 8-12mm. do not use GLM, if you do it, you want t

8、o .3*3*3 brain module. Your anotomical data is high revolution than your function data. . fMRI: lectures from Frank:Presentation: tell the presentation to start-presentation starttell the scan start.What the final analysis are going to be. Planned everything, know in advance what analysis software y

9、ou are Gonne use. Fmri safety course, you should take the safety course, they will show all the worst thing that could go wrong. Video frequency in the scanner, that is quite dangerous. Minimize the bad things. Projector, high resolution, eye trakler. Programme to run the computer: Computer will con

10、trol the delivery of the stimuli, potential programes that could run the computer is : presentation （which is the one we generally use）, eprime, and matlab, each one of those is ok. Show things into the scanner, need the PC and scan talk to each other. Once we go into the brainvoyager, brianvoyager

11、always give an option to skip several volumes. It is good to get rid it. The reason is : If you look at the statistic analysis, all the data that incluse some conditions that sometimes goes to your baseline, and if your baseline includes these noise and it annoys your baseline, so just skip some vol

12、umes that does not contribute at all. But it is important to keep track of the data if multi people work on the same data.Presentation log file: it is good to have the log file from the stimulus delivery. So the computers is showing the stimulu, it is really handy if keeping track of the log of what

13、 is going on. When it is showing, what is up the scanning and what is hearing from the scanner. You need have the log file from the scanning session. if you have the log file and have it logged : log the response , log in all information, you can go back and check everything find everything（we did n

14、ot log one of our participants responses, and then we want to analyse, but we did not have these responses since we did not log in）, one word, if you do not have these stuff at the beginning, then you do not have these at all. Two ways to do timing with brainvoyager: uniform time,2000ms TR=2. If you

15、 want to see the brain in ms, you really need to do it by yourself, otherwise, the scanner just take the brain every 2s.When the subject was in the scanner, what happened to the scanner or computer. At the end of the session or at the beginning （it is up to you）, we require the anatomic data. It wil

16、l take 4-8mins to collect the anatomical data, the differences between 4-8mins is the longer time, the higher contrast between the white matter and the grey matter. In Friday, we did 2 functional runs and 1 aunotomic run. Every time, there is a run always produce one file, but the functional runs al

17、ways produce 2 files, one is raw data, the other is motion corrected （moco） data. We general use the raw data （franks prefers to use the raw data, but in some other manuals, some of them use the motion corrected data, which is the second one of each run ）. The process: （these steps are ubtertwined）P

18、lanning, stimulus presentation, measurement, pre-processing and statistic analysis Synchronisations : scanner waits for 7s, until signals to be stable, press button of stimulus computer and scanner at the same time. So skip first 1 or 2 volumes this synchronisation issue need to be decided since lat

19、er in preprocessing BVQx will ask you if you want to skip. Log file : format is text, every 2 seconds.# Anatomical run: 192 sclies, 1*1*1 mm （the whole head）Functional run: 32 sclices, 3*3*3 mm and a whole brain volume acquires every 2 seconds.Preprocessing: Anatomical preprocessing : talariaki the

20、brain , filter the brain in the same way （covert the brain to the talariake space） Functional preprocessing: CorregistrationCreat PRT file when you want to contrast different conditions.Brain normalization is to put brain in the talariaki space. The contrast of the brain activity when you see scramb

21、led person and intact person.We use the wizard to put in the data. 32slices, if you have some area that you really interested in in particular, you may change the functional run to the specific brain, but we would be a little bit open to see the whole brain, to see what other brain areas may be invo

22、lved. We try to measure the whole brain. Typically, you can do 32 sclices, 3*3*3 voxels and acquire the whole brain every 2 sceonds. If people have small brains, that is enough, but if people have larger brain, maybe there is something has missed. You have the option of either missing the sop superi

23、or frontal corxet on the top or the temporal cortex. All the anotomic data, everyone almost get the same thing. No matter the brain size. Where these kinds of issues become important , you want to see what happens on average about 20 brains , here you need to use the normalization . that all 20 brai

24、ns at somehow should be aligned . there are techniques to allow you .present one brain at a time, you give preliminary the region you are interested. .But we usually do is to average all the brain together, then somehow you need a space that combine all these brains. All the brains have different sh

25、apes and size, even we talariki these correctly, cortex based alignment . .there is still a little chance to have brains . Create the VMR anatomical data. Create the VMR in the step 9, page 41, check the number of sclices（192）-next, check the resolution of anatomical scan/images （256*256）. Then chec

26、k these slices and resolutions. -check the contrast and brightness （generally the default is ok, so keep the options remain there and then press OK）. After creating the VMR, you can just change the intensity of the brain. Which is inhomogeneity correction, V16 Tools. Original VMR volumesinhomogeneit

27、y correction-load v6just click the V16 file （we can also do this step before talairach）.Create the FMR, Create name the first vmr （the raw data） as R1（here, it is important to use the _ underscore to avoid the confusion of file names）, choose the number of volumes is 243, （keep everything as default

28、）. And then create FMR R2, here the original design for the experiment is 243 （the first one -first）, but frances always run the scan longer than the experiment design, and then just press stop when it is ok. In order to be equal as to our design, let us go for 243. Then for number of volumes , let

29、us go for 243. Then , we still not quite trust the first two volumes, so we go skip the first two volumes. To see the time course movie: go to the optionstime course movies （give the qualities of the movie）.Attach PRT file: open the fmr we just created, go to FMR properties, choose the fmr run 1choo

30、se the PRT file （choose the run 1 PRT file） closeThen open the fmr run 2, go to FMR properties, choose the fmr run 2choose the PRT file （choose the run 2 PRT file） closeThus, our PRT file is attached to out fmr.Preprocessing the functional data, close other file and only keep the fmr open, go to optionspreprocessing Fmriclick preprocessing slice scan time correction, 3D motion correction spatial smoothing -temporal filtering （ the mean intensity adjustment, while is not need in most cases, so dont choose this） -spatial smoothing is the one general can be down a