Difference between revisions of "Lab Manual:FMRI Data Analysis"
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(→Exercise for new neuroimagers) |
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==Preprocessing== | ==Preprocessing== | ||
* [[Functional_Preprocessing| Functional preprocessing]] | * [[Functional_Preprocessing| Functional preprocessing]] | ||
| − | * [[Anatomical_Preprocessing| Anatomical preprocessing (nudging and warping)]] | + | * [[Anatomical_Preprocessing| Anatomical preprocessing (nudging and warping by hand)]] |
* [[Checking_Motion| Checking for motion]] | * [[Checking_Motion| Checking for motion]] | ||
| − | * [[artifacts| Troubleshooting | + | * [[artifacts| Troubleshooting]] |
==Modeling== | ==Modeling== | ||
| − | * [[Modeling_Introduction| | + | * [[Modeling_Introduction|Background]] |
* [[Regressors|Making regressors]] | * [[Regressors|Making regressors]] | ||
| − | * [[the_GLM|Running | + | * [[the_GLM|Running a general linear model (GLM)]] |
| − | * [[Lab Manual:MSSD | | + | * [[Lab Manual:MSSD | Calculating Mean Squared Successive Deviation (MSSD -- an optional measure of temporal variance)]] |
==Group Maps== | ==Group Maps== | ||
| Line 20: | Line 20: | ||
*[[Making VOI masks|Making VOI Masks]] | *[[Making VOI masks|Making VOI Masks]] | ||
*[[Warping VOI masks|Warping VOI Masks]] | *[[Warping VOI masks|Warping VOI Masks]] | ||
| − | * | + | * Plotting Timecourses |
| − | + | ||
** [[Dumping Raw Timecourse Data|Raw Timecourses]] | ** [[Dumping Raw Timecourse Data|Raw Timecourses]] | ||
| + | ** [[Iresp_Method| Generating Fitted Timecourses (iresp)]] | ||
** [[Dumping Regression Coefficients| Regression Coefficients]] | ** [[Dumping Regression Coefficients| Regression Coefficients]] | ||
*[[Plotting_Timecourses|Plotting timecourses]] | *[[Plotting_Timecourses|Plotting timecourses]] | ||
| Line 28: | Line 28: | ||
* [[Mediation|Mediation Analysis]] | * [[Mediation|Mediation Analysis]] | ||
| − | == | + | ==AFNI command help== |
| − | *[[Roundup of Useful AFNI Programs and Plugins|AFNI Programs and Plugins]]: | + | *[[Roundup of Useful AFNI Programs and Plugins|AFNI Programs and Plugins]]: Here is a list of useful AFNI commands and their functions. You can also google commands on the AFNI discussion board, or type in the afni command at the command prompt. |
==General Program Guides== | ==General Program Guides== | ||
| Line 36: | Line 36: | ||
*[[Stata|Stata]] | *[[Stata|Stata]] | ||
| − | ==Exercise for | + | ==Exercise for newbies== |
If you're new to FMRI data analysis, you could first try the following: <br> | If you're new to FMRI data analysis, you could first try the following: <br> | ||
1. Find a recent neuroimaging paper (for example [http://www-psych.stanford.edu/~span/Publications/bk05jn.pdf Knutson et. al. 2005] or [http://www-psych.stanford.edu/~span/Publications/bk07n.pdf Knutson et. al. 2007] would work well). First give the paper a quick read through to get the main idea of the paper. <br> | 1. Find a recent neuroimaging paper (for example [http://www-psych.stanford.edu/~span/Publications/bk05jn.pdf Knutson et. al. 2005] or [http://www-psych.stanford.edu/~span/Publications/bk07n.pdf Knutson et. al. 2007] would work well). First give the paper a quick read through to get the main idea of the paper. <br> | ||
Latest revision as of 23:32, 10 July 2023
Contents
Preprocessing
- Functional preprocessing
- Anatomical preprocessing (nudging and warping by hand)
- Checking for motion
- Troubleshooting
Modeling
- Background
- Making regressors
- Running a general linear model (GLM)
- Calculating Mean Squared Successive Deviation (MSSD -- an optional measure of temporal variance)
Group Maps
- Group anatomical (optional)
- Group level t-tests
- Individual differences
- Making activation tables
Volume of Interest Analysis
- Making VOI Masks
- Warping VOI Masks
- Plotting Timecourses
- Plotting timecourses
- Logistic regression
- Mediation Analysis
AFNI command help
- AFNI Programs and Plugins: Here is a list of useful AFNI commands and their functions. You can also google commands on the AFNI discussion board, or type in the afni command at the command prompt.
General Program Guides
Exercise for newbies
If you're new to FMRI data analysis, you could first try the following:
1. Find a recent neuroimaging paper (for example Knutson et. al. 2005 or Knutson et. al. 2007 would work well). First give the paper a quick read through to get the main idea of the paper.
2. Next, slowly and carefully read through the methods section.
3. Finally, try to identify all of the steps required to run the analyzes in the paper. See if you can match the steps you found in the methods section to the steps in the above pipeline.
This should give you a good sense of the overall flow of data processing from start to finish.
