Computer Reference Portal
From SpanLabWiki
Your dental expertise, our commitment at edu.dental. dental upenn edu ==General==
Contents
- 1 Backing up data to BIAC servers
- 2 Plotting timecourses in Excel, SPSS, and Deltagraph
- 3 Using the General Linear Model Regression script
- 4 EPrime
- 5 Scanner Computer
- 6 AFNI
- 6.1 Reconstrucing anatomicals using the to3d function
- 6.2 Guide to nudging
- 6.3 Guide to warping
- 6.4 Running a GLM Regression in AFNI
- 6.5 Neurofeedback IRESP script for use with 3ddeconvolve
- 6.6 How to make canonical VOI masks
- 6.7 How to make individual VOI masks
- 6.8 How to draw VOI masks
- 6.9 Dumping your regression coefficients using 3dmaskave
- 6.10 Old process script instructions
- 6.11 Viewing your group contrast data in AFNI
- 6.12 AFNI Functions
- 7 MATLAB
- 8 Python
- 9 Stata
Backing up data to BIAC servers[edit]
Plotting timecourses in Excel, SPSS, and Deltagraph[edit]
Using the General Linear Model Regression script[edit]
- The script will automatically loop through your subjects and run individual regressions on each subjects.
EPrime[edit]
Guide to designing studies with EPrime and some EPrime Basics[edit]
- You should be familiar with the information in this guide.
Drift adjustment in EPrime[edit]
EPrime BIAS Task Data Cleaning and Analysis[edit]
Guide to within- and between-group analyses on FMRI data with scripts[edit]
Scanner Computer[edit]
- It is recommended you be familiar with all of the scanning page.
How to prepare the Signa Operation Program on the scanner computer[edit]
Steps for scanning procedure and different scans[edit]
Moving files from the scanner to server[edit]
AFNI[edit]
Reconstrucing anatomicals using the to3d function[edit]
Guide to nudging[edit]
Guide to warping[edit]
Running a GLM Regression in AFNI[edit]
Neurofeedback IRESP script for use with 3ddeconvolve[edit]
- Needs description/context
How to make canonical VOI masks[edit]
- See: VOI Masks
How to make individual VOI masks[edit]
- See: VOI Masks
How to draw VOI masks[edit]
- See: VOI Masks
Dumping your regression coefficients using 3dmaskave[edit]
Old process script instructions[edit]
Viewing your group contrast data in AFNI[edit]
AFNI Functions[edit]
3dclust[edit]
- 3dclust is an afni function that finds clusters of an experimenter-specified size. 3dclust tests those clusters for statistical strength at a p value specified by the experimenter. Then outputs regions meeting both of these criteria to a .txt file.
- See: Activation Tables
3dmaskave[edit]
- 3dmaskave takes your mask and the dataset, created after preprocessing, and dumps out the data only for the voxels designated by your maskfile. The values for these voxels are then averaged across the VOI.
AlphaSim[edit]
- AlphaSim is used to do a monte carlo simulation to estimate false discovery rates.
- See: Activation Tables
MATLAB[edit]
Plotting tutorial in MATLAB[edit]
Plotting timecourses in MATLAB[edit]
Checking motion in MATLAB[edit]
- It’s necessary to check your subject’s motion to make sure there aren’t any big jumps that could really fudge up your data. Generally, gradual drifts and movements under 2mm are acceptable (be sure to check your units; small jumps can be stretched to look quite large). There is a matlab function called "inspectMotion" that you can use to view all 6 motion directions at once and get an exact measure of the largest jumps in your data. (Note: inspectMotion is not a built in function. See the lab manual scripts page if matlab doesn't recognize this command)
Python[edit]
Organizing your group coefficient data using the makecoeftable.py script[edit]
- See also: Dumping regression coefficients with AFNI and VOI masks
tableDump.py[edit]
- This script is for creating tables in csv format from 3dclust output.
- See Activation Tables
Stata[edit]
Running Stata and Stata Basics[edit]
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