Getting Start with
Data Processing
AFNI How-To for GE Datasets. (Edited from Lisa T. Eyler original
How-To).
1. Converting anatomical into 3D brik:
a. cd to the directory where your image files are located in.
b. to3d -prefix [anatbrikname] i*
2. Converting functional images into 3D brik:
a. Change directory to your first run for example
b. These are time dependent datasets, so we have to feed the
to3d command some parameter, here is an example
to3d -prefix XXX -time:zt #slices #timepts TR sliceorder i*
to3d -prefix run1 -time:zt 35 200 3000 alt+z i*
3. Images Registration:
· In the date directory, enter afni -R (this
recursively searches for any AFNI datasets in or below the
current directory)
· Afni widget window, click on Switch Underlay
- Choose the functional file name that you just created (e.g,
0320run1+orig).
- Under axial (plane that images were
collected) click on graph
- A window with voxels of graphs should appear.
· To look for large movements by the patient during the task,
you need to scroll through the graph over time (x-axis on
graph), and watch for large changes in the head position on the
images.
- to do this, use following keys on the keyboard, while your
arrow for the mouse is placed within the graph.
- > moves U forward in time (the red dot on the graph line )
- < moves U back in time
- + increases the amplitude
- - decreases the amplitude of the graph
- if large movement in head, note approx. time it occurred, may
need this later.
· Now, time to register image.
- In the AFNI widget window, click on Define
Datamode, then Plugins, then
3-D Registration, and whichever base image you
choose (we usually pick one in the middle or use a program by
martin Paulus to help choose the most typical base image). Click
on Dataset and choose your functional dataset.
- Output file name run1_reg (remember use same name as
experiment)
- Now, review graph of registered images to see if head motion
has improved.
· Or, one can do the same thing on the command line
- 3dvolreg -base 43 -dfile 0320runbs43.mot -prefix
0320_reg3dbs43 0320+orig
- -base 43 means register to the 43rd image
- the dfile flag outputs the parameters dx, dy, dz, pitch,
roll, yaw into a file (named 0230runbs43.mot) so can use these
as a quantitative index of the amount of movement
- -prefix tells the output prefix
- run1.* is the input to register
4. Reference function creation
· Options for creating reference functions
- Text editor
- (click with Right mouse button on wallpaper, under Programs,
you will find this)
"0" for no stimulus
"1" for stimulus on
· All reference functions must be created with a file name that
has suffix of .1D or .1Dx (for sets of multiple
reference functions) for AFNI to recognize it.
5. Correlating functionals to reference functions
·
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In graph window, click on FIM, then
click on Pick Ideal
· Choose reference function from file that you created
for this image analysis
· Click on Set
· Examine shape of reference function in graph window to
make sure it looks like you expected
· Click on FIM, Compute
FIM+, click on FBUC
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6. Looking at your functional data
· Switch Underlay pick the anatomical brik
(e.g., 0230anat+orig)
· Click Define Overlay, and See Overlay
· Switch threshold (Thr) to #3 correlation;
switch OLay to #0 Fit Coefficient
· Slide correlation slider all the way to 0 and look at pixels
to make sure your functional brick is in a logical position
relative to the anatomy
· Move cursor up & down the multi-colored columns to find a
correlation point with minimal artifact.
7. Shifted reference functions
· In AFNI graph window, click on FIM, then
click on Pick Ideal, and choose your unshifted
reference function
· Then click on FIM, Edit Ideal, Shift
Ideal
- Choose the increment (in TRs ΰ e.g., 0.5 with TR = 3 sec
means 1.5 sec increments)
- Choose the number of steps (usually to the right, and [number
of steps X increment (in seconds)] should be less than length of
one half-cycle)
- Click Set
· Save your set of reference functions using FIM, Edit
Ideal, Write Ideal.
- Give the reference function the .1Dx suffix and include info
about the increment and number of steps (e.g.,
run149_lrn-rpt_s6_1.5s.1Dx)
· Do FIM, Compute FIM+, FBUC
· Look at data as above
· Also, look at which shift was picked for each pixel
- For OLay, pick #1 Best Index; for Thr, pick
#3 Correlation
- Change the Intensity color bar so that the values increment at
(1/# of reference functions). E.g., if you used 7 reference
functions (a 0 shift plus 6 shifts), then you would have the
colors change at 0.14, 0.28, 0.42, etc.
- Change the colors by clicking on them to make neighboring
colors very distinct
- Slide correlation down to 0 and then back up slowly to see
which shifts were associated with the highest correlations
8. Renaming functional datasets
· AFNI outputs the results of each FIM+ as a filename like
run1_reg+orig@1.
· To rename the filename to be more informative:
- Click on Define Datamode, Plugins, Dataset Rename
- Choose input file, and provide new output prefix
9. Saving images to .jpg format
| Step 1 - Make the AFNI window of interest look like you want (e.g., turn off crosshairs, etc). note the button 'Sav1.ppm' is the save button. |
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| Step 2 - right click on the save button, select Save.jpg for jpeg format and click on the 'set' button. |
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| Step 3 - left click on the save button and enter in a filename that you want to name the file. note to save the image in your home directory instead of directory where your dataset is located in, type ~[Home]/[image name].jpg where [Home] is your home directory which is usually your user name. |
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10. For more AFNI program -help
go to the AFNI website
http://afni.nimh.nih.gov/afni/doc
Last after all the subjects are to be analyzed together you may Tailarach the images
Last modified
August 28, 2009
