I think I'm having a normalization problem. I have 2 group with 3 experiments
in each (wnw, stut, oral). 1 group has 3 subjects and the other has 2 (we've
just started our experiments). In the jpegs(0.99 threshold) that I've attached,
it shows that the normalization is off in the z axis (not stretched enough) and
shifted to the left axially, and overstretched into the eyeballs! Since each
experiment and group shows the same skew, it must be in my normalization
procedure?
Here is my procedure (taken from my manual that I'm building)
slice timing
Reorient anatomic and functional
· use display to bring up a.img
· set pitch and roll to 1.57
· find Anterior Commisure
· record AC numbers in mm. Eg (0.0 –8.8 –1.2)
· enter into Right, forward & up, REVERSE numbers (0.0 8.8 1.2)
· put 0 0 0 in mm box.
· Check and make sure that crosshairs are on AC
· Reorient image a.img
· Use display to bring up functional
· Use unix program to get numbers (this usually shifts x-axis by about
0.7 of a mm).
· enter into Right, forward & up the numbers the program gives (0.7 8.8
1.2)
· put 0 0 0 in mm box.
· Check and make sure that crosshairs are on AC
· Reorient image af*.img
Use check reg to make sure transformations are correct
Coregister (this moves the anatomic into the space of the functional)
· Need to register anatomic (a.img) to functionals (af*.img)
· Select coregister button
· Number of subjects=1
· Option coregister only
· Modality of first target image=T1 MRI
· Modality of first object image=T1 MRI
· Select target image ****use 1st image of the run that was performed the
closest in time to the anatomic
· Select Object image, a.img for that subject
· Select other images for subject 1 just press: DONE
Realign
· number of subjects 1
· number of sessions 3
· select af*.img for all 3 experiments make sure to select the first run
closest to a.img as the first run (all others in order of expt).
· method- coregister ONLY
use checkreg again to check all af*.img and a.img for correct location
go to defaults and change normalization, parameter estimation to R is R
Normalize- Anatomic
· press normalize button
· determine + write normalize
· 1 subject, select a.img
· select again a.img
· use T1 as template
· SINC interpolation
· Use display to look at na.img to make sure crosshairs still on AC
Normalize- functionals
· press normalize button and select write normalize only
· select all af*.img files for ONE experiment for same subject
· SINC interpolation
· Do each run for that subject separately
Does anyone have any ideas as to why my overall brain activation doesn't look
right? Are there certain default parameters I should be changing?
voxel size, reiterations etc...
thanks sophie
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