AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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December 02, 2003 07:10PM
I can't see anything obviously wrong, but here are a few things you could check:

(1) The option '-exp' in 3dcalc should be '-expr';
(2) Do you only have ONE run of original dataset with 554 TR's? I mean, did you run 3dDeconvolve with option '-concat'?
(3) Make sure those three subbricks [0], [2], and [50] are really the corresponding coefficients.
(4) You may consider adding a step function in the expression so that some noisy voxels outside the brain could be filtered out, which could be exactly the reason why you got those huge numbers of percent signal change (by the way, you could use ANFI to locate some of the voxels with absurdly huge % signal change). Do something like this:

3dcalc \
-a Decon${subject}_18view554Tr30SAN+orig[0] \
-b Decon${subject}_18view554Tr30SAN+orig[2] \
-c Decon${subject}_18view554Tr30SAN+orig[50] \
-d Decon${subject}_18view554Tr30SAN+orig[Number] \ ## put in the number for the whole-F subbrick
-expr "100*c/(a+b*(554/2))*step(d-F_value)" \ ##Use AFNI to find out a threshold F-value so that those significantly inactive voxels would be ignored during the percent signal conversion process
-fscale \
-prefix ${subject}_18view_Prcnt_AvN

(5) Personally I prefer normalizing the original dataset before running 3dDeconvolve. Check out Doug Ward's following message:

[afni.nimh.nih.gov]

Gang
Subject Author Posted

% change

Cendri Hutcherson December 02, 2003 06:33PM

Re: % change

Gang Chen December 02, 2003 07:10PM