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

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bob cox
November 04, 2003 01:49PM
Yes, since the registration is done by intensity matching. The program does include an attempt to match intensity scales as well as positions, but it probably won't deal well with intensity mismatches of over a factor of 2 or so. You have a factor of about 10, which is the cause of the problem. Basically, I've never seen this problem before, so didn't allow for this possibility.

I could put a fix in for this, but until that is done, the only real fix is for you to manually scale the inputs to match (roughly). One way to do that would be to create a separate template for matching. For example, if you want to use sub-brick #3 from run 1 as the template, but it needs to be scaled up by a factor of 10, then
3dcalc -a 'run1+orig[3]' -expr '10*a' -prefix run1_Xtemplate
will produce a 1 sub-brick dataset that you could use as the base dataset for 3dvolreg.

bob cox
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Subject Author Posted

does intensity affect 3dvolreg?

David Soltysik November 04, 2003 12:16PM

Re: does intensity affect 3dvolreg?

bob cox November 04, 2003 01:49PM