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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April 07, 2023 07:35AM
3dQwarp (the engine inside our nonlinear warping scripts) also has two options that let you give extra weight to registration in a particular small region. From the -help output of 3dQwarp:
-wball x y z r f =
                Enhance automatic weight from '-useweight' by a factor
                of 1+f*Gaussian(FWHM=r) centered in the base image at
                DICOM coordinates (x,y,z) and with radius 'r'. The
                goal of this option is to try and make the alignment
                better in a specific part of the brain.
               * Example:  -wball 0 14 6 30 40
                 to emphasize the thalamic area (in MNI/Talairach space).
               * The 'r' parameter must be positive (in mm)!
               * The 'f' parameter must be between 1 and 100 (inclusive).
               * '-wball' does nothing if you input your own weight
                 with the '-weight' option :(
               * '-wball' does change the binary weight created by
                 the '-noweight' option.
               * You can only use '-wball' once in a run of 3dQwarp.
             *** The effect of '-wball' is not dramatic. The example
                 above makes the average brain image across a collection
                 of subjects a little sharper in the thalamic area, which
                 might have some small value. If you care enough about
                 alignment to use '-wball', then you should examine the
                 results from 3dQwarp for each subject, to see if the
                 alignments are good enough for your purposes.

 -wmask ws f  = Similar to '-wball', but here, you provide a dataset 'ws'
                that indicates where to increase the weight.
               * The 'ws' dataset must be on the same 3D grid as the base
                  dataset.
               * 'ws' is treated as a mask -- it only matters where it
                 is nonzero -- otherwise, the values inside are not used.
               * After 'ws' comes the factor 'f' by which to increase the
                 automatically computed weight. Where 'ws' is nonzero,
                 the weighting will be multiplied by (1+f).
               * As with '-wball', the factor 'f' should be between 1 and 100.
               * You cannot use '-wball' and '-wmask' together!

If the region defined by -wball or -wmask is small (the usual case), the factor 'f' should be large-ish -- 40 or more -- otherwise the effect will not be noticeable. In my experiments with the human thalamus, the effects were small in any case, but visible.
Subject Author Posted

Macaque warping refinement Attachments

El_suri March 20, 2023 08:15AM

Re: Macaque warping refinement

Daniel Glen March 22, 2023 07:01PM

Re: Macaque warping refinement

RWCox April 07, 2023 07:35AM