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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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Hi pt,
Here are my answers to your questions:
0) are these 3D volumes, or 2D slices? - 2D slices
1) what are the voxel dimensions of the data? - anisotropic 1x1x3 mm voxels (1x1 in the axial plane)
2) how much distortion/difference is there from time point to time point? - it depends on the task, but the cord can regularly move 0-3 mm (mostly in the ventral-dorsal direction)
3) how you
by
Kim
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AFNI Message Board
Thank you both -
My goal is to do spinal cord fMRI motion correction. Specifically, it is a slicewise alignment of each timepoint to a base, so it is a like to like alignment as you mentioned, Daniel. The alignment is limited to just XY translations.
This is an example of the command I am trying to translate:
3dWarpDrive -affine_general \
-parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6
by
Kim
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AFNI Message Board
Hello,
I would like to know if there are input options (such as the cost function, etc.) that can be set in the function 3dAllineate to have it behave as 3dWarpDrive does. I can set all of the inputs used in 3dWarpDrive in 3dAllineate, but because of the added options and functionality of the newer function, the result was not as desired. There are likely some defaults of 3dWarpDrive that I am
by
Kim
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AFNI Message Board
Hi! Thanks for the reply. The reason I would to smooth anisotropically is because we are analyzing functional spinal cord data (with anisotropic voxels too), which others have shown to have improved sensitivity of task activation when using anisotropic kernels to increase smoothing along the longitudinal axis of the cord.
As far as I can tell, none of those others have used an anisotropic met
by
Kim
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AFNI Message Board
Thanks! That function sounds like what I want, but I'm not sure how to make it work or if it does what I am intending.
Specifically what I'm looking for is what you mentioned first - to do anisotropic smoothing. For example, I would like to define my own smoothing kernel such as a Gaussian FWHM 2x2x6mm^3. So I'd like my smoothing along the z-axis to be greater.
by
Kim
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AFNI Message Board
Hello,
I have been using the 3dBlurInMask function to smooth my fMRI data with a mask of the spinal cord. There is currently only the option to enter a FWHM to define an isotropic kernel. I would like to be able to use an anisotropic kernel with a mask, but there is currently no option in this function. (Nor can I do it in 3dBlurToFWHM, which I gather can perform the same/similar function to
by
Kim
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AFNI Message Board