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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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Dear AFNI experts,
I have two related questions:
(1) Does 3dFWHMx work on a single volume?
(2) Does 3dFWHMx work well on PET images?
Based on my reading of the help menu, I am using this command to estimate the smoothness on amyloid PET images:
3dFWHMx -2difMAD -mask brain_mask+tlrc subject_718b_suvr+tlrc
Thank you.
David
by
DavidZhu
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AFNI Message Board
Dear Rick and Daniel,
Thanks for clarification and suggestion.
The linear interpolation option works better for my case. I want to simulate 2D from the 3D images.
Based on my data, when the slice of 2D is right at the 3D slice location, the voxel values are very close to each other, but not exactly the same. It seems some interpolation still happens.
"The contribution of the nei
by
DavidZhu
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AFNI Message Board
Dear AFNI experts:
I used 3dresample to downsize the slice resolution from 321 slices to 53 slices via -dxyz, specifying 6 x slice thickness. I use "-rmode Linear". Specifically,
3dresample -dxyz 1.042 1.042 3.36 -rmode Linear -prefix ....
I checked the source codes but I was not sure the exact equation.
Is it a simple linear fit over 6 slices with a straight line?
Could
by
DavidZhu
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AFNI Message Board
Hi Bob,
Thank you for your discussion and the Brain Connectivity paper from your team. I think your paper puts fMRI clustering analysis in a well balanced perspective.
Thanks for maintaining AFNI and continuing to improve it.
David
by
DavidZhu
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AFNI Message Board
Dear AFNI experts,
When combing DICOM image files to a single AFNI/NIFTI file in fMRI time series, does the "Dimon" command automatically detect the slice timing order based on the DICOM header file?
My understand is that "Dimon" relies on the "-sp SLICE_PATTERN" for the information, either through the default "alt+z" or input.
Could someone clari
by
DavidZhu
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AFNI Message Board
Hi Rick,
Thank you for pointing this out.
I can see the effect of "-2difMAD" now.
For a related question: My understanding of "3dFWHMx" is that it estimates the smoothness of each sub-brick first, and then it generates the means of all sub-bricks as the output. In calculating the smoothness of a sub-brick, are other sub-bricks used in the calculation?
Thank you.
by
DavidZhu
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AFNI Message Board
Dear AFNI expert:
I want to estimate the smoothness of a single volume (with structure).
3dFWHMx seems to get me a reasonable result. According to the 3dFWHMx help manual, I tried with and without the "-2difMAD' option as below. The results are the same. Could you please suggest me the appropriate steps?
Thank you.
David
3dFWHMx -mask automask_DTIwhole_T2+tlrc fdt_paths_F
by
DavidZhu
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AFNI Message Board