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
May 22, 2005 02:33PM
3drefit only affects the .HEAD file -- you are just telling AFNI what way the data is oriented as it is stored in the .BRIK file. If some of your datasets are actually stored in RAI orientation, say, and some in LAI, then you cannot flip the RAI ones to LAI just by using 3drefit -orient.

3dDeconvolve (or 3dTcat) simply catenates the datasets in time, VOXEL BY VOXEL. The output will have the same physical orientation, grid spacing, et cetera, as the first input. If in fact some of your input datasets are not stored in the same orientation, you will not get correct results from the program -- it does not attempt to flip input datasets to match one another.

If you want to physically flip a dataset to a different orientation, the 3dresample program can be used.
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Subject Author Posted

Head orientation in 3DDeconvolve

Spiegelhalder, Kai May 22, 2005 11:32AM

Re: Head orientation in 3DDeconvolve

Bob Cox May 22, 2005 02:33PM

Re: Head orientation in 3DDeconvolve

Spiegelhalder, Kai May 23, 2005 04:46AM