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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Daniel Glen
October 28, 2009 04:47PM
If you want the dimensions and grid of the aligned EPI to match the anatomical reference, use -master_epi BASE. If you want a different voxel size, then you can also use -master_epi_dxyz 'nn' to set the voxel cubic dimension to a particular size. Note EPI output at what is usually the fine grid of the anatomical data will result in a very large dataset, as you have seen, and is usually not very useful.

You do not need to apply the matrix on your own, though you can if you want to. The aligned dataset is one of the outputs of the script. If you are doing the epi2anat alignment, it will share the same name as the original but have the suffix appended.

For visualization of the alignment, you can use the -AddEdge option for align_epi_anat.py and the AFNI GUI.
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Subject Author Posted

Align BOLD to T1

Leo Ai October 28, 2009 01:02PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 01:10PM

Re: Align BOLD to T1

Leo Ai October 28, 2009 01:56PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 02:57PM

Re: Align BOLD to T1

Leo Ai October 28, 2009 03:56PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 04:47PM