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
September 28, 2021 12:34PM
A few ways to do this:

1. Align your anatomical to the EPI dataset first, then redo Freesurfer processing using that anatomical dataset. Then repeat @SUMA_Make_Spec_FS, etc.

2. Align EPI data to anatomical dataset as part of your processing with afni_proc.py. If you're doing motion correction anyway, interpolation effects should be minimal.

3. Align your anatomical to the EPI dataset using align_epi_anat.py. Then use that volume as the -sv volume option to align to experiment.

4. Align your anatomical data to the EPI dataset using align_epi_anat.py. Transform the ROI data using the transformation computed with "3dAllineate -NN -1Dmatrix_apply" (using the transformation 1D file output from align_epi_anat.py).
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Align mask with EPI image Attachments

Alireza September 27, 2021 06:33PM

Re: Align mask with EPI image

Daniel Glen September 28, 2021 12:34PM

Re: Align mask with EPI image

Alireza October 03, 2021 05:55PM

Re: Align mask with EPI image

Daniel Glen October 04, 2021 12:47AM

Re: Align mask with EPI image Attachments

Alireza October 05, 2021 05:39PM

Re: Align mask with EPI image

Daniel Glen October 07, 2021 01:04PM

Re: Align mask with EPI image

Alireza November 02, 2021 06:11PM