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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monarch
April 20, 2018 09:26AM
Hello,

I am trying to reconstruct functional MRI images using AFNI through the (siemenstoafni) commands. I am still very new to fMRI preprocessing, so I was wondering if these first steps are correct in terms of processing both my anatomical and EPI DICOMS. I want to be able to produce a niftii file for both my original anat DICOMS and my EPI DICOMS so I can conduct a coregistration check later.

siemenstoafni -norot -prefix anat ./anat/DICOM/

3dWarp -oblique2card -prefix anat1 -newgrid 3.5 anat+orig

siemenstoafni -prefix rest -rotobrick anat+orig ./epi/rs/DICOM/

Any help would be very much appreciated. Thanks!
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Subject Author Posted

AFNI fMRI Preprocessing / 3dWarp

monarch April 20, 2018 09:26AM

Re: AFNI fMRI Preprocessing / 3dWarp

Peter Molfese April 20, 2018 09:51AM

Re: AFNI fMRI Preprocessing / 3dWarp

ptaylor April 21, 2018 09:15AM

Re: AFNI fMRI Preprocessing / 3dWarp

monarch April 23, 2018 02:43PM

Re: AFNI fMRI Preprocessing / 3dWarp

Peter Molfese April 24, 2018 04:22PM