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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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Peter Molfese
February 20, 2014 06:36AM
I hit post and then saw that Daniel beat me to it!

3dresample will not warp your data to TT_N27 space, for that you will need to use another @auto_tlrc step. Assuming that your resting state data is already aligned with your anatomical data in subject space, you could do the following: 

#warp anatomical to TT_N27 space
@auto_tlrc -base TT_N27+tlrc -input AnaT.nii.gz
#apply that warp to your resting state data
@auto_tlrc -apar AnaT_at.nii -input rest.nii.gz -dxyz 2
#apply the warp again to your seed region
@auto_tlrc -apar AnaT_at.nii -input pcc.nii.gz -dxyz 2 -rmode NN


If you haven't yet aligned your resting state to the anatomical, I would suggest using align_epi_anat.py 

#convert everything to AFNI dataset
3dcopy AnaT.nii.gz anat
3dcopy rest.nii.gz rest
3dcopy pcc.nii.gz pcc

#get warp to TT_N27
@auto_tlrc -base TT_N27+tlrc -input anat+orig

#Align resting state to anatomic and then warp to TT_N27 space
align_epi_anat.py -anat anat+orig -epi rest+orig     \
-epi_base 0 -epi2anat -suffix _alTT  \
-tlrc_apar anat+tlrc

#warp seed region as before
@auto_tlrc -apar AnaT_at.nii -input pcc.nii.gz -dxyz 2 -rmode NN

These steps can be accomplished using afni_proc.py if you feel like preprocessing your data in AFNI.



Edited 1 time(s). Last edit at 02/20/2014 06:39AM by Peter Molfese.
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Subject Author Posted

Talairach transformation

Arvind February 20, 2014 02:08AM

Re: Talairach transformation

Daniel Glen February 20, 2014 06:31AM

Re: Talairach transformation

Peter Molfese February 20, 2014 06:36AM