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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Pawel
June 14, 2021 06:34PM
Hello,

I have a simple monkey/animal_warper/afni_proc.py question. I am modifying the MACAQUE_DEMO_REST pipeline.
If I want to use eroded WM signal as a nuisance regressor in afni_proc (whether via anaticor or as averaged WM), and I have WM mask from the NMT template, I should import the mask in NMT space into afni_proc, correct?

So this: 

afni_proc.py                                                              \
[...]
        -mask_import             WM_mask ${additional_path}/WMe_mask+tlrc     \
[...]
        -regress_ROI             WM_mask                                      \

or this 

afni_proc.py                                                              \
[...]
        -mask_import             WM_mask ${additional_path}/WMe_mask+tlrc     \
[...]
        -regress_anaticor_fast                                                \
        -regress_anaticor_radius  20                                          \
        -regress_anaticor_label   WM_mask                                      \

instead of 
afni_proc.py                                                              \
[...]
        -anat_follower_ROI       WMmask epi ${odir_aw}'/'WM_anat_mask+orig    \
        -anat_follower_erode     WMmask                                       \
[...]                       
        -regress_anaticor_fast                                                \
        -regress_anaticor_radius  20                                          \
        -regress_anaticor_label   WMmask                                      \

because the latter would involve warping the WM mask from the NMT to individual space in animal warper and then warping it back to NMT space in afni_proc, right?
Reply Quote
RSS
Subject Author Posted

regressing out WM in afni_proc.py

Pawel June 14, 2021 06:34PM

Re: regressing out WM in afni_proc.py

rick reynolds July 15, 2021 10:47AM

Re: regressing out WM in afni_proc.py

Pawel July 15, 2021 10:52AM