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
|
MayaSa
March 19, 2023 07:59AM
Hi,
I am trying to perform proc.py command on output data from tedana (ts_OC.nii file).
I want to do only some blocks - mask scale regress.
The problem is that the input is already in +tlrc and the files from FreeSurfer are in +orig.
How can I overcome this issue?

Thank you!
Maya

Attached here my proc.py script: 

3dcopy $resultsPath/tedana_r01/ts_OC.nii.gz $path/$subject.$session.$scan.OC

afni_proc.py                                                                   \
   -subj_id $subject.$session.$scan.OC                                        \
   -blocks mask scale regress            \
   -copy_anat anatSS.$subject.$session.$scan.ME.nii                            \
   -anat_has_skull no                                                          \
   -anat_follower anat_w_skull anat anatU.$subject.$session.$scan.ME.nii       \
   -anat_follower_ROI aaseg anat $path/Freesurfer/$subject/SUMA/aparc.a2009s+aseg.nii.gz    		\
   -anat_follower_ROI aeseg epi $path/Freesurfer/$subject/SUMA/aparc.a2009s+aseg.nii.gz          \
   -anat_follower_ROI FSvent epi $path/Freesurfer/$subject/SUMA/fs_ap_latvent.nii.gz             \
   -anat_follower_ROI FSWe epi $path/Freesurfer/$subject/SUMA/fs_ap_wm.nii.gz                    \
   -anat_follower_erode FSvent FSWe                                            \
   -dsets $subject.$session.$scan.OC+tlrc.HEAD                                 \
   -mask_epi_anat yes                                                          \
   -mask_apply anat \
   -regress_motion_per_run                                                     \
   -regress_ROI_PC FSvent 3                                                    \
   -regress_ROI_PC_per_run FSvent                                              \
   -regress_make_corr_vols aeseg FSvent                                        \
   -regress_anaticor_fast                                                      \
   -regress_anaticor_label FSWe                                                \
   -regress_apply_mot_types demean deriv                                       \
   -regress_est_blur_epits                                                     \
   -regress_est_blur_errts                                                     \
   -html_review_style pythonic
Reply Quote
RSS
Subject Author Posted

proc.py on tlrc data

MayaSa March 19, 2023 07:59AM

Re: proc.py on tlrc data

ptaylor March 19, 2023 11:42AM

Re: proc.py on tlrc data

rick reynolds March 20, 2023 03:44PM