proc.py on tlrc data

AFNI Message Board
1

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
2

Hi-

Is that data already in Talairach or MNI space, or is the +tlrc there just because of some qform_code/sform_code value from whatever program did the OC?

Also, I’m curious if is there a particular reason you don’t want to input the ME-FMRI data into afni_proc.py, and do the OC within it?

–pt

3

Indeed, afni_proc.py can be used with “-combine_method m_tedana” to run the MEICA group’s tedana as part of the step to combine echoes. See
APMULTI_Demo1_rest/scripts_desktop/do_26_ap_me_bT.tcsh for an afni_proc.py command script, including use of that combine method.

In any case, tedana creates the NIFTI datasets generally using nibabel, which writes an sform_code of 2, which has an ambiguous space (orig vs standard). AFNI can be told to interpret that as being in orig space by setting AFNI_NIFTI_VIEW to “orig” (in the command, the shell environment or the ~/.afnirc file). If you continue to run afni_proc.py only after tedana, it would be reasonable to set it at the top of that command script (or in your .afnirc).

  • rick