Dear AFNI experts and developers,
Hopefully I’m just missing something basic, but this one has me stumped.
I’m trying to use afni_proc.py to pre-process some resting state fMRI data. For a couple of the subjects, alignment of the structural to the functional was giving me trouble until I used the “-edge” option. That fixed the alignment in separate testing using align_epi_anat.py. However, when I simply replace the “-cost lpc+” argument that I was using before with “-edge” in the relevant part of afni_proc.py, it throws this error:
cat_matvec -ONELINE anatQQ.28864.aff12.1D anatSS.28864_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
** ERROR: mri_read_ascii: couldn’t open file anatSS.28864_al_junk_mat.aff12.1D
** FATAL ERROR: Can’t read file ‘anatSS.28864_al_junk_mat.aff12.1D’
** Program compile date = May 11 2021
Here’s the afni_proc.py command that produces that error:
afni_proc.py
-subj_id $subj
-dsets rest+orig
-blocks despike tshift align tlrc volreg blur mask scale regress
-copy_anat ./anat_warped/anatSS.$subj.nii
-anat_has_skull no
-anat_follower anat_w_skull anat ./$subj/SUMA/${subj}_SurfVol.nii
-anat_follower_ROI aaseg anat ./$subj/SUMA/aparc.a2009s+aseg.nii.gz
-anat_follower_ROI aeseg epi ./$subj/SUMA/aparc.a2009s+aseg.nii.gz
-anat_follower_ROI FSvent epi ./$subj/SUMA/fs_ap_latvent.nii.gz
-anat_follower_ROI FSWe epi ./$subj/SUMA/fs_ap_wm.nii.gz
-anat_follower_erode FSvent FSWe
-tcat_remove_first_trs 2
-align_opts_aea -epi_strip 3dSkullStrip -edge -check_flip
-tlrc_base /usr/lib/afni/bin/MNI152_2009_template_SSW.nii.gz
-tlrc_NL_warp
-tlrc_NL_warped_dsets ./anat_warped/anatQQ.$subj.nii ./anat_warped/anatQQ.$subj.aff12.1D ./anat_warped/anatQQ.${subj}_WARP.nii
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-mask_epi_anat yes
-regress_censor_motion 0.3
-regress_censor_outliers 0.1
-regress_apply_mot_types demean deriv
-regress_est_blur_epits
-regress_est_blur_errts
-scr_overwrite
-html_review_style pythonic
-execute
Again, all I have to do is replace “-edge” with “-cost lpc+” to make the error go away. But then the alignment isn’t as good! I’d appreciate any help you can give.
Best,
Will