Hi, Matthew-
Thanks for posting the AP command. I have a few comments on the options there.
I think you might have a small bug in the file paths. Most paths in your command contain something like:
/home/hoptman/neurodesktop-storage/TSIB
... but your blip-forward dataset has:
/home/hoptman/neurodesktop/storage/TSIB
Note the "-" after neurodesktop in the first case, and a "/" after it in the second.
Note you also seem to include -blip_forward_dset .. and -blip_reverse_dset .. twice. One of those has the buggy path.
You also have -blur_in_mask yes twice, as well as -regress_3dD_stop twice.
It also appears like the same FMRI dataset is input 4 times after -dsets_me_run:
/home/hoptman/neurodesktop-storage/TSIB/MultiEcho/TSIB/derivatives/sub-xxxx/ses-MRI1/func/sub-xxxx_ses-MRI1_task-rest_echo-1_part-mag_nordicNoNoise_bold_deob.nii.gz
I assume the number after "echo-" should change each time?
Also, we typically recommend running sswarper2 prior to afni_proc.py, for both nonlinear alignment and anatomical skullstripping. Then the results are passed to afni_proc.py. This saves time during any re-runs, and the skullstripping tends to be better than what 3dSkullStrip alone will do (which is what AP will use), as well as better anatomical-to-template alignment. Your command could be adjusted to do that.
Because the command is so large and file paths are long, I did run it through a script to vertically align opts, and then also tried to pull out common file path pieces to make it easier to scan. This is the result, with reductions of duplicate options listed above and a guess at some file path correction, as noted above (I guessed at replacing the echo-? number, too in the ME-FMRI dset inputs). I also bunched options by processing block---it isn't necessary, but it was a bit easier for me to read. Please check this for correctness.
#!/bin/tcsh
set subj = sub-xxxx
set p1 = /home/hoptman/neurodesktop-storage/TSIB
set p2 = ${p1}/MultiEcho/TSIB/derivatives
set p3 = ${p2}/${subj}/ses-MRI1
set p4 = ${p2}/fmriprep_out/sourcedata/freesurfer
afni_proc.py \
-subj_id ${subj}_ses-MRI1 \
-blocks despike ricor align tlrc volreg mask combine \
blur scale regress \
-radial_correlate_blocks tcat volreg \
-blip_forward_dset "${p1}/subjects/${subj}/AP_prescan_rest_009/TSIB_xxxx_AP_prescan_rest_9_ph_deob.nii.gz[0]" \
-blip_reverse_dset "${p1}/subjects/${subj}/PA_prescan_rest_012/TSIB_xxxx_PA_prescan_rest_12_ph_deob.nii.gz[0]" \
-copy_anat ${p3}/anat/${subj}_ses-MRI1_acq-MEMPRAGEnoRemeas4ep21mmisoRMS_T1w.nii.gz \
-anat_has_skull yes \
-dsets_me_run ${p3}/func/${subj}_ses-MRI1_task-rest_echo-1_part-mag_nordicNoNoise_bold_deob.nii.gz \
${p3}/func/${subj}_ses-MRI1_task-rest_echo-2_part-mag_nordicNoNoise_bold_deob.nii.gz \
${p3}/func/${subj}_ses-MRI1_task-rest_echo-3_part-mag_nordicNoNoise_bold_deob.nii.gz \
${p3}/func/${subj}_ses-MRI1_task-rest_echo-4_part-mag_nordicNoNoise_bold_deob.nii.gz \
-echo_times 12.8 32.87 52.94 73.01 \
-reg_echo 2 \
-anat_follower_ROI FSvent epi \
${p4}/${subj}/SUMA/fs_ap_latvent.nii.gz \
-anat_follower_ROI FSWe epi \
${p4}/${subj}/SUMA/fs_ap_wm.nii.gz \
-anat_follower_ROI aaseg anat \
${p4}/${subj}/SUMA/aparc+aseg_REN_all.nii.gz \
-anat_follower_ROI aseg epi \
${p4}/${subj}/SUMA/aparc+aseg_REN_all.nii.gz \
-anat_follower_erode FSvent FSWe \
-align_unifize_epi local \
-align_opts_aea -cost lpc+ZZ \
-giant_move \
-check_flip \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_compute_tsnr yes \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-ricor_regs ${p3}/func/physio_calc2/physio_slibase.1D \
-combine_method OC \
-combine_opts_tedana --tedpca aic \
-mask_epi_anat yes \
-blur_size 4 \
-blur_in_mask yes \
-regress_3dD_stop \
-regress_reml_exec \
-regress_compute_fitts \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_anaticor_fast \
-regress_opts_3dD -jobs 8 \
-regress_motion_per_run \
-regress_censor_outliers 0.05 \
-regress_apply_mot_types demean deriv \
-regress_anaticor_label FSWe \
-regress_ROI_PC FSvent 3 \
-regress_ROI_PC_per_run FSvent \
-regress_run_clustsim no \
-html_review_style pythonic \
-script ./17.${subj}_ses-MRI1_rest
--pt