When I did 11b in the past, I still did SSWarper first, and just then used that (and anat has no skull). Basically I made 11b just like 11, except for anything having to do with the ventricle mask creation type stuff.

All this being said, you are correct that whether it is pythonic or not does not make a difference as I just tried it with basic again and I did not get the correct files in index.html. So this must be a new issue, because data I ran sswarper on even a week or so ago had all the right alignment showing up, but not today for me. I did notice when I ran SSwarper I got a ton of the message "/home/username/anaconda3/conda/bin/complete: is not a directory" like 15ish times in a row near the beginning, before it continued to run. That looked new to me.

Also, is blur something we can apply after the fact (given the removal of the blur block and blur_size). I'm used to hearing that blur is required before analysis (makes sense with voxel analysis). I have also used SPM12 where you smooth with a blur of [7 7 7] typically at the end, and I have also heard that overall blur should be about 1.5x your voxel size (my voxel size might be around 3x3x3 I think... need to double check). So anyways, I now feel a little unclear when smoothing becomes necessary -- but regardless I would think/hope we could just apply a blur post-preprocessing as needed for different analysis (e.g. not ROI based)? In which case [7x7x7] or maybe 1.5*3=[5x5x5] -- I assume the choice of blur to add at the end would also depend on if any other previous steps applied some blur (like SSwarper for instance?).

Here is my afni_proc.py command based on 11 specifically. I have tried to remove the blur block and -blur_size 5, but kept the regress_est_blur_errts and regress_est_blur_epits because I assume that's fine even if it has blur in the name? Anyway, it is almost exactly like example 11, except I had to remove "-radial_correlate_blocks tcat volreg" because it kept erroring out by thinking that -radial_correlate_blocks was a part of the -blocks command, and then blur_size was 5 (because I had larger voxels) and I set regress_censor_motion to 0.25 because our subjects move a lot and even at 0.25 I still lose a lot of data... I know functional can be 0.3, but with resting 0.2 is preferred, but 0.2 just was too much. Hopefully 0.25 is still valid.

   # to not blur (if we want to do ROI analysis later) I removed the blur block in between volreg and mask, as well as -blur* options)
   # so removed -blur_size 5 after volreg_tlrc_warp and -mask_epi_anat yes
   # blurring makes sense for voxel wise analysis
  afni_proc.py                                                 \
    -subj_id ${sid}.${naming}                        	       \
    -blocks despike tshift align tlrc volreg mask scale regress  \
    -copy_anat ${ss_path}/anatSS.${sid}.nii                    	       \
    -anat_has_skull no                                         \
    -anat_follower anat_w_skull anat ${ss_path}/anatU.${sid}.nii	       \
    -anat_follower_ROI aaseg anat ${suma_path}/aparc.a2009s+aseg.nii        \
    -anat_follower_ROI aeseg epi ${suma_path}/aparc.a2009s+aseg.nii         \
    -anat_follower_ROI FSvent epi ${suma_path}/fs_ap_latvent.nii.gz         \
    -anat_follower_ROI FSWe epi ${suma_path}/fs_ap_wm.nii.gz                \
    -anat_follower_erode FSvent FSWe 			       \
    -dsets ${ss_path}/${sid}_rest+orig.HEAD                    	       \
    -tcat_remove_first_trs 0                                   \
    -align_opts_aea -cost lpc+ZZ -ginormous_move -check_flip   \
    -tlrc_base ${template}                                     \
    -tlrc_NL_warp                                              \
    -tlrc_NL_warped_dsets ${ss_path}/anatQQ.${sid}.nii ${ss_path}/anatQQ.${sid}.aff12.1D ${ss_path}/anatQQ.${sid}_WARP.nii  \
    -volreg_align_to MIN_OUTLIER                               \
    -volreg_align_e2a                                          \
    -volreg_tlrc_warp                                          \
    -mask_epi_anat yes                                         \
    -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_censor_motion 0.25                                \
    -regress_censor_outliers 0.05                              \
    -regress_apply_mot_types demean deriv                      \
    -regress_est_blur_epits                                    \
    -regress_est_blur_errts                                    \
    -html_review_style pythonic

Related question -- to get the appropriate Freesurfer files, I run recon-all, which takes nearly 4-5 hours per subject. Is there another way to get the necessary freesurfer files per subject, without having to run all of it and wait for that long that you know of by chance?

I emailed you the files you requested. Please let me know if you do not get them. Thanks!



Edited 3 time(s). Last edit at 08/26/2021 06:46PM by kxd344.