Table 1.
Current processing blocks in afni_proc.py, with brief descriptions.
| Automatic blocks setup and initialization; not user specified, always used | |
| setup: | check args, set run list, make output directory, copy stim files |
| tcat: | copy input datasets and remove unwanted initial TRs |
| Default blocks standard steps; user may skip, modify or rearrange | |
| tshift: | slice timing alignment on volumes |
| volreg: | volume registration (for reduction of subject motion effects) |
| blur: | blur each volume (default is 4 mm FWHM) |
| mask: | create a “brain” mask from the EPI data |
| scale: | scale each run mean to 100, for each voxel (max of 200)a |
| regress: | regression analysis (stimulus model, filter, censor, etc.) |
| Optional blocks default is to not apply these blocks, but the user can add | |
| align: | align EPI and anatomy (linear affine) |
| combine: | combine echoes into one |
| despike: | truncate spikes in each voxel’s time series |
| empty: | placeholder for some other user command |
| ricor: | RETROICORb - removal of cardiac/respiratory regressors |
| surf: | project volumetric data into the surface domain (via SUMAc) |
| tlrc: | warp anatomical volume to a standard space or template |
| Implicit blocks not user-specified, but performed when appropriate | |
| blip: | perform B0 distortion correction |
| outcount: | temporal outlier detection |
| QC_review: | generate QC review scripts and HTML report (APQC HTML) |
| anat_unif: | anatomical uniformity correction |
The automatic and implicit blocks are not specified by the user in the “-blocks” option list; the former will always be performed, and the user can still manage their behavior with options, such as “-tcat_remove_first_trs” and more. The implicit blocks will be automatically added in an appropriate spot within the processing stream when the user adds a relevant option, such as “-blip_forward_dset” for the blip block. The users can see where and how these blocks are performed in detail within the created processing script.