Update README

README.md

@@ -251,7 +251,9 @@ The docker execution has very similar syntax to the singularity execution, excep
 ```
 usage: rabies preprocess [-h] [-e] [--bias_cor_method {otsu_reg,thresh_reg}]
                          [--disable_anat_preproc] [--apply_despiking]
-                         [--apply_slice_mc] [--detect_dummy]
+                         [--HMC_option {intraSubjectBOLD,0,1,2,3}]
+                         [--HMC_transform {Rigid,Affine}] [--apply_slice_mc]
+                         [--detect_dummy]
                          [--data_type {int16,int32,float32,float64}] [--debug]
                          [--coreg_script COREG_SCRIPT]
                          [--anat_reg_script ANAT_REG_SCRIPT]
@@ -299,6 +301,14 @@ optional arguments:
   --apply_despiking     Whether to apply despiking of the EPI timeseries based
                         on AFNI's 3dDespike https://afni.nimh.nih.gov/pub/dist
                         /doc/program_help/3dDespike.html. (default: False)
+  --HMC_option {intraSubjectBOLD,0,1,2,3}
+                        Select an option for head motion realignment among the
+                        pre-built options from https://github.com/ANTsX/ANTsR/
+                        blob/60eefd96fedd16bceb4703ecd2cd5730e6843807/R/ants_m
+                        otion_estimation.R. (default: intraSubjectBOLD)
+  --HMC_transform {Rigid,Affine}
+                        Select between Rigid and Affine registration for head
+                        motion realignment. (default: Rigid)
   --apply_slice_mc      Whether to apply a slice-specific motion correction
                         after initial volumetric rigid correction. This second
                         motion correction can correct for interslice
@@ -383,29 +393,29 @@ Specify Slice Timing Correction info that is fed to AFNI 3dTshift
 Provided commonspace atlas files.:
   --anat_template ANAT_TEMPLATE
                         Anatomical file for the commonspace template.
-                        (default: /home/gabriel/RABIES-0.2.1/rabies/../tem
-                        plate_files/DSURQE_40micron_average.nii.gz)
+                        (default: /home/gabriel/RABIES-0.2.1/rabies/../templat
+                        e_files/DSURQE_40micron_average.nii.gz)
   --brain_mask BRAIN_MASK
                         Brain mask for the template. (default: /home/gabriel/R
-                        ABIES-0.2.1/rabies/../template_files/DSURQE_100mic
-                        ron_mask.nii.gz)
+                        ABIES-0.2.1/rabies/../template_files/DSURQE_100micron_
+                        mask.nii.gz)
   --WM_mask WM_MASK     White matter mask for the template. (default: /home/ga
-                        briel/RABIES-0.2.1/rabies/../template_files/DSURQE
-                        _100micron_eroded_WM_mask.nii.gz)
+                        briel/RABIES-0.2.1/rabies/../template_files/DSURQE_100
+                        micron_eroded_WM_mask.nii.gz)
   --CSF_mask CSF_MASK   CSF mask for the template. (default: /home/gabriel/RAB
-                        IES-0.2.1/rabies/../template_files/DSURQE_100micro
-                        n_eroded_CSF_mask.nii.gz)
+                        IES-0.2.1/rabies/../template_files/DSURQE_100micron_er
+                        oded_CSF_mask.nii.gz)
   --vascular_mask VASCULAR_MASK
                         Can provide a mask of major blood vessels for
                         computing confound timeseries. The default mask was
                         generated by applying MELODIC ICA and selecting the
                         resulting component mapping onto major veins.
                         (Grandjean et al. 2020, NeuroImage; Beckmann et al.
-                        2005) (default: /home/gabriel/RABIES-0.2.1/rabies/
-                        ../template_files/vascular_mask.nii.gz)
+                        2005) (default: /home/gabriel/RABIES-0.2.1/rabies/../t
+                        emplate_files/vascular_mask.nii.gz)
   --labels LABELS       Atlas file with anatomical labels. (default: /home/gab
-                        riel/RABIES-0.2.1/rabies/../template_files/DSURQE_
-                        40micron_labels.nii.gz)
+                        riel/RABIES-0.2.1/rabies/../template_files/DSURQE_40mi
+                        cron_labels.nii.gz)
 ```
 
 ## Outputs