initial pass at cross bold documentation

docs/global.rst

@@ -1,26 +1,69 @@
+.. |br| raw:: html
+
+    </br>
+
 .. csh script params file data dictionary
-.. |params_header| replace:: **Required variables** (:ref:`params`)
+.. |params_header| replace:: :ref:`params` variables
+
+.. |day1_path_vals| replace:: <str>
+.. |day1_path_desc| replace:: path to day1 atlas directory (if patid is not patient's first session)
+
+.. |day1_patid_vals| replace:: <str>
+.. |day1_patid_desc| replace:: patient directory for first session (if patid is not patient's first session)
 
 .. |fcbolds_vals| replace:: <array>
 .. |fcbolds_desc| replace:: list of bold run folders
 
+.. |FMbases_vals| replace:: <img>
+.. |FMbases_desc| replace:: ??
+
+.. |FMmag_vals| replace:: <img>
+.. |FMmag_desc| replace:: field map magnitude image
+
+.. |FMmean_vals| replace:: <img>
+.. |FMmean_desc| replace:: mean field map image
+
+.. |FMphase_vals| replace:: <img>
+.. |FMphase_desc| replace:: field map phase image
+
+.. |fstd_vals| replace:: <int array>
+.. |fstd_desc| replace:: list of scan numbers that map to run folders
+
+.. |gre_vals| replace:: <array>
+.. |gre_desc| replace:: gradient echo measured field map scan numbers (magnitude image should be first, followed by phase image)
+
+.. |irun_vals| replace:: <str array>
+.. |irun_desc| replace:: list of run folders
+
+.. |mprs_vals| replace:: <int array>
+.. |mprs_desc| replace:: list of mprage scan numbers
+
 .. |patid_vals| replace:: <str>
 .. |patid_desc| replace:: participant folder
 
+.. |pdt2_vals| replace:: <array>
+.. |pdt2_desc| replace:: list containing one study number for ptd
+
+.. |sefm_vals| replace:: <array>
+.. |sefm_desc| replace:: spin echo measured field maps
+
 .. |srcdir_vals| replace:: <str>
 .. |srcdir_desc| replace:: source directory path (contains run directories)
 
 .. |workdir_vals| replace:: <str>
 .. |workdir_desc| replace:: working directory path
 
 .. csh script instruction file data dictionary
-.. |inst_header| replace:: **Optional variables** (:ref:`instructions`)
+.. |inst_header| replace:: :ref:`instructions` variables
 
 .. |anat_aveb_vals| replace:: <flt>
 .. |anat_aveb_desc| replace:: run_dvar_4dfp preblur in mm
 
 .. |anat_avet_vals| replace:: <flt>
-.. |anat_avet_desc| replace:: run_dvar_4dfp_criterion
+.. |anat_avet_desc| replace:: run_dvar_4dfp criterion
+
+.. |BiasField_vals| replace:: 0,1
+.. |BiasField_desc| replace:: perform bias field correction
 
 .. |blur_vals| replace:: <flt>
 .. |blur_desc| replace:: f_half for spatial blur (no blurring if unspecified)
@@ -31,6 +74,9 @@
 .. |conc_vals| replace:: <str>
 .. |conc_desc| replace:: pre-existing conc file to use
 
+.. |cross_day_nostretch_vals| replace:: 0,1
+.. |cross_day_nostretch_desc| replace:: disable stretch for cross-day transform
+
 .. |CSF_excl_lim_vals| replace:: <flt>
 .. |CSF_excl_lim_desc| replace:: mask threshold for CSF (default = .126)
 
@@ -40,11 +86,17 @@
 .. |dwell_vals| replace:: <flt>
 .. |dwell_desc| replace:: EPI dwell time/echo spacing (ms)
 
-.. |economy_vals| replace:: 1-6
+.. |E4dfp_vals| replace:: 0,1
+.. |E4dfp_desc| replace:: if 4dfp files already exist (skips :ref:`dcm_to_4dfp`)
+
+.. |economy_vals| replace:: 2-7
 .. |economy_desc| replace:: level of removal for intermediate files created during execution (higher economy will remove more files)
 
 .. |epi2atl_vals| replace:: 0,1,2
-.. |epi2atl_desc| replace:: if EPI to atlas transform is required (0 = no transform, 1 = transform to 333 space, 2 = proceed to t4_xr3d_4dfp)
+.. |epi2atl_desc| replace:: if EPI to atlas transform is required (0 = no transform, 1 = transform to 333 space, 2 = skip to resampling step)
+
+.. |epi_zflip_vals| replace:: 0,1
+.. |epi_zflip_desc| replace:: flip z when unpacking (:ref:`unpack_4dfp`)
 
 .. |epidir_vals| replace:: 0,1
 .. |epidir_desc| replace:: direction of EPI slices (0 = inferior to superior, 1 = superior to inferior)
@@ -64,17 +116,32 @@
 .. |FWHM_vals| replace:: <int>
 .. |FWHM_desc| replace:: full-width half maximum for spatial blur (default = 6)
 
+.. |Gad_vals| replace:: 0,1
+.. |Gad_desc| replace:: if gadolinium contrast was used
+
 .. |go_vals| replace:: 0,1
 .. |go_desc| replace:: if calls should be executed (if 0, statements will only be printed, not executed)
 
-.. |MB_vals| replace:: 0,1
-.. |MB_desc| replace:: enable slicing timing correction and debanding (choices=0,1)
+.. |goto_UNWARP_vals| replace:: 1
+.. |goto_UNWARP_desc| replace:: immediately go to unwarp step (will happen if variable is defined)
+
+.. |interleave_vals| replace:: -S
+.. |interleave_desc| replace:: sequential slice acquisition (:ref:`frame_align_4dfp`)
+
+.. |lomotil_vals| replace:: <int>
+.. |lomotil_desc| replace:: lowpass filter specified motion parameter (:ref:`mat2dat`)
+
+.. |MB_enable_vals| replace:: 0,1
+.. |MB_enable_desc| replace:: enable slicing timing correction and debanding
+
+.. |MB_skip_vals| replace:: 0,1
+.. |MB_skip_desc| replace:: skip slice timing correction and debanding
 
 .. |MBfac_vals| replace:: <int>
 .. |MBfac_desc| replace:: multiband factor (default = 1)
 
 .. |min_frames_vals| replace:: <int>
-.. |min_frames_desc| replace:: minimum number of remaining frames after scrubbing for participant to be included
+.. |min_frames_desc| replace:: minimum number of remaining frames after scrubbing for participant to be included (default = 240)
 
 .. |movement_regressors_vals| replace:: raw,bpss,none
 .. |movement_regressors_desc| replace:: (default="bpss")
@@ -88,6 +155,9 @@
 .. |normode_vals| replace:: 0,1
 .. |normode_desc| replace:: if per-frame volume intensity should be modified
 
+.. |nounpack_vals| replace:: 0,1
+.. |nounpack_desc| replace:: skips unpacking step
+
 .. |nx_vals| replace:: <int>
 .. |nx_desc| replace:: number of voxels on the x-axis
 
@@ -100,13 +170,28 @@
 .. |ped_vals| replace:: x,x-,y,y-,z,z-
 .. |ped_desc| replace:: EPI phase encoding direction (default = y-)
 
+.. |rsam_cmnd_vals| replace:: <str>
+.. |rsam_cmnd_desc| replace:: script to use for resampling
+
+.. |scrdir_vals| replace:: <str>
+.. |scrdir_desc| replace:: scratch directory to be used if desired
+
+.. |Siemens_interleave_vals| replace:: 0,1
+.. |Siemens_interleave_desc| replace:: enables Siemens interleave order (:ref:`frame_align_4dfp`)
+
 .. |skip_vals| replace:: <int>
 .. |skip_desc| replace:: number of pre-steady state frames
 
 .. |sorted_vals| replace:: 0,1
 .. |sorted_desc| replace:: if dcm sort already been run (if 0, dcm_sort will be run)
 
-.. |target_vals| replace:: <str>
+.. |sx_vals| replace:: <int>
+.. |sx_desc| replace:: unpacked x-dimension squeeze factor (:ref:`unpack_4dfp`)
+
+.. |sy_vals| replace:: <int>
+.. |sy_desc| replace:: unpacked y-dimension squeeze factor (:ref:`unpack_4dfp`)
+
+.. |target_vals| replace:: <img>
 .. |target_desc| replace:: atlas to be used for alignment
 
 .. |task_regressor_vals| replace:: <str>
@@ -115,11 +200,17 @@
 .. |TE_vol_vals| replace:: <int>
 .. |TE_vol_desc| replace:: echo time (ms)
 
+.. |to_MNI152_vals| replace:: 0,1
+.. |to_MNI152_desc| replace:: transform to MNI152 atlas space
+
 .. |TR_slc_vals| replace:: <flt>
 .. |TR_slc_desc| replace:: time per slice (s)
 
 .. |TR_vol_vals| replace:: <flt>
 .. |TR_vol_desc| replace:: time per frame (s)
 
-.. |usescr_vals| replace:: <str>
-.. |usescr_desc| replace:: if a scratch directory should be used
+.. |use_anat_ave_vals| replace:: 0,1
+.. |use_anat_ave_desc| replace:: use _anat_ave epi image (default is _func_vols_ave)
+
+.. |uwrp_cmnd_vals| replace:: <str>
+.. |uwrp_cmnd_desc| replace:: script to use for unwarping