Params/Instructions files

Many of the csh scripts take one or two text files as input (called “params” and “instructions”). The two files are for convenience. You can specify settings all in one file (“params”), or specify some in one (“params”) and more in another (“instructions”). A typical, convenient use case would be putting subject- or session-specific settings (e.g. patid, scan series numbers, etc.) in the “params” file and study-specific settings that don’t change across subjects (e.g. target atlas, BOLD scan TR, etc.) in the “instructions” file.

Because the instructions file is sourced after the params file, you can reference settings from the params file in the instructions file:

# in params
set patid = TM201

# in instructions
set inpath =  /some/study/path/${patid}

Params file

# TM201.params

set patid = TM201
set mprs = ( 8 )
set t2ws = ( 10 )
set irun = ( thumb1 browthumb blink1  brow1 blink2 brow2 thumb2 thumbbrow )
set fstd = ( 14     16        18      20    22     24    26     28        )
set sefm = ( 11 12 )

Instructions file

# TM_instructions.txt

@ sorted = 1
@ economy = 5
@ go = 1
@ usescr = 0
set target = $REFDIR/TRIO_Y_NDC
@ nx = 72
@ ny = 72
set TR_vol = 0.6
set TE_vol = 33
set TR_slc = 0
set delta = ""
set ped = "y-"
set dwell = "0.59"
@ MBfac = 6
@ epidir = 0
@ skip = 5
@ epi2atl = 1
@ normode = 1
set tse = ( ${t2ws[1]} ) # for bold pp

set FDthresh = 0.2
@ min_frames = 120

set srcdir = $cwd

#####################
# FM unwarping
#####################
set datain = /data/nil-bluearc/black/scripts/TicModel_fieldmap_topup_datain.txt
set FMmag = $srcdir/sefm/${patid}_sefm_mag.nii.gz
set FMphase = $srcdir/sefm/${patid}_sefm_fieldmap.nii.gz
set uwrp_cmnd   = /data/gizmo/data1/NEWT_phantom/kqa778_20_vs_64/fmri_unwarp_se.csh
set rsam_cmnd   = /data/nil-bluearc/benzinger2/Tyler/scripts/one_step_resample.tcsh