fixto1809c

#!/usr/bin/env bash
# make .18_09c.nii.gz from input file
# optionally, if given second argument "mask", will use NN interp instead of sinc
fixto1809c() { 
  [ $# -lt 1 ] && echo "usage: $FUNCNAME to_correct.nii.gz [-mask] [-mkbad] [-out newfile.nii.gz]" && return 1

  local reffolder="/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c"
  local newname="18_09c"
  local mask=""
  local output="";

  local input=$1; shift
  while [ $# -ne 0 ]; do
     case $1 in
        -mask) mask=1; shift;;
        -out) shift; output=$1; shift;;
        -mkbad) 
           reffolder="/opt/ni_tools/standard_old/mni_icbm152_nlin_asym_09c"
           newname="bad_09c"
           shift;;
         *) echo "unkown argument $1! no args for help"; return 1;;
    esac
  done

  [ $# -eq 2 ] && [ "$2" != "ismask" ] && echo "only valid second argument is 'ismask', you gave $2" && return 1

  # output name cannot be changed, requires input be .nii.gz
  [ -z "$output" ] && output="${input/.nii.gz/.$newname.nii.gz}"
  #output="$(dirname $input)/$(basename "$input" .nii.gz).18_09c.nii.gz"

  # checks
  [ -z "$input" -o ! -r "$input" ] && echo "$FUNCNAME needs nifti to warp. given '$input'" >&2 && return 1
  ! 3dinfo -space $input | grep -iq mni && echo "$input is not in mni space!" >&2 && return 1

  dim=$(3dinfo -adj $input|sed 's/0\+$//;s/\.$//')
  [ $dim != "1" ] && dim=_${dim}mm

  local ref=$reffolder/mni_icbm152_t1_tal_nlin_asym_09c${dim}.nii 
  # /opt/ni_tools/standard/09cFix/gen_mats.bash
  local mat=/opt/ni_tools/standard_old/09cFix/2mm_luna_to_fixed.mat 
  # file is identity:
  # 1  0  0  0  
  # 0  1  0  0  
  # 0  0  1  0  
  # 0  0  0  1  

  [ ! -r $ref -o ! -r $mat ] && echo "$FUNCNAME cannot find ref or mat ($ref $mat)" >&2 && return 1
  [ -z "$REDOWARP" -a -r "$output" ] && echo "have $output" >&2 && return 0
  echo "creating $output ($dim)"
  cmd="applyxfm4D '$input'  $ref '$output'  $mat -singlematrix" # default to sinc
  [ -n "$mask" ] && cmd="flirt -ref '$ref' -in '$input' -applyxfm -init '$mat' -out '$output' -interp nearestneighbour"
  if command -v rel >/dev/null; then
     rel "$cmd # $(pwd)" c
  else
     echo "$cmd # $(pwd)"
  fi
  eval "$cmd" && 3dNotes -h "[$FUNCNAME] $cmd" "$output"
}

if [ "$(basename $0)" == fixto1809c ]; then
   fixto1809c $@
fi
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