thomas_csh_mv

#!/bin/tcsh
set c = (1 2 4 5 6 7 8 9 10 11 12 13 14)

if ( $?THOMAS_HOME ) then
    echo "THOMAS_HOME setting of $THOMAS_HOME"
    set Thomas = $THOMAS_HOME
else
    echo "Environment variable THOMAS_HOME variable not set, add it to .cshrc or .bashrc and try again"
    exit 1
endif

if ( $?OSTYPE) then
    if ( "$OSTYPE" =~ "*linux*" ) then 
        set Ismac = 0
        echo "Linux OS detected"
    else if ( "$OSTYPE" =~ "*darwin*" ) then
        set Ismac = 1
        echo "Mac OS detected, running ANTS jointfusion" 
    else
        echo "Invalid OS $OSTYPE, only linux or Darwin supported"
        exit 1
    endif
endif

if ( $#argv >= 1 && $#argv <= 2 ) then
    set x = $1
    set y = $1:t
    if ( $x == $y) then
        echo "File name OK"
        set fileok = 1
    else
        set fileok = 0
        echo "First argument has to be just the WMn MPRAGE file name without the full path"
        echo "Please call $0:t in the directory containing the MPRAGE/T1 file"
	exit 1
    endif
else
     set fileok = 0
     echo "Usage: thomas mprage/T1 <lo>"
     echo "Optional argument lo is for just running left side"
     exit 1
endif

if ( $#argv == 1 ) then
  echo "Running left and right thalamus MV big"
  if (-d temp) then
    echo "Deleting temp"
    \rm -rf temp
  endif
  ${Thomas}/THOMASmib.py -a v2 -p 4 -v -M --tempdir temp -B $1 ALL
  mkdir left
  cp -rf temp/crop_* .
  mv ?-*.nii.gz left
  mv ??-*.nii.gz left
  mv 4567* left
  mv 6_* left
  mv san* left
  mv mask* left
  mv crop_* left
  mv rigid* left
  mv temp/*Warp* temp/*Aff* left
  mv temp/registered.nii.gz left
  mv left/$1 .

  cd left
  ${Thomas}/fuselabels
  python2 ${Thomas}/uncrop.py thomas.nii.gz thomasfull.nii.gz mask_inp.nii.gz
  set h = $1:t:r:r
  antsApplyTransforms -d 3 -i ${Thomas}/templ_93x187x68.nii.gz -r crop_{$1} -o regn.nii.gz -t \[${h}0GenericAffine.mat, 1\] -t ${h}1InverseWarp.nii.gz
  foreach z ($c)
  foreach zz ($z-*.nii.gz)
    echo $zz:r:r
  end
  set x = `fslstats $zz -V | awk '{print $2}'`
  echo $zz:r:r $x >> nucleiVols.txt
  end   
  cd ..
  echo "Done; segmentation results in directory left"

 # Now do the right side 
  if (-d tempr) then
    echo "Deleting tempr"
    \rm -rf tempr
  endif

  ${Thomas}/THOMASmib.py -a v2 -p 4 -v -R -M --tempdir tempr -B $1 ALL

      mkdir right
#     THOMAS flips so we want the original crop not the flipped
#     cp -rf tempr/crop_* .
      mv ?-*.nii.gz right
      mv ??-*.nii.gz right
      mv 4567* right
      mv 6_* right
      mv san* right
      mv mask* right
      mv crop_* right
      mv rigid* right
      mv tempr/*Warp* tempr/*Aff* right
      mv tempr/registered.nii.gz right
      mv right/$1 .

      cd right
      ${Thomas}/fuselabels
      python2 ${Thomas}/uncrop.py thomas.nii.gz thomasfull.nii.gz mask_inp.nii.gz
      mv thomas.nii.gz thomasr.nii.gz
      mv thomasfull.nii.gz thomasrfull.nii.gz
      set h = $1:t:r:r
      antsApplyTransforms -d 3 -i ${Thomas}/templ_93x187x68.nii.gz -r crop_{$1} -o regn.nii.gz -t \[${h}0GenericAffine.mat, 1\] -t ${h}1InverseWarp.nii.gz
      foreach z ($c)
      foreach zz ($z-*.nii.gz)
        echo $zz:r:r
      end
      set x = `fslstats $zz -V | awk '{print $2}'`
      echo $zz:r:r $x >> nucleiVols.txt
      end   
      cd ..
  echo "Done; segmentation results in directory right"
endif

  if ( $#argv == 2) then
    if ($2 == lo) then
  if (-d temp) then
    echo "Deleting temp"
    \rm -rf temp
  endif
      echo "Running only left thalamus MV big"

  ${Thomas}/THOMASmib.py -a v2 -p 4 -v -M --tempdir temp -B $1 ALL
      mkdir left
      cp -rf temp/crop_* .
      mv ?-*.nii.gz left
      mv ??-*.nii.gz left
      mv 4567* left
      mv 6_* left
      mv san* left
      mv mask* left
      mv crop_* left
      mv rigid* left
      mv temp/*Warp* temp/*Aff* left
      mv temp/registered.nii.gz left
      mv left/$1 .

      cd left
      {$Thomas}/fuselabels
      python2 {$Thomas}/uncrop.py thomas.nii.gz thomasfull.nii.gz mask_inp.nii.gz
      set h = $1:t:r:r
      antsApplyTransforms -d 3 -i ${Thomas}/templ_93x187x68.nii.gz -r crop_{$1} -o regn.nii.gz -t \[${h}0GenericAffine.mat, 1\] -t ${h}1InverseWarp.nii.gz
      foreach z ($c)
      foreach zz ($z-*.nii.gz)
        echo $zz:r:r
      end
      set x = `fslstats $zz -V | awk '{print $2}'`
      echo $zz:r:r $x >> nucleiVols.txt
      end   
      echo "Done; segmentation results in directory left"
      cd ..
    endif
 # Now do the right side 
  if (-d tempr) then
    echo "Deleting tempr"
    \rm -rf tempr
  endif

    if ($2 == ro) then
      echo "Running only right thalamus MV big"
  ${Thomas}/THOMASmib.py -a v2 -p 4 -v -R -M --tempdir tempr -B $1 ALL

      mkdir right
#     THOMAS flips so we want the original crop not the flipped
#     cp -rf tempr/crop_* .
      mv ?-*.nii.gz right
      mv ??-*.nii.gz right
      mv 4567* right
      mv 6_* right
      mv san* right
      mv mask* right
      mv crop_* right
      mv rigid* right
      mv tempr/*Warp* tempr/*Aff* right
      mv tempr/registered.nii.gz right
      mv right/$1 .

      cd right
      ${Thomas}/fuselabels
      python2 ${Thomas}/uncrop.py thomas.nii.gz thomasfull.nii.gz mask_inp.nii.gz
      mv thomas.nii.gz thomasr.nii.gz
      mv thomasfull.nii.gz thomasrfull.nii.gz
      set h = $1:t:r:r
      antsApplyTransforms -d 3 -i ${Thomas}/templ_93x187x68.nii.gz -r crop_{$1} -o regn.nii.gz -t \[${h}0GenericAffine.mat, 1\] -t ${h}1InverseWarp.nii.gz
      foreach z ($c)
      foreach zz ($z-*.nii.gz)
        echo $zz:r:r
      end
      set x = `fslstats $zz -V | awk '{print $2}'`
      echo $zz:r:r $x >> nucleiVols.txt
      end   
      cd ..
  echo "Done; segmentation results in directory right"
  endif

    if ( ($2 == lo) || ($2 == ro)) then
    else
      echo "Unrecognized second argument; usage: thomas mprage/T1file or thomas mprage/T1file lo/ro"
    endif
  endif