UNNIFTI

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# A command to rummage about 
# a subject and convert NIFTI files
# into ANALYZE
#
# Note, images that exist in "NIFTI" directory 
# will be ignored.
# 
#
# run_XX/
#    ANALZE/
#      apimg/
#         aprvol_XXXX.img, hdr
#    NIFIT/
#      aprun_XX.nii
#
# will turn into
#
# run_XX/
#    aprun_XX.nii
#
# And anatomy directory this is
#
#   anatomy/
#     NIFTI/
#       ...
#     ANALZE/
#       ...
#
# will become
#
#   anatomy/
#
#                         Robert C. Welsh
#                         Copyright 2007
#
#
#
#  Modified to do flipping by default.
#
# # # # # # # # # # # # # # # # # #

# 
# Main UNNIFTI function.
#

VERSION="2.0"
VERSIONDATE="2011-09-14"

# Find out where the current command lives and execute some common code.

theFullCommand="$0 $*"
execDIR=`pwd`

theCommand=`which $0`
thisDir=`dirname $theCommand`

# Find out where the current command lives and execute some common code.

theCommand=`which $0`
thisDir=`dirname $theCommand`

thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`

allowedOptions=" f M V "

# This piece of code all of the spm12Batch scripts will use
. ${thisDir}/auxiliary/commonCode_AllScriptsStart

# Validate that we have FSL installed.
. ${thisDir}/auxiliary/commonCode_FSL_01

# This is common in-line code for all spm12Batch script to make sure arguments were passed
. ${thisDir}/auxiliary/commonCode_checkIfArgsPassed


# The actual function.
#

. ${thisDir}/auxiliary/parse_arguments

#

. ${thisDir}/auxiliary/superDebugStatus

#
# Ok - let's start displaying things back to the terminal
#

. ${thisDir}/auxiliary/shellScriptInfo

#
# Prepare to write the script.
#

# Makes sure they speficied some subjects.
. ${thisDir}/auxiliary/checkInputForSubjects

# Write out debug status
. ${thisDir}/auxiliary/debugStatus

# Get the name of this experiment.

expDIR=`pwd`

# Now start building the automatic scripts.

theDate=`date`

HOSTCOMPUTER=`echo $HOSTNAME | awk -F. '{print $1}'`

echo
echo " UNNIFTI. Version ${VERSION} ${VERSIONDATE}"
echo " Running on ${HOSTCOMPUTER} at ${theDate}"
echo " Will perform move NIFTI back to where they need to be for spm12 processing."
echo
echo " Verify Flag     : ${verifyFLAG}"
echo " fMRI Path       : ${fmriPATH}"
echo " Subjects in     : ${SUBJDIR}"
    

# Print out the list of subjects that we operate upon.
. ${thisDir}/auxiliary/printSubjectsList

# Now do the work.

echo 
echo " Starting...."
echo
for (( ii=1 ; ii<=$nSubjects ; ii++ ))
  do
  echo 
  echo " Processing subject : ${subjects[$ii]}"
  echo
  cd ${expDIR}/${SUBJDIR}/${subjects[$ii]}
  echo "  ANATOMY"
  echo
  if [ -e "anatomy" ] 
  then
      cd anatomy
	    # just go ahead and move the ginx format files.
      mkdir -p ginx/
      mv e????s*i* ginx/ 2> /dev/null
      NNII=`ls *.nii 2> /dev/null| wc | awk '{print $1}'`
      if [ ${NNII} -gt 0 ]
      then
	  echo 
	  echo "    Found nifti files in anatomy directory"
      fi
      if [ ! -d NIFTI ]
      then
	  echo "    No anatomy/NIFTI directory"
      else
	  echo "      Found anatomy/NIFTI"
	  cd NIFTI
	  NNII=`ls *.nii 2> /dev/null| wc | awk '{print $1}'`
	  if [ ${NNII} -gt 0 ]
	  then
	      echo 
	      echo "        Found nifti files in anatomy/NIFTI directory"
	      for FILE in `ls *.nii 2> /dev/null`
	      do 
		  if [ -e ../$FILE ]
		  then
		      echo
		      echo "Potential conflict, found $FILE in anatomy/NIFTI and it also exists in anatomy"
		      echo
		      echo "ABORTING"
		      echo
		      exit 0
		  fi
	      done
	      if [ "${verifyFLAG}" -eq 0 ]
	      then
		  mv *.nii ../
	      else
		  echo
		  echo List of anatomy files to be moved : 
		  for FILE in `ls *.nii 2> /dev/null`
		  do
		      echo "  $FILE"
		  done
	      fi
	  else
	      echo
	      echo "      NO NIFTI FILES IN ANATOMY DIRECTORY"
	      echo
	  fi
	  cd ../
      fi
      cd ..
  else
      echo
      echo " * * * ANATOMY DIRECTORY IS MISSING * * * "
      echo 
  fi
  
  # Now the runs
  
  #
  # now do the functional directories
  #
  echo
  echo "  FUNCTIONALS"
  echo
  if [ -d "${fmriPATH}" ]
  then
      echo
      echo "    Working on time-series NIFTI files."
      echo
      cd ${fmriPATH}
      nRUNS=`ls 2> /dev/null | wc | awk '{print $1}'`
      if [ $nRUNS -gt 0 ] 
      then
	  for RUN in `ls -l | grep drw | grep run | awk '{print $9}'`
	  do
	      if [ -d ${RUN} ]
	      then
		  echo "      Found run : ${RUN}"
		  cd ${RUN}		    
		  nRUNFILES=`ls *run*.nii 2> /dev/null | wc | awk '{print $1}'`
		  echo "         has    : $nRUNFILES NIFTI files"
		  if [ ! -d NIFTI ]
		  then
		      echo "             but no NIFTI subdirectory"
		  else
		      cd NIFTI
		      nRUNFILES=`ls *run*.nii 2> /dev/null | wc | awk '{print $1}'`
		      echo "             NIFTI/    : $nRUNFILES NIFTI files"
		      if [ "${nRUNFILES}" != "0" ]
		      then
			  for FILE in `ls *run*.nii 2> /dev/null`
			  do 
			      if [ -e ../$FILE ]
			      then
				  echo
				  echo "Potential conflict, found $FILE in ${RUN}/NIFTI and it also exists in ${RUN}"
				  echo
				  echo "ABORTING"
				  echo
				  exit 0
			      fi
			  done
			  if [ "${verifyFLAG}" -eq 0 ]
			  then
			      mv *run*.nii ../
			  else
			      echo
			      echo "          List of run files to be moved : "
			      for FILE in `ls *run*.nii 2> /dev/null`
			      do
				  echo "            $FILE"
			      done
			  fi
		      fi
		      cd ../
		  fi
		  cd ../
	      fi
	  done
      else
	  echo
	  echo "        NO RUN FILES PRESENT."
	  echo
      fi
      cd ../
  else
      echo
      echo " * * * FUNCTIONAL DIRECTORY IS MISSING * * * "
      echo
  fi
done

echo 
echo " All done."
echo