spm8Batch/daisyChained to be pulled into spm8Batch_alpha etc.

spm8Batch/INSTALL_README.txt

@@ -1,6 +1,6 @@
 # # # # # # # # # # # # # # # # # #
 #
-# This is the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
+# This is a modified version of the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
 #
 # Copyright 2002-2012
 #
@@ -29,29 +29,21 @@
 #
 # INSTALLATION INSTRUCTIONS:
 #
-# Move the spm8Batch tar distribution file to the directory where you wish the code to 
-# reside. Then untar using
-# 
-# tar -xvf [tarfile]
 #
-# Next you will need to adjust your PATH environmental variable to include 
+# You will need to adjust your PATH environmental variable to include
 # the spm8Batch distribution
 #
-# For bash you can add this to your .bashrc or .bash_profile
-#
-#     export PATH=[spm8Batch_distribution_location]:${PATH}
-#
-# On tcsh you can add this to your .cshrc file.
+# You can do this on the fly by running "source spm8Setup" while in this directory.
+# You can also edit your .bashrc, .bash_profile, or /etc/bashrc startup scripts to source this automatically
+# for all or just some users.
 #
-#     setenv PATH [spm8Batch_distribution_location]:${PATH}
 # 
-# Next you need to implement the localization changes in spm8Batch_Global that are
-# described below. Remember the native language of the spm8Batch system is bash. An
+# Remember the native language of the spm8Batch system is bash. An
 # excellent site for BASH help is:
 # 
 #     http://tldp.org/LDP/abs/html/
 #
-# You will need to have spm8 distribution
+# You will need to have spm8 distribution (Included in this distribution)
 # 
 # You will need to have fsl, at least 4.1.7, it's known to work with 4.1.7 and 4.1.8
 #
@@ -73,7 +65,7 @@
 # -----------------------------------------------------------------
 # -----------------------------------------------------------------
 #
-# LOCALIZATION
+# LOCALIZATION (No longer needs to be edited. This section retained for developer documentation)
 #
 # The only file that has to be modified for local distrubution is the scripts "spm8Batch_Global"
 # 

spm8Batch/auxiliary/help/help_case_TGLOBAL

@@ -0,0 +1,3 @@
+    echo "    -G TGLOBAL           change the TGLOBAL parameters for fsl/slicetimer, "
+    echo "                         default is 0.50"
+    echo 

spm8Batch/auxiliary/help/help_case_flirt_options

@@ -1,5 +1,7 @@
-    echo "    -m \"flirt options\"   enable super debug flag."
+    echo "    -m \"fsl options\"     Give options to mcflirt or slicetimer."
     echo "                         Be sure to specify inside of quotes."
     echo "                         do \"mcflirt --help\" for help."
-    echo "                         default is \"-cost normcorr -stats -plots\""
+    echo "                         do \"slicetimer --help\" for help."
+    echo "                         default for mcflirt is \"-cost normcorr -stats -plots\""
+    echo "                         default for slicetimer is \"\""
     echo 

spm8Batch/auxiliary/help/help_case_no_background_job

@@ -0,0 +1,2 @@
+    echo "    -B                   run in the foreground, need for daisy chaining jobs."
+    echo 

spm8Batch/auxiliary/help/help_case_warpmethod

@@ -1,3 +1,5 @@
     echo "    -W                   Enable VBM8 warping for fMRI, you need to run vbm8HiRes first."
     echo "                         Default is to use standard SPM8 normalization."
+    echo "                         This will set the output name to 'vbm8_', so use '-w' after"
+    echo "                         you specificy '-W' if you wish to use 'w' as the prepend name."
     echo

spm8Batch/auxiliary/help/help_options_end

@@ -2,6 +2,8 @@
     echo "${helpComment} functional images path    : $fmriPATH"
     echo "${helpComment} Subject directory         : ${SUBJDIR}"
     echo
+    echo "${helpComment} Back(1)/fore(0)ground     : ${BACKGROUNDJOBFLAG}"
+    echo 
     echo "${helpComment} spm8 is located in        : $SPM8B1"
     echo "${helpComment} spm8Batch is located in   : $SPM8B2"
     echo "${helpComment} spm8 patch is located in  : $SPM8B3"

spm8Batch/auxiliary/help/help_options_start

@@ -54,6 +54,9 @@
 	    "a") 
 	        . ${thisDir}/auxiliary/help/help_case_anatomy_path
 	        ;;
+	    "B")
+                . ${thisDir}/auxiliary/help/help_case_no_background_job
+		;;
 	    "b") 
    	        . ${thisDir}/auxiliary/help/help_case_bet_best_flag
 	        ;;
@@ -69,6 +72,9 @@
 	    "f") 
 	        . ${thisDir}/auxiliary/help/help_case_functional_path
 	        ;;
+	    "G") 
+	        . ${thisDir}/auxiliary/help/help_case_TGLOBAL
+	        ;;
 	    "g") 
 	        . ${thisDir}/auxiliary/help/help_case_BET_gradient
 	        ;;

spm8Batch/auxiliary/help/help_sliceTime_Options

@@ -1,6 +1,7 @@
     echo "${helpComment} Sub-directory             : ${subPATH}"
     echo "${helpComment} Volume Wildcard           : ${volumeWILD}"
     echo "${helpComment} fMRI TR                   : ${TR}"
+    echo "${helpComment} TGLOBAL                   : ${TGLOBAL}"
     echo "${helpComment} FSLOUTPUTTYPE             : ${FSLOUTPUTTYPE}"
     echo "${helpComment} Number of runs to realign : ${nRUN}"
 

spm8Batch/auxiliary/initialization_all

@@ -92,6 +92,10 @@ SLICETIMEROPT=
 
 BATCHCOMMAND=1
 
+# Is this command to run in the background
+
+BACKGROUNDJOBFLAG=1
+
 #
 # Now the process specific initialization
 #

spm8Batch/auxiliary/initialization_sliceTime

@@ -9,6 +9,8 @@ FSL_COMMENT_B="Slice time correcting subject"
 
 outputName=a
 
+mcOPT=""
+
 #
 # all done
 #

spm8Batch/auxiliary/parse_arguments

@@ -67,6 +67,15 @@ do
 		    . ${thisDir}/auxiliary/setAnatomyPath
 		    ;;
 
+              # case_no_background_job
+              #
+              # don't launch the job into the background, but run in the foreground, 
+              # this will facilitate daisy-chaining jobs.
+              #
+                "B")
+                    . ${thisDir}/auxiliary/setNoBackgroundJob
+		    ;;
+
               # case_bet_best_flag 
 	      #
 	      # look at the BET best flag
@@ -107,6 +116,13 @@ do
 		    . ${thisDir}/auxiliary/setFunctionalPath
 		    ;;
 
+              # case_set_TGLOBAL
+              #
+              # Set the TGLOBAL value for slice time
+              #
+		"G")
+                    . ${thisDir}/auxiliary/setTGlobalValue
+                    ;;
               # case_set_BET_gradient
               #
               # Set the gradient scale for bestBET

spm8Batch/auxiliary/setNoBackgroundJob

@@ -0,0 +1,7 @@
+
+# The user wants to run the job in the foreground, only recommended for daisy-chaining.
+# We also set the mail account to be null that way jobs in foreground do not by default send 
+# out email. However, this can be overridden with the -U flag.
+
+		  BACKGROUNDJOBFLAG=0
+		  USEREMAIL="NOMAIL"

spm8Batch/auxiliary/setTGlobalValue

@@ -0,0 +1,20 @@
+#
+# Set the value of TGLOBAL
+#
+		  shift
+		  let argn++
+		  if (( $argn >= $args ))
+		      then
+		      echo "Missing parameter for setting TGLOBAL"
+	              . ${thisDir}/auxiliary/exit_w_removal
+		  else
+	              isnumber $1
+		      retVal=$?
+		      if [ "$retVal" != "0" ]
+		      then
+			echo "TGLOBAL needs to be numeric, you entered : $1"
+			. ${thisDir}/auxiliary/exit_w_removal
+		      fi
+		      TGLOBAL=`echo $1 | awk '{printf "%2.2f",$1}'`
+		      isnumber $TGLOBAL
+		  fi

spm8Batch/auxiliary/shellScriptFinalize

@@ -33,8 +33,12 @@ echo "# ${execDIR}"
 echo "#"                                                                               >> ${FULLSCRIPTNAME}.sh
 
 BATCHVERSION=`cat ${thisDir}/.spm8BatchVersion`
+[[ -f ${thisDir}/../.local/CurrentVersionSHA ]] && mcSHA=`cat ${thisDir}/../.local/CurrentVersionSHA`
+[[ -f ${thisDir}/../.local/mc_releasetag ]] && mc_releasetag=`cat ${thisDir}/../.local/mc_releasetag`
 
 echo "# spm8Batch Version : ${BATCHVERSION}"                                           >> ${FULLSCRIPTNAME}.sh
+echo "# MethodsCore Release Tag : ${mc_releasetag}"                                    >> ${FULLSCRIPTNAME}.sh
+echo "# MethodsCore Repository SHA-ID: $mcSHA"                                         >> ${FULLSCRIPTNAME}.sh
 echo "#"                                                                               >> ${FULLSCRIPTNAME}.sh
 echo "# All done"                                                                      >> ${FULLSCRIPTNAME}.sh
 echo "#"                                                                               >> ${FULLSCRIPTNAME}.sh

spm8Batch/auxiliary/shellScriptLaunch

@@ -11,10 +11,22 @@ echo "${FULLSCRIPTNAME}.sh" > ${thisDir}/Usage/${SANDBOXHOST}/${theYearMonth}/${
 
 if [ ! "$debugFLAG" == "1" ]
 then
-    echo
-    echo "   Lauching script into background."
-    echo
-    nohup ${FULLSCRIPTNAME}.sh &> ${FULLSCRIPTNAME}.log &
+   if [ "${BACKGROUNDJOBFLAG}" == "1" ]
+   then
+       echo
+       echo "   Lauching script into background."
+       echo
+       nohup ${FULLSCRIPTNAME}.sh &> ${FULLSCRIPTNAME}.log &
+   else
+       echo
+       echo "   Launching script into foreground."
+       echo 
+       ${FULLSCRIPTNAME}.sh &> ${FULLSCRIPTNAME}.log
+       echo
+       echo "   Script ${FULLSCRIPTNAME}.sh is finished"
+       echo "   Script LOGFILE is : ${FULLSCRIPTNAME}.log"
+       echo    
+   fi
 else
     echo
     echo "   Script can now be launched by hand."

spm8Batch/bestBET

@@ -35,7 +35,7 @@ thisDir=`dirname $theCommand`
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
 #allowedOptions="aDdfhMnOoRrtUw"
-allowedOptions="aDdghMtU"
+allowedOptions="aBDdghMtU"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/coregHiRes

@@ -40,7 +40,7 @@ thisDir=`dirname $theCommand`
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
 #allowedOptions="aDdfhMnOoRrtUw"  - reslice only is NOT working with other images.
-allowedOptions="aDdfhMnOorrtUw"
+allowedOptions="aBDdfhMnOorrtUw"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/coregOverlay

@@ -43,7 +43,7 @@ thisDir=`dirname $theCommand`
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
 #allowedOptions="aDdfMnOoRrstUvw"
-allowedOptions="aDdfMnOorstUvw"
+allowedOptions="aBDdfMnOorstUvw"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/isnumber.sh

@@ -27,22 +27,15 @@ isdigit()
 	fi
 }
 
+# New code for determining is an input is a number - 2012-07-27 - RCWelsh
+
 isnumber ()   # Test if the parameter is a number (integer or float)
 {
     retVal=1;
-    nPeriod=`echo $1 | awk -F . '{print NF}'`
-    if [ "$nPeriod" -ne "1" -a "$nPeriod" -ne "2" ]
-	then
-	return $FAILURE
-    fi
-    theNumber=`echo $1 | sed 's/\.//g' `
-    isdigit $theNumber
+    # do it by trying to printf the number fo get error if bad
+    printf "%2.2f" $1 2> /dev/null > /dev/null
     retVal=$?
-    if [ "$retVal" == "0"  ]
-	then
-	return $SUCCESS
-    else
-	return $FAILURE
-    fi
+    return $retVal
 }
 
+

spm8Batch/matlabScripts/UMBatchWarpVBM8.m

@@ -219,6 +219,10 @@
 
   [Images2WriteUnique Images2WriteCount] = uniqueNII(Images2Write);
 
+  % If the prefix is "w" then we just need to report the images that
+  % vbm8 has already generated. - RCWelsh 2012-07-27
+  tmpNewImages2WriteUnique = [];
+
   for iNII = 1:size(Images2WriteUnique,1)
     [d1 d2 d3 d4] = spm_fileparts(strtrim(Images2WriteUnique(iNII,:)));
     newFile = fullfile(d1,['w' d2 d3]);
@@ -229,6 +233,9 @@
       fprintf('\n\n* * * * * * * * * * * * \n\n');
       return
     end
+    % If the prefix is "w" then we just need to report the images that
+    % vbm8 has already generated. - RCWelsh 2012-07-27
+    tmpNewImages2WriteUnique = strvcat(tmpNewImages2WriteUnique, newFile);
   end
 
   % Everything up to this point is okay
@@ -253,6 +260,10 @@
           end
           newImages2WriteUnique = strvcat(newImages2WriteUnique, newFile);
       end
+  else
+    % If the prefix is "w" then we just need to report the images that
+    % vbm8 has already generated. - RCWelsh 2012-07-27
+    newImages2WriteUnique = tmpNewImages2WriteUnique;
   end
 
   ImageDirectory = fileparts(Images2Write(1,:));

spm8Batch/physioCorr

@@ -38,7 +38,7 @@ thisDir=`dirname $theCommand`
 
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
-allowedOptions="ADdfFiMnpPtUv#"
+allowedOptions="ABDdfFiMnpPtUv#"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/realignfMRI

@@ -32,7 +32,7 @@ thisDir=`dirname $theCommand`
 
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
-allowedOptions="ADdfiMmnStUv#"
+allowedOptions="BADdfiMmnStUv#"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/segHiRes

@@ -38,7 +38,7 @@ thisDir=`dirname $theCommand`
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
 #allowedOptions="DdfhMnTtUw"
-allowedOptions="DdfhMTtUw"
+allowedOptions="BDdfhMTtUw"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart

spm8Batch/sliceTime

@@ -35,7 +35,7 @@ thisDir=`dirname $theCommand`
 
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
-allowedOptions="ADdfiMntUv#"
+allowedOptions="ABDdFfGiMmntUv#"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart
@@ -141,15 +141,15 @@ echo "          CURRUN4D=\`ls ${volumeWILD}*.nii 2> /dev/null\`  "
 echo "          if [ -e \"\${CURRUN4D}\" ] "                                                          >> ${FULLSCRIPTNAME}.sh
 echo "          then"                                                                                 >> ${FULLSCRIPTNAME}.sh
 echo "            FSLOUTPUTTYPE=NIFTI"                                                                >> ${FULLSCRIPTNAME}.sh
-echo "            echo \"slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} -r ${TR}  --tglobal=${TGLOBAL}\"">> ${FULLSCRIPTNAME}.sh
-echo "            slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} -r ${TR} --tglobal=${TGLOBAL}"          >> ${FULLSCRIPTNAME}.sh
+echo "            echo \"slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} ${mcOPT} -r ${TR}  --tglobal=${TGLOBAL}\"">> ${FULLSCRIPTNAME}.sh
+echo "            slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} ${mcOPT} -r ${TR} --tglobal=${TGLOBAL}"          >> ${FULLSCRIPTNAME}.sh
 echo "            logTheUMProcess sliceTime ${FULLSCRIPTNAME} \${CURRUN4D} ${outputName}\${CURRUN4D}"            >> ${FULLSCRIPTNAME}.sh
 echo "          else"                                                                                 >> ${FULLSCRIPTNAME}.sh
 echo "             echo \"Can't find a 4D ${volumeWILD}*.nii for this run \${CURRUN}\" "              >> ${FULLSCRIPTNAME}.sh
 echo "          fi"                                                                                   >> ${FULLSCRIPTNAME}.sh
 echo "       else"                                                                                    >> ${FULLSCRIPTNAME}.sh
 echo "          echo \"Test mode.\"  "                                                                >> ${FULLSCRIPTNAME}.sh
-echo "          echo \"slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} -r ${TR} --tglobal=${TGLOBAL}\" "  >> ${FULLSCRIPTNAME}.sh
+echo "          echo \"slicetimer -i \${CURRUN4D} -o ${outputName}\${CURRUN4D} ${mcOPT} -r ${TR} --tglobal=${TGLOBAL}\" "  >> ${FULLSCRIPTNAME}.sh
 echo "       fi"                                                                                      >> ${FULLSCRIPTNAME}.sh
 echo "       cd ../"                                                                                  >> ${FULLSCRIPTNAME}.sh
 echo "    done"                                                                                       >> ${FULLSCRIPTNAME}.sh

spm8Batch/smoothfMRI

@@ -32,7 +32,7 @@ thisDir=`dirname $theCommand`
 
 thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`
 
-allowedOptions="DdfMntUv"
+allowedOptions="BDdfMntUv"
 
 # This piece of code all of the spm8Batch scripts will use
 . ${thisDir}/auxiliary/commonCode_AllScriptsStart