MEICA Scripts

rsfMRI/S01_AnatPrep_RR.sh

@@ -0,0 +1,128 @@
+# ===============================================================   
+# Date: 11/12/2015
+# Authors: Javier Gonzalez-Castillo
+#
+# Inputs:
+#   * SubjectID is the only input parameter
+#
+# Outputs:
+#   * Skull-strip PD
+#   * Intracranial mask based on PD
+#   * Create Skull Stripped and Bias Corrected MP-RAGE
+#   * Perform trasformation to MNI space
+#
+# ===============================================================   
+
+# COMMON STUFF
+# ============
+source ./00_CommonVariables.sh
+set -e
+minp=11      # Minimum patch size as recommended by BOB for the NL Alignment
+usePD4mask=0 # Use PD for computing intra-cranial mask (helps keep the TLs)
+
+# READ INPUT PARAMETERS
+# =====================
+# INPUT VARIABLES REQUIRED
+# ========================
+if [[ -z "${SBJ}" ]]; then
+        echo "You need to provide SBJ as an environment variable"
+        exit
+fi
+### if [ $# -ne 1 ]; then
+###  echo "Usage: $basename $0 SBJID"
+###  exit
+### fi
+### SBJ=$1
+
+
+# CREATE DIRECTORIES AND COPY FILES
+# =================================
+cd ${PRJDIR}/PrcsData/${SBJ}
+echo -e "\033[0;33m++ INFO: Creating D01_Anatomical Directory and linking necessary files.\033[0m"
+if [ ! -d D01_Anatomical ]; then mkdir D01_Anatomical; fi
+cd D01_Anatomical
+ln -fvs ${PRJDIR}/Scripts/MNI152_T1_2009c_uni+tlrc.* .
+ln -fvs ../D00_OriginalData/${SBJ}_t1_memprage*.nii.gz .
+
+# COMBINE THE DIFFERNET ECHOES
+# ============================
+echo -e "\033[0;33m++ INFO: Averaging all ME-MEMPRAGE datasets into $SBJ_Anat+orig.\033[0m"
+3dMean -overwrite -prefix ${SBJ}_Anat ${SBJ}_t1_memprage.nii.gz
+# CREATE INTRACRANIAL MASK
+# ========================
+echo -e "\033[0;33m++ INFO: Intensity Bias Correction for Anatomical scan.\033[0m"
+3dUnifize -overwrite -prefix ${SBJ}_Anat_bc -input ${SBJ}_Anat+orig. -GM -ssave ${SBJ}_Anat.UN.Bias
+
+if [ "${noisyANAT}" -eq "1" ]; then
+   if [ "${usePD4mask}" -eq "1" ]; then
+     echo -e "\033[0;33m++ INFO: Skull-stripping via noisy appraoach [BASED ON PD]\033[0m"
+     @NoisySkullStrip -input ${SBJ}_Anat_PD_bc+orig 
+     3dcalc -a ${SBJ}_Anat_PD_bc.ns+orig -expr 'step(a)' -overwrite -prefix ${SBJ}_Anat_mask
+     rm ${SBJ}_Anat_PD_bc.ns+orig.*
+     rm ${SBJ}_Anat_PD_bc.skl+orig.*
+     rm ${SBJ}_Anat_PD_bc.nsm+orig.*
+     rm ${SBJ}_Anat_PD_bc.ma+orig.*
+     rm ${SBJ}_Anat_PD_bc.lsp+orig.*
+     rm ${SBJ}_Anat_PD_bc.ls+orig.* 
+     rm ${SBJ}_Anat_PD_bc.air+orig.*
+     rm __MA_h.1D
+     rm __MA_hd.1D
+   else 
+     echo -e "\033[0;33m++ INFO: Skull-stripping via noisy appraoach [BASED ON MPRAGE]\033[0m"
+     @NoisySkullStrip -input ${SBJ}_Anat_bc+orig 
+     3dcalc -a ${SBJ}_Anat_bc.ns+orig -expr 'step(a)' -overwrite -prefix ${SBJ}_Anat_mask
+     rm ${SBJ}_Anat_bc.ns+orig.*
+     rm ${SBJ}_Anat_bc.skl+orig.*
+     rm ${SBJ}_Anat_bc.nsm+orig.*
+     rm ${SBJ}_Anat_bc.ma+orig.*
+     rm ${SBJ}_Anat_bc.lsp+orig.*
+     rm ${SBJ}_Anat_bc.ls+orig.* 
+     rm ${SBJ}_Anat_bc.air+orig.*
+     rm __MA_h.1D
+   fi
+else
+   echo -e "\033[0;32m++ INFO: Skull-stripping via regular approach \033[0m"
+   3dSkullStrip -prefix ${SBJ}_Anat_mask -ld 33 -niter 777 -shrink_fac_bot_lim 0.777 -exp_frac 0.0666 -input ${SBJ}_Anat_bc+orig
+   3dcalc -a ${SBJ}_Anat_mask+orig. -expr 'step(a)' -overwrite -prefix ${SBJ}_Anat_mask
+fi
+
+###echo -e "\033[0;33m++ MANUAL INTERVENTION NEEDED: Check that the mask is ok, and correct when necessary [${SBJ}_Anat_mask] \033[0m"
+###read -n1 -rsp $'Press ENTER to continue:'
+3dcalc -overwrite -a ${SBJ}_Anat_bc+orig -m ${SBJ}_Anat_mask+orig -expr 'a*m' -prefix ${SBJ}_Anat_bc_ns
+# CONVERT ANATOMICAL TO MNI SPACE
+# ===============================
+if [ "${doNL}" -eq "1" ]; then
+  echo -e "\033[0;33m++ INFO: Alignment to MNI space will be via non-linear registration \033[0m"
+  3dQwarp -overwrite \
+          -allineate \
+          -blur -3 -3  -iwarp -duplo \
+          -workhard:0:4 \
+          -noneg \
+          -pblur \
+          -minpatch ${minp} \
+          -base MNI152_T1_2009c_uni+tlrc \
+          -source ${SBJ}_Anat_bc_ns+orig \
+          -prefix ${SBJ}_Anat_bc_ns
+
+else
+  echo -e "\033[0;33m++ INFO: Alignment to MNI space will be via linear registration \033[0m"
+  @auto_tlrc -overwrite -base MNI152_T1_2009c_uni+tlrc -input ${SBJ}_Anat_bc_ns+orig. -no_ss -twopass
+  cat_matvec -ONELINE ${SBJ}_Anat_bc_ns+tlrc::WARP_DATA > ${SBJ}_MNI2Anat.Xaff12.1D
+  cat_matvec -ONELINE ${SBJ}_MNI2Anat.Xaff12.1D -I      > ${SBJ}_Anat2MNI.Xaff12.1D
+  rm ${SBJ}_Anat_bc_ns_WarpDrive.log
+  rm ${SBJ}_Anat_bc_ns.Xaff12.1D
+  rm ${SBJ}_Anat_bc_ns.Xat.1D
+fi
+
+# Create Autobox version for visualization
+# ========================================
+3dAutobox -overwrite -input ${SBJ}_Anat_bc_ns+tlrc -prefix  ${SBJ}_Anat_bc_ns.AB
+
+# GZIP All files
+# ==============
+gzip ${SBJ}_Anat*BRIK
+echo -e "\033[0;32m++ INFO: =================================================  \033[0m"
+echo -e "\033[0;32m++ INFO: =========  SCRIPTS FINISHED SUCCESSFULY    ======  \033[0m"
+echo -e "\033[0;32m++ INFO: =================================================  \033[0m"
+
+