FIXED func mask overestimates, REMOVED filtering for multi-echo

functions/02_proc-func.sh

@@ -6,7 +6,8 @@
 # and incorporation to mica-pipe by Raul (August-September 2020)
 # and addition of a bunch of fancy flags by Jessica (October-November 2020)
 # and updated mapping by Jordan (March 2023)
-#
+# 
+
 # Resting state fMRI processing with bash:
 #
 # Preprocessing workflow for func.
@@ -82,7 +83,8 @@ else
   BIDSanat="${idBIDS}"
   dir_anat="${proc_struct}"
 fi
-subject_dir
+
+
 dir_volum="${subject_dir}/parc"
 T1_seg_subcortex="${dir_volum}/${BIDSanat}_space-nativepro_T1w_atlas-subcortical.nii.gz"
 T1_seg_cerebellum="${dir_volum}/${BIDSanat}_space-nativepro_T1w_atlas-cerebellum.nii.gz"
@@ -454,19 +456,15 @@ if [[ ! -f "${func_volum}/${idBIDS}${func_lab}_preproc".nii.gz ]]; then
         tmp_t1w_brain_res="${tmp}/nativepro_brain_rescaled.nii.gz"
         tmp_affineStr="${tmp}/from-nativepro_to-mainScan01_"
         tmp_aff_mat="${tmp_affineStr}0GenericAffine.mat"
+        tmp_func_strip="${tmp}/mainScan01_mean_stripped.nii.gz"
         tmp_func_mask="${tmp}/mainScan01_mean_mask.nii.gz"
 
-        # Create a loose mask for tedana
+        # Create a tight mask for tedana
         fslmaths "${scans4tedana[0]}" -Tmean "${tmp_func_mean}"
-        voxels=$(mrinfo "${tmp_func_mean}" -spacing); voxels="${voxels// /,}"
-        Do_cmd flirt -applyisoxfm "${voxels}" -in "${T1nativepro_brain}" -ref "${T1nativepro_brain}" -out "${tmp_t1w_brain_res}"
-        # [fixedImage,movingImage,initializationFeature]
-        centeralign="[${tmp_func_mean},${tmp_t1w_brain_res},0]"
-        Do_cmd antsRegistrationSyNQuick.sh -d 3 -m "$tmp_t1w_brain_res" -f "$tmp_func_mean" -o "$tmp_affineStr" -t a -n "$threads" -p d -i ${centeralign}
-        Do_cmd antsApplyTransforms -d 3 -i "$T1nativepro_mask" -r "$tmp_func_mean" -t "$tmp_aff_mat" -o "${tmp_func_mask}" -u int
+        Do_cmd mri_synthstrip -i "${tmp_func_mean}" -o "${tmp_func_strip}" -m "${tmp_func_mask}"
 
         # Run tedana
-        tedana -d $(printf "%s " "${scans4tedana[@]}") -e $(printf "%s " "${EchoTime[@]}") --out-dir "${tedana_dir}" --mask "${tmp_func_mask}"
+        tedana -d $(printf "%s " "${scans4tedana[@]}") -e $(printf "%s " "${EchoTime[@]}") --out-dir "${tedana_dir}" --mask "${tmp_func_mask}"        
 
         # Overwite the motion corrected to insert this into topup.
         ## TODO: func_topup should take proper input arguments instead of relying on architecture implemented in other functions.
@@ -507,13 +505,18 @@ else
     Info "Subject ${id} has a brain masked from func"; ((Nsteps++)); ((N++))
 fi
 
-# High-pass filter - Remove all frequencies EXCEPT those in the range
-if [[ ! -f "${func_volum}/${idBIDS}${func_lab}_tSNR.nii.gz" ]]; then ((N++))
-    Info "High pass filter"
-    Do_cmd 3dTproject -input "${func_nii}" -prefix "$fmri_HP" -passband 0.01 666
-        if [[ -f "${fmri_HP}" ]] ; then ((Nsteps++)); fi
+# High-pass filter - Remove all frequencies in the range (only for single echo processing)
+# retaining frequencies above 0.01Hz
+if [[ ${acq} == "se" ]]; then 
+    if [[ ! -f "${func_volum}/${idBIDS}${func_lab}_tSNR.nii.gz" ]]; then ((N++))
+        Info "High pass filter"
+        Do_cmd 3dTproject -input "${func_nii}" -prefix "$fmri_HP" -stopband 0 0.0099
+            if [[ -f "${fmri_HP}" ]] ; then ((Nsteps++)); fi
+    else
+        Info "Subject ${id} has Highpass filter"; ((Nsteps++)); ((N++))
+    fi
 else
-    Info "Subject ${id} has High-pass filter"; ((Nsteps++)); ((N++))
+    fmri_HP=${func_nii} # no need to filter post tedana
 fi
 
 #------------------------------------------------------------------------------#