run_fastsurfer.sh

- Fix for bash-3.2 (|& => 2&>1 |)
- Add warning if T2 is passed, but biasfield is skipped --no_biasfield

run_fastsurfer.sh

@@ -859,7 +859,7 @@ if [[ "$run_seg_pipeline" == "1" ]]
       then
         printf "INFO: Copying T2 file to %s..." "${t2_copy_file}" | tee -a "$seg_log"
         cmd=("nib-convert" "$t2" "$t2_copy_file")
-        "${cmd[@]}" |& tee -a "$seg_log"
+        "${cmd[@]}" 2>&1 | tee -a "$seg_log"
         echo "Done." | tee -a "$seg_log"
     fi
 
@@ -918,7 +918,7 @@ if [[ "$run_seg_pipeline" == "1" ]]
           echo "INFO: Running N4 bias-field correction of the t2" | tee -a "$seg_log"
           cmd=($python "${reconsurfdir}/N4_bias_correct.py" "--in" "$t2"
                --out "$norm_name_t2" --threads "$threads" --uchar)
-          echo "${cmd[@]}" |& tee -a "$seg_log"
+          echo "${cmd[@]}" | tee -a "$seg_log"
           "${cmd[@]}"
           if [[ "${PIPESTATUS[0]}" -ne 0 ]]
             then
@@ -933,7 +933,11 @@ if [[ "$run_seg_pipeline" == "1" ]]
         echo "INFO: Robustly rescaling $t2 to uchar ($norm_name_t2), which is assumed to already be biasfield corrected." | tee -a "$seg_log"
         cmd=($python "${fastsurfercnndir}/data_loader/conform.py" --no_force_lia
              --no_force_vox_size --no_force_img_size "$t2" "$norm_name_t2")
-        "${cmd[@]}" |& tee -a "$seg_log"
+        echo "WARNING: --no_biasfield is activated, but FastSurfer does not check, if "
+        echo "  passed T2 image is properly scaled and typed. T2 needs to be uchar and"
+        echo "  robustly scaled (see FastSurferCNN/utils/data_loader/conform.py)!"
+        # TODO implement/validate no changes to affine parameters for conform
+        # "${cmd[@]}" 2>&1 | tee -a "$seg_log"
       fi
     fi
 
@@ -978,11 +982,11 @@ if [[ "$run_seg_pipeline" == "1" ]]
           cmd+=("$t1")
           if [[ -n "$t2" ]] ; then cmd+=(--t2 "$t2"); fi
         fi
-        echo "${cmd[@]}" |& tee -a "$seg_log"
+        echo "${cmd[@]}" 2>&1 | tee -a "$seg_log"
         "${cmd[@]}"
         if [[ "${PIPESTATUS[0]}" -ne 0 ]]
           then
-            echo "ERROR: Hypothalamus Segmentation failed" |& tee -a "$seg_log"
+            echo "ERROR: Hypothalamus Segmentation failed" | tee -a "$seg_log"
             exit 1
         fi
     fi