Merge 62f2fe3 into 7347e4c

installer/install_shimming_toolbox.sh

@@ -51,10 +51,14 @@ print info "Creating launchers for Python scripts. List of functions available:"
 mkdir -p "$ST_DIR/$BIN_DIR"
 
 for file in "$ST_DIR"/"$PYTHON_DIR"/bin/*st_*; do
-  cp "$file" "$ST_DIR/$BIN_DIR/" # || die "Problem creating launchers!"
+  cp "$file" "$ST_DIR/$BIN_DIR/" || die "Problem creating launchers!"
   print list "$file"
 done
 
+# Dcm2niix is called by dcm2bids through subprocess, we need to create a launcher for it to be found when called from
+# outside the environment (when using st_dicom_to_nifti)
+cp ""$ST_DIR"/"$PYTHON_DIR"/bin/dcm2niix" "$ST_DIR/$BIN_DIR/" || die "Problem creating launchers!"
+
 # Activate the launchers
 export PATH="$ST_DIR/$BIN_DIR:$PATH"
 

shimmingtoolbox/cli/prepare_fieldmap.py

@@ -46,12 +46,18 @@ def prepare_fieldmap_cli(phase, fname_mag, unwrapper, fname_output, autoscale, f
                          gaussian_filter, sigma, verbose):
     """Creates fieldmap (in Hz) from phase images.
 
-    This function accommodates multiple echoes (2 or more) and phase difference. This function also
+    This function accommodates multiple echoes (2 or more) and phase difference. It also
     accommodates 4D phase inputs, where the 4th dimension represents the time, in case multiple
     field maps are acquired across time for the purpose of real-time shimming experiments.
     For non Siemens phase data, see --autoscale-phase option.
 
-    PHASE: Input path of phase nifti file(s), in ascending order: echo1, echo2, etc.
+    PHASE: Input path of phase NIfTI file(s), in ascending order: echo1, echo2, etc. The BIDS metadata JSON file
+    associated with each phase file is required, it will be fetched automatically using the same name as the NIfTI file.
+
+    Example of use (Multiple echoes) : st_prepare_fieldmap phase_echo1.nii.gz phase_echo2.nii.gz phase_echo3.nii.gz
+    --mag mag.nii.gz
+
+    Example of use (Phase difference): st_prepare_fieldmap phasediff.nii.gz --mag mag.nii.gz
     """
     # Set logger level
     set_all_loggers(verbose)