Updated command line parsing and added hint for common error

README.md

@@ -68,7 +68,8 @@ Use `--help` to see all options.
 Notes on the steps: 
 * Overall, make sure your scripts are executable:
 
-      chmod -R 777 _/enigma/Parent_Folder/scripts
+      chmod -R +x _/enigma/Parent_Folder/scripts
+* If the error `./enigma_fs_wrapper_script.sh: line 143: printf: ****.*: invalid number` appears try running the script again with the prefix `LC_NUMERIC=C`.
 * The extraction steps (i.e., Step 1 & 2) have been updated in April 2021 to correctly extract the full intracranial volume (ICV) value using %f to avoid rounding up of the values when the CSV is opened and edited. The result of these steps will be three comma-separated (CSV) files (“LandRvolumes.csv” for the subcortical measures, “CorticalMeasuresENIGMA_ThickAvg.csv” and “CorticalMeasuresENIGMA_SurfAvg.csv” for the cortical measures) that can be opened in your favorite spreadsheet application (i.e., Excel). After running the script, open the CSV files and make sure that only subjects are listed in the rows of the file. Sometimes if there are other folders in your parent directory those folders can sometimes become included in your final files, if that happens just delete those from your CSV files and save. [When you edit the files in Excel, be sure to keep them in CSV format when you save!] The first row in all csv's are headers describing the extracted regions and names for each column. Each row after the first gives the subcortical volumes (in mm3), cortical thickness average or total surface area measures respectively for each subject found in your FreeSurfer directory.  
 * To make the visual QC process faster, this script will create webpages in the same folder as your respective QC outputs: multiple webpages (e.g. "ENIGMA_Amyg_volume_QC.html") and one per subcortical ROI and one called "ENIGMA_Subortical_QC.html" for the Subcortical PNGs, "ENIGMA_Cortical_QC.html" for the Cortical Internal PNGs, and "QC_external.html" for the Cortical External PNGs.
 You can open these in any browser, just make sure all of the .png files are in the same folder if you decide to move the html file to a different location (like a local computer). Zoom in and out of the window to adjust the size of the images per row, or click on a subject’s file to see a larger version. To open the webpage in a browser in a Linux environment you can probably just type the following from the QC folder, e.g.,:

enigma_fs_wrapper_script.sh

@@ -9,7 +9,7 @@ function Usage(){
 
 Usage:
 
-`basename $0` --subjects <subject.txt> --fsdir </freesufer/path> --outdir <output/directory> --script <ENIGMA/scripts/path> --matlab <MATLAB/path> --step_N 1 <other options>
+`basename $0` --subjects <subject.txt> --fsdir </freesufer/path> --outdir <output/directory> --script <ENIGMA/scripts/path> --matlab <MATLAB/path> --step_N 1 <other options> --fs7 <other options>
 
 Mandatory arguments:
 	--subjects	Provide a list of subjects stored in a text file
@@ -109,7 +109,25 @@ done
 
 # Checking mandatory arguments
 if [[ -z ${subjectIDs} || -z ${fs_dir} ||  -z ${scripts_dir} || -z ${matlab_dir} || -z ${out_dir} || -z ${fs_version} ]]; then
-	echo "ERROR: --subjects --fsdir, --script, --matlab, --outdir are mandatory arguments. Please see usage: \n"
+  if [[ -z ${subjectIDs} ]]; then
+    echo "--subjects missing" >&2
+  fi
+  if [[ -z ${fs_dir} ]]; then
+    echo "--fsdir missing"
+  fi
+  if [[ -z ${scripts_dir} ]]; then
+    echo "--script missing"
+  fi
+  if [[ -z ${matlab_dir} ]]; then
+    echo "--matlab missing";
+  fi
+  if [[ -z ${out_dir} ]]; then
+    echo "--outdir missing"
+  fi
+  if [[ -z ${fs_version} ]]; then
+    echo "--fs7 missing"
+  fi
+	echo "ERROR: --subjects --fsdir, --script, --matlab, --outdir, --fs7 are mandatory arguments. Please see usage:"
     Usage >&2
 fi