Update README.md

Update README.md from mfcsc.m

README.md

@@ -8,6 +8,10 @@
           Civier O, Sourty M, Calamante F (2023) MFCSC: Novel method to calculate mismatch between functional and structural brain connectomes, 
           and its application for detecting hemispheric functional specialisations. Scientific Reports https://doi.org/10.1038/s41598-022-17213-z
 
+     VERSION
+
+          1.1
+
      USAGE
 
          From Neurodesk (no Matlab license required!):
@@ -28,8 +32,14 @@
 
      PREREQUISITES:
 
+         Matlab 9.8.0.1721703 (R2020a) Update 7 or newer (older versions of Matlab should work as well, but not tested)
          Matlab's Curve Fitting toolbox
 
+             OR
+
+         Neurodesktop 20230324 or newer 
+         (older versions of Neurodesktop should work as well, but not tested; to use in older versions, load from the terminal using: 'ml mfcsc/1.1')
+
      DESCRIPTION
 
          mfcsc receive pairs of functional and structural connectivity
@@ -84,7 +94,7 @@
 
      MANDATORY ARGUMENTS
 
-         FC_SC_LIST
+         FC_SC_LIST (path)
 
          Path to a tab-separated file with two columns.
          The first column lists the files with the connectivity matrices of the FC connectomes
@@ -103,42 +113,42 @@
              paste /tmp/fc_list /tmp/sc_list > path_to_filename
          6) Provide path_to_filename as the FC_SC_LIST argument
 
-         FC_INPUT_DIR
+         FC_INPUT_DIR (path)
 
          The directory containing the files with the FC connectivity matrices
 
-         SC_INPUT_DIR
+         SC_INPUT_DIR (path)
 
          The directory containing the files with the SC connectivity matrices
 
-         OUPTUT_DIR
+         OUPTUT_DIR (path)
 
          The output directory where the mask and mFCSC files are to be
          saved
 
      OPTIONAL ARGUMENTS
 
-         not_in_mask_value
+         not_in_mask_value (any number)
 
          Value that will be assigned to cells in the output matrices that are
          not in the mask. By deafult it is set to -99 to make sure
          people do not report the values in these cells.
          Can be set to 0 to prevent this value from affecting color scaling of plots.    
 
-         is_contra
+         is_contra (true or false)
          
          By default, mFCSC is calculated for ipsilateral connections
          (is_contra = false or omitted)
          set is_contra to true to calculate mFCSC for contralateral connections instead.
 
-         is_keep_neg_fc
+         is_keep_neg_fc (true or false)
 
          By default, mFCSC removes cells that have negative mean FC before 
          fitting the model used to transform SC
          (is_remove_negative_fc = false or omitted)
          set is_keep_negative_fc to true to keep them
 
-         is_symmetrical
+         is_symmetrical (true or false)
 
          By default, only the upper right triangle of the output matrices is
          populated, with the lower triangle being zeroed out.
@@ -147,14 +157,14 @@
          mirroring the upper right triangle into the bottom left triangle
          In both cases, the main diagonal is zeroed out.
 
-         is_figures
+         is_figures (true or false)
 
          By default, do not show figures.
          (is_figures = false or omitted)
          set is_figures to true to print verbose figures with information for QC and debg.
          Not tested. Use at your own risk!
 
-         bct_dir
+         bct_dir (path)
 
          If specified, Matlab will look for the Brain Connectome Toolbox (BCT)
          in this directory instead of the BCT version supplied with
@@ -176,8 +186,8 @@
 
       EXAMPLE
 
-             For the processing performed in the journal article, see:
-             https://osf.io/d7j9n/ under "TESTING MFCSC INSTALLATION"
+         For the processing performed in the journal article, see:
+         https://osf.io/d7j9n/ under "TESTING MFCSC INSTALLATION"
 
       DEVELOPER