update cli for preprocess

demos/openneuro/ds000001_run.sh

@@ -0,0 +1,10 @@
+#! /bin/bash
+
+# script to run the demo via the command line
+cd ../..
+
+bidspm demos/openneuro/inputs/ds000001 demos/openneuro/outputs/ds000001/derivatives subject \
+    --action preprocess \
+    --task balloonanalogrisktask \
+    --fwhm 8 \
+    --participant_label 01 02 03

src/bidspm.py

@@ -429,9 +429,11 @@ def run_command(cmd: str, platform: str | None = None) -> int:
 
     if platform is None:
         if Path(matlab()).exists():
+            log.info(f"Using matlab found at: {matlab()}")
             platform = matlab()
             cmd = cmd.replace(new_line, ", ")
         else:
+            log.info("Using octave")
             platform = "octave"
 
     if platform == "octave":

src/cli/cliPreprocess.m

@@ -26,6 +26,21 @@ function cliPreprocess(varargin)
   validate(args);
 
   opt = getOptionsFromCliArgument(args);
+
+  if iscellstr(opt.taskName)
+    if numel(opt.taskName) > 1
+      logger('WARNING', ...
+             ['Too many tasks for preprocessing.\n', ...
+              'bidspm can only preprocess one task at time.\n', ...
+              'To preprocess several tasks at once use fMRIprep.\n', ...
+              'Only taking the first one: ', opt.taskName{1}], ...
+             'options', opt, ...
+             'filename', mfilename, ...
+             'id', id);
+    end
+    opt.taskName = opt.taskName{1};
+  end
+
   opt.pipeline.type = 'preproc';
   opt = checkOptions(opt);
 

src/cli/inputParserForPreprocess.m

@@ -10,11 +10,11 @@
   isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
   isLogical = @(x) islogical(x) && numel(x) == 1;
   isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);  %#ok<*ISCLSTR>
-  isEmptyOrisChar = @(x) isempty(x) || ischar(x);  %#ok<*ISCLSTR>
+  isEmptyOrisCharOrCellstr = @(x) isempty(x) || ischar(x) || iscellstr(x);  %#ok<*ISCLSTR>
   isCellStr = @(x) iscellstr(x);
 
   addParameter(args, 'space', {}, isCellStr);
-  addParameter(args, 'task', '', isEmptyOrisChar);
+  addParameter(args, 'task', '', isEmptyOrisCharOrCellstr);
   addParameter(args, 'fwhm', 6, isPositiveScalar);
   addParameter(args, 'dry_run', false, isLogical);
   addParameter(args, 'anat_only', false, isLogical);

src/matlab.py

@@ -10,4 +10,4 @@ def matlab() -> str:
 
     The 'matlab' executable is usually in the 'bin' subdirectory.
     """
-    return "/usr/local/MATLAB/R2018a/ bin/matlab"
+    return "/usr/local/MATLAB/R2018a/bin/matlab"