Add -first_dir option to multiple Python commands

Original commit message:
"Added option to provide FSL FIRST data to three scripts which would otherwise run that step repeatedly.
Also takes away the FSL dependency in labelsgmfix for Windows users."
Manual cherry-pick of dc6d87b by: Robert E. Smith <robert.smith@florey.edu.au>

python/mrtrix3/commands/5ttgen/fsl.py

@@ -58,6 +58,14 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
                        action='store_true',
                        default=None,
                        help='Indicate that brain masking has already been applied to the input image')
+  options.add_argument('-first_dir',
+                       metavar='/path/to/first/dir',
+                       help='use pre-calculated output of FSL FIRST previously run on input T1-weighted image; '
+                            'data must be defined in the same space as input T1w')
+  options.add_argument('-fast_dir',
+                       metavar='/path/to/fast/dir',
+                       help='use pre-calculated output of FSL FAST previously run on input T1-weighted image; '
+                            'data must be defined in the same space as input T1w')
   parser.flag_mutually_exclusive_options( [ 'mask', 'premasked' ] )
 
 
@@ -190,10 +198,22 @@ def execute(): #pylint: disable=unused-variable
   # Finish branching based on brain masking
 
   # FAST
-  if fast_t2_input:
-    run.command(f'{fast_cmd} -S 2 {fast_t2_input} {fast_t1_input}')
-  else:
-    run.command(f'{fast_cmd} {fast_t1_input}')
+  if not app.args.fast_dir:
+    if fast_t2_input:
+      run.command(f'{fast_cmd} -S 2 {fast_t2_input} {fast_t1_input}')
+    else:
+      run.command(f'{fast_cmd} {fast_t1_input}')
+  if app.args.fast_dir:
+    if not os.path.isdir(os.path.abspath(app.args.fast_dir)):
+      app.error('FAST directory cannot be found, please check path')
+    else:
+      fast_output_prefix = fast_t1_input.split('.')[0]
+      fast_csf_input = fsl.find_image(app.args.fast_dir + '/' + fast_output_prefix + '_pve_0.nii.gz')
+      fast_gm_input = fsl.find_image(app.args.fast_dir + '/' + fast_output_prefix + '_pve_1.nii.gz')
+      fast_wm_input = fsl.find_image(app.args.fast_dir + '/' + fast_output_prefix + '_pve_2.nii.gz')
+      run.command('cp ' + fast_csf_input + ' .' )
+      run.command('cp ' + fast_gm_input + ' .' )
+      run.command('cp ' + fast_wm_input + ' .' )
 
   # FIRST
   first_input = 'T1.nii'
@@ -205,10 +225,19 @@ def execute(): #pylint: disable=unused-variable
   first_brain_extracted_option = ['-b'] if app.ARGS.premasked else []
   first_debug_option = [] if app.DO_CLEANUP else ['-d']
   first_verbosity_option = ['-v'] if app.VERBOSITY == 3 else []
-  run.command([first_cmd, '-m', 'none', '-s', ','.join(sgm_structures), '-i', first_input, '-o', 'first']
-              + first_brain_extracted_option
-              + first_debug_option
-              + first_verbosity_option)
+  if not app.args.first_dir:
+    run.command([first_cmd, '-m', 'none', '-s', ','.join(sgm_structures), '-i', first_input, '-o', 'first']
+                + first_brain_extracted_option
+                + first_debug_option
+                + first_verbosity_option)
+  elif app.args.first_dir:
+    if not os.path.isdir(os.path.abspath(app.args.first_dir)):
+      app.error('FIRST directory cannot be found, please check path')
+    else:
+      for struct in sgm_structures:
+        vtk_in_path = 'first-' + struct + '_first.vtk'
+        run.command('cp ' + app.args.first_dir + '/' + vtk_in_path + ' .')
+      run.command('cp -r ' + app.args.first_dir + '/first.logs' + ' .')
   fsl.check_first('first', sgm_structures)
 
   # Convert FIRST meshes to partial volume images

python/mrtrix3/commands/5ttgen/hsvs.py

@@ -56,6 +56,10 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
                       action='store_true',
                       default=None,
                       help='Classify the brainstem as white matter')
+  parser.add_argument('-first_dir',
+                      metavar='/path/to/first/dir',
+                      help='utilise pre-calculated output of FSL FIRST run on input T1-weighted image; '
+                           'must have been computed in the same space as FreeSurfer T1w')
   parser.add_citation('Smith, R.; Skoch, A.; Bajada, C.; Caspers, S.; Connelly, A. '
                       'Hybrid Surface-Volume Segmentation for improved Anatomically-Constrained Tractography. '
                       'In Proc OHBM 2020')
@@ -102,6 +106,7 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
                     (57,  5, 'Right-Lesion'),
                     (62,  4, 'Right-vessel'),
                     (72,  4, '5th-Ventricle'),
+		                (77,  5, 'WM-Hypointensities'),
                     (250, 3, 'Fornix') ]
 
 
@@ -189,7 +194,6 @@ def execute(): #pylint: disable=unused-variable
   mri_dir = os.path.join(app.ARGS.input, 'mri')
   check_dir(surf_dir)
   check_dir(mri_dir)
-  #aparc_image = os.path.join(mri_dir, 'aparc+aseg.mgz')
   aparc_image = 'aparc.mif'
   mask_image = os.path.join(mri_dir, 'brainmask.mgz')
   reg_file = os.path.join(mri_dir, 'transforms', 'talairach.xfm')
@@ -557,7 +561,16 @@ def execute(): #pylint: disable=unused-variable
       from_first = { key: value for key, value in from_first.items() if 'Hippocampus' not in value and 'Amygdala' not in value }
     if thalami_method != 'first':
       from_first = { key: value for key, value in from_first.items() if 'Thalamus' not in value }
-    run.command([first_cmd, '-s', ','.join(from_first.keys()), '-i', 'T1.nii', '-b', '-o', 'first'])
+    if not app.ARGS.first_dir:
+        run.command([first_cmd, '-s', ','.join(from_first.keys()), '-i', 'T1.nii', '-b', '-o', 'first'])
+    elif app.ARGS.first_dir:
+      if not os.path.isdir(os.path.abspath(app.ARGS.first_dir)):
+        app.error('FIRST directory cannot be found, please check path')
+      else:
+        for key, value in from_first.items():
+          vtk_in_path = 'first-' + key + '_first.vtk'
+          run.command('cp ' + app.ARGS.first_dir + '/' + vtk_in_path + ' .')
+          run.command('cp -r ' + app.ARGS.first_dir + '/first.logs' + ' .')
     fsl.check_first('first', from_first.keys())
     app.cleanup(glob.glob('T1_to_std_sub.*'))
     progress = app.ProgressBar('Mapping FIRST segmentations to image', 2*len(from_first))

python/mrtrix3/commands/labelsgmfirst.py

@@ -54,6 +54,10 @@ def usage(cmdline): #pylint: disable=unused-variable
                        default=None,
                        help='Consider the amygdalae and hippocampi as sub-cortical grey matter structures,'
                             ' and also replace their estimates with those from FIRST')
+  cmdline.add_argument('-first_dir',
+                       metavar='/path/to/first/dir',
+                       help='use pre-calculated output of FSL FIRST previously run on T1-weighted image; '
+                            'must be defined in the same space as input FreeSurfer parcellation')
 
 
 
@@ -63,23 +67,24 @@ def usage(cmdline): #pylint: disable=unused-variable
 def execute(): #pylint: disable=unused-variable
   from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
   from mrtrix3 import app, fsl, image, path, run, utils #pylint: disable=no-name-in-module, import-outside-toplevel
-
-  if utils.is_windows():
-    raise MRtrixError('Script cannot run on Windows due to FSL dependency')
+  if not app.ARGS.first_dir:
+  	if utils.is_windows():
+    	  raise MRtrixError('Script cannot run on Windows due to FSL dependency')
 
   image.check_3d_nonunity(app.ARGS.t1)
 
-  fsl_path = os.environ.get('FSLDIR', '')
-  if not fsl_path:
-    raise MRtrixError('Environment variable FSLDIR is not set; '
-                      'please run appropriate FSL configuration script')
+  if not app.ARGS.first_dir:
+    fsl_path = os.environ.get('FSLDIR', '')
+    if not fsl_path:
+      raise MRtrixError('Environment variable FSLDIR is not set; '
+                        'please run appropriate FSL configuration script')
 
-  first_cmd = fsl.exe_name('run_first_all')
+  	first_cmd = fsl.exe_name('run_first_all')
 
-  first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin')
-  if not os.path.isdir(first_atlas_path):
-    raise MRtrixError('Atlases required for FSL\'s FIRST program not installed; '
-                      'please install fsl-first-data using your relevant package manager')
+    first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin')
+    if not os.path.isdir(first_atlas_path):
+      raise MRtrixError('Atlases required for FSL\'s FIRST program not installed; '
+                        'please install fsl-first-data using your relevant package manager')
 
   # Want a mapping between FreeSurfer node names and FIRST structure names
   # Just deal with the 5 that are used in ACT; FreeSurfer's hippocampus / amygdala segmentations look good enough.
@@ -118,8 +123,17 @@ def execute(): #pylint: disable=unused-variable
   first_input_is_brain_extracted = ''
   if app.ARGS.premasked:
     first_input_is_brain_extracted = ' -b'
-  structures_string = ','.join(structure_map.keys())
-  run.command(f'{first_cmd} -m none -s {structures_string} -i T1.nii {first_input_is_brain_extracted} -o first')
+  if not app.ARGS.first_dir:
+	  structures_string = ','.join(structure_map.keys())
+    run.command(f'{first_cmd} -m none -s {structures_string} -i T1.nii {first_input_is_brain_extracted} -o first')
+  elif app.ARGS.first_dir:
+    if not os.path.isdir(os.path.abspath(app.ARGS.first_dir)):
+      app.error('FIRST directory cannot be found, please check path')
+    else:
+      for key, value in structure_map.items():
+          vtk_in_path = 'first-' + key + '_first.vtk'
+          run.command('cp ' + app.ARGS.first_dir + '/' + vtk_in_path + ' .')
+          run.command('cp -r ' + app.ARGS.first_dir + '/first.logs' + ' .')
   fsl.check_first('first', structure_map.keys())
 
   # Generate an empty image that will be used to construct the new SGM nodes