Refinements to 99af403

Manual application of changes in #2330 by: Robert E. Smith <robert.smith@florey.edu.au>

docs/reference/commands/5ttgen.rst

@@ -213,6 +213,10 @@ Options specific to the "fsl" algorithm
 
 - **-premasked** Indicate that brain masking has already been applied to the input image
 
+- **-first_dir /path/to/first/dir** 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
+
+- **-fast_dir /path/to/fast/dir** 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; filename prefix must be "T1_BET"
+
 Options common to all 5ttgen algorithms
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -401,6 +405,8 @@ Options
 
 - **-white_stem** Classify the brainstem as white matter
 
+- **-first_dir /path/to/first/dir** utilise pre-calculated output of FSL FIRST run on input T1-weighted image; must have been computed in the same space as FreeSurfer T1w
+
 Options common to all 5ttgen algorithms
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

docs/reference/commands/labelsgmfirst.rst

@@ -27,6 +27,8 @@ Options
 
 - **-sgm_amyg_hipp** Consider the amygdalae and hippocampi as sub-cortical grey matter structures, and also replace their estimates with those from FIRST
 
+- **-first_dir /path/to/first/dir** use pre-calculated output of FSL FIRST previously run on T1-weighted image; must be defined in the same space as input FreeSurfer parcellation
+
 Additional standard options for Python scripts
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

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

@@ -65,7 +65,8 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
   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')
+                            'data must be defined in the same space as input T1w; '
+                            'filename prefix must be "T1_BET"')
   parser.flag_mutually_exclusive_options( [ 'mask', 'premasked' ] )
 
 
@@ -198,22 +199,21 @@ def execute(): #pylint: disable=unused-variable
   # Finish branching based on brain masking
 
   # FAST
-  if not app.args.fast_dir:
+  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 + ' .' )
+  if app.ARGS.fast_dir:
+    if not os.path.isdir(os.path.abspath(app.ARGS.fast_dir)):
+      raise MRtrixError('FAST directory cannot be found, please check path')
+    fast_output_prefix = fast_t1_input.split('.')[0]
+    fast_csf_input = fast_output_prefix + 'pve_0.nii.gz'
+    fast_gm_input = fast_output_prefix + '_pve_1.nii.gz'
+    fast_wm_input = fast_output_prefix + '_pve_2.nii.gz'
+    run.command('cp ' + path.from_user(fast_csf_input) + ' ' + path.to_scratch(fast_csf_input))
+    run.command('cp ' + path.from_user(fast_gm_input) + ' ' + path.to_scratch(fast_gm_input))
+    run.command('cp ' + path.from_user(fast_wm_input) + ' ' + path.to_scratch(fast_wm_input))
 
   # FIRST
   first_input = 'T1.nii'
@@ -225,19 +225,18 @@ 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 []
-  if not app.args.first_dir:
+  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' + ' .')
+  elif app.ARGS.first_dir:
+    if not os.path.isdir(os.path.abspath(app.ARGS.first_dir)):
+      raise MRtrixError('FIRST directory cannot be found, please check path')
+    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

@@ -13,8 +13,6 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-
-
 import glob, os, re, shutil
 from mrtrix3 import MRtrixError
 from mrtrix3 import app, fsl, image, path, run
@@ -566,11 +564,10 @@ def execute(): #pylint: disable=unused-variable
     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' + ' .')
+      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

@@ -68,8 +68,8 @@ 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 not app.ARGS.first_dir:
-  	if utils.is_windows():
-    	  raise MRtrixError('Script cannot run on Windows due to FSL dependency')
+    if utils.is_windows():
+      raise MRtrixError('Script cannot run on Windows due to FSL dependency')
 
   image.check_3d_nonunity(app.ARGS.t1)
 
@@ -79,7 +79,7 @@ def execute(): #pylint: disable=unused-variable
       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):
@@ -124,7 +124,7 @@ def execute(): #pylint: disable=unused-variable
   if app.ARGS.premasked:
     first_input_is_brain_extracted = ' -b'
   if not app.ARGS.first_dir:
-	  structures_string = ','.join(structure_map.keys())
+    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)):