diff --git a/python/mrtrix3/commands/5ttgen/fsl.py b/python/mrtrix3/commands/5ttgen/fsl.py
index 9eaf631d8d..98dcde4d17 100644
--- a/python/mrtrix3/commands/5ttgen/fsl.py
+++ b/python/mrtrix3/commands/5ttgen/fsl.py
@@ -59,10 +59,12 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
                        default=None,
                        help='Indicate that brain masking has already been applied to the input image')
   options.add_argument('-first_dir',
+                       type=app.Parser.DirectoryIn(),
                        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',
+                       type=app.Parser.DirectoryIn(),
                        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; '
@@ -81,11 +83,42 @@ def execute(): #pylint: disable=unused-variable
     raise MRtrixError('Environment variable FSLDIR is not set; '
                       'please run appropriate FSL configuration script')
 
+  sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ]
+  if app.ARGS.sgm_amyg_hipp:
+    sgm_structures.extend([ 'L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp' ])
+
   bet_cmd = fsl.exe_name('bet')
-  fast_cmd = fsl.exe_name('fast')
-  first_cmd = fsl.exe_name('run_first_all')
   ssroi_cmd = fsl.exe_name('standard_space_roi')
 
+  fast_cmd = None
+  fast_pve_images = []
+  if app.ARGS.fast_dir:
+    pve_candidates = sorted(app.ARGS.fast_dir.glob('*_pve_*.nii*'))
+    if len(pve_candidates) != 3:
+      raise MRtrixError(f'Expected three partial volume images in FAST directory {app.ARGS.fast_dir}; '
+                        f'found {len(pve_candidates)}')
+    for index, filepath in enumerate(pve_candidates):
+      if not f'_pve_{index}.nii' in filepath:
+        raise MRtrixError('Expected FAST PVE image "*_pve_*.nii*"; '
+                          f'found "{filepath.name}"')
+      fast_pve_images.append(filepath.name)
+  else:
+    try:
+      fast_cmd = fsl.exe_name('fast')
+    except MRtrixError as e:
+      raise MRtrixError('FSL program "fast" is requisite if -fast_dir option is not used') from e
+
+  first_cmd = None
+  first_object_files = []
+  if app.ARGS.first_dir:
+    first_prefix = fsl.check_first_input(app.ARGS.first_dir, sgm_structures)
+    first_object_files = [app.ARGS.first_dir / f'{first_prefix}{struct}_first.vtk' for struct in sgm_structures]
+  else:
+    try:
+      first_cmd = fsl.exe_name('run_first_all')
+    except MRtrixError as e:
+      raise MRtrixError('FSL program "run_first_all" is requisite if -first_dir option is not used') from e
+
   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; '
@@ -107,15 +140,20 @@ def execute(): #pylint: disable=unused-variable
       raise MRtrixError('Provided T2w image does not match input T1w image')
     run.command(['mrconvert', app.ARGS.t2, 'T2.nii', '-strides', '-1,+2,+3'],
                 preserve_pipes=True)
-
-  sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ]
-  if app.ARGS.sgm_amyg_hipp:
-    sgm_structures.extend([ 'L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp' ])
+  if app.ARGS.fast_dir:
+    for name in fast_pve_images:
+      shutil.copyfile(app.ARGS.fast_dir / name, app.SCRATCH_DIR / name)
+  if app.ARGS.first_dir:
+    progress = app.ProgressBar('Importing pre-calculated FIRST segmentations', len(sgm_structures))
+    for filename in first_object_files:
+      run.function(shutil.copyfile, app.ARGS.first_dir / filename, app.SCRATCH_DIR / filename)
+      progress.increment()
+    progress.done()
 
   t1_spacing = image.Header('input.mif').spacing()
   upsample_for_first = False
   # If voxel size is 1.25mm or larger, make a guess that the user has erroneously re-gridded their data
-  if math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0/3.0) > 1.225:
+  if not app.ARGS.first_dir and math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0/3.0) > 1.225:
     app.warn(f'Voxel size larger than expected for T1-weighted images ({t1_spacing}); '
              f'note that ACT does not require re-gridding of T1 image to DWI space, and indeed '
              f'retaining the original higher resolution of the T1 image is preferable')
@@ -200,53 +238,41 @@ def execute(): #pylint: disable=unused-variable
 
   # FAST
   if not app.ARGS.fast_dir:
+    assert not fast_pve_images
     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)):
-      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))
+    for index in range(0, 3):
+      fast_pve_images.append(fsl.find_image(f'{fast_t1_input}_pve_{index}'))
 
   # FIRST
-  first_input = 'T1.nii'
-  if upsample_for_first:
-    app.warn('Generating 1mm isotropic T1 image for FIRST in hope of preventing failure, '
-             'since input image is of lower resolution')
-    run.command('mrgrid T1.nii regrid T1_1mm.nii -voxel 1.0 -interp sinc')
-    first_input = 'T1_1mm.nii'
-  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 []
+  # TODO Preferably find a suitable reference image inside the FIRST directory
+  first_reference = 'T1.nii'
   if not app.ARGS.first_dir:
-    run.command([first_cmd, '-m', 'none', '-s', ','.join(sgm_structures), '-i', first_input, '-o', 'first']
+    assert not first_object_files
+    if upsample_for_first:
+      app.warn('Generating 1mm isotropic T1 image for FIRST in hope of preventing failure, '
+              'since input image is of lower resolution')
+      run.command('mrgrid T1.nii regrid T1_1mm.nii -voxel 1.0 -interp sinc')
+      first_reference = 'T1_1mm.nii'
+    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_reference, '-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)):
-      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)
+    fsl.check_first_output('first', sgm_structures)
+    first_object_files = [f'first-{struct}_first.vtk' for struct in sgm_structures]
 
   # Convert FIRST meshes to partial volume images
   pve_image_list = [ ]
   progress = app.ProgressBar('Generating partial volume images for SGM structures', len(sgm_structures))
-  for struct in sgm_structures:
+  for struct, vtk_in_path in zip(sgm_structures, first_object_files):
     pve_image_path = f'mesh2voxel_{struct}.mif'
-    vtk_in_path = f'first-{struct}_first.vtk'
     vtk_temp_path = f'{struct}.vtk'
-    run.command(['meshconvert', vtk_in_path, vtk_temp_path, '-transform', 'first2real', first_input])
+    run.command(['meshconvert', vtk_in_path, vtk_temp_path, '-transform', 'first2real', first_reference])
     run.command(['mesh2voxel', vtk_temp_path, fast_t1_input, pve_image_path])
     pve_image_list.append(pve_image_path)
     progress.increment()
@@ -255,24 +281,20 @@ def execute(): #pylint: disable=unused-variable
                'mrcalc', '-', '1.0', '-min', 'all_sgms.mif'])
 
   # Combine the tissue images into the 5TT format within the script itself
-  fast_output_prefix = fast_t1_input.split('.')[0]
-  fast_csf_output = fsl.find_image(f'{fast_output_prefix}_pve_0')
-  fast_gm_output = fsl.find_image(f'{fast_output_prefix}_pve_1')
-  fast_wm_output = fsl.find_image(f'{fast_output_prefix}_pve_2')
   # Step 1: Run LCC on the WM image
-  run.command(f'mrthreshold {fast_wm_output} - -abs 0.001 | '
+  run.command(f'mrthreshold {fast_pve_images[2]} - -abs 0.001 | '
               f'maskfilter - connect - -connectivity | '
               f'mrcalc 1 - 1 -gt -sub remove_unconnected_wm_mask.mif -datatype bit')
   # Step 2: Generate the images in the same fashion as the old 5ttgen binary used to:
   #   - Preserve CSF as-is
   #   - Preserve SGM, unless it results in a sum of volume fractions greater than 1, in which case clamp
   #   - Multiply the FAST volume fractions of GM and CSF, so that the sum of CSF, SGM, CGM and WM is 1.0
-  run.command(f'mrcalc {fast_csf_output} remove_unconnected_wm_mask.mif -mult csf.mif')
+  run.command(f'mrcalc {fast_pve_images[0]} remove_unconnected_wm_mask.mif -mult csf.mif')
   run.command('mrcalc 1.0 csf.mif -sub all_sgms.mif -min sgm.mif')
-  run.command(f'mrcalc 1.0 csf.mif sgm.mif -add -sub {fast_gm_output} {fast_wm_output} -add -div multiplier.mif')
+  run.command(f'mrcalc 1.0 csf.mif sgm.mif -add -sub {fast_pve_images[1]} {fast_pve_images[2]} -add -div multiplier.mif')
   run.command('mrcalc multiplier.mif -finite multiplier.mif 0.0 -if multiplier_noNAN.mif')
-  run.command(f'mrcalc {fast_gm_output} multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif')
-  run.command(f'mrcalc {fast_wm_output} multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif')
+  run.command(f'mrcalc {fast_pve_images[1]} multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif')
+  run.command(f'mrcalc {fast_pve_images[2]} multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif')
   run.command('mrcalc 0 wm.mif -min path.mif')
   run.command('mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | '
               'mrconvert - combined_precrop.mif -strides +2,+3,+4,+1')
diff --git a/python/mrtrix3/commands/5ttgen/hsvs.py b/python/mrtrix3/commands/5ttgen/hsvs.py
index 7ab4e59713..a71a7364d9 100644
--- a/python/mrtrix3/commands/5ttgen/hsvs.py
+++ b/python/mrtrix3/commands/5ttgen/hsvs.py
@@ -55,6 +55,7 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable
                       default=None,
                       help='Classify the brainstem as white matter')
   parser.add_argument('-first_dir',
+                      type=app.Parser.DirectoryIn(),
                       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')
@@ -182,7 +183,9 @@ def execute(): #pylint: disable=unused-variable
 
   # Most freeSurfer files will be accessed in-place; no need to pre-convert them into the temporary directory
   # However convert aparc image so that it does not have to be repeatedly uncompressed
-  run.command(['mrconvert', os.path.join(app.ARGS.input, 'mri', 'aparc+aseg.mgz'), 'aparc.mif'],
+  # TODO See if this can be deferred until later
+  aparc_image = 'aparc.mif'
+  run.command(['mrconvert', os.path.join(app.ARGS.input, 'mri', 'aparc+aseg.mgz'), aparc_image],
               preserve_pipes=True)
   if app.ARGS.template:
     run.command(['mrconvert', app.ARGS.template, 'template.mif', '-axes', '0,1,2'],
@@ -192,10 +195,8 @@ 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 = 'aparc.mif'
   mask_image = os.path.join(mri_dir, 'brainmask.mgz')
   reg_file = os.path.join(mri_dir, 'transforms', 'talairach.xfm')
-  check_file(aparc_image)
   check_file(mask_image)
   check_file(reg_file)
   template_image = 'template.mif' if app.ARGS.template else aparc_image
@@ -220,17 +221,22 @@ def execute(): #pylint: disable=unused-variable
       else:
         fast_suffix = '.nii.gz'
     else:
-      app.warn('Could not find FSL program fast; script will not use fast for cerebellar tissue segmentation')
-    # Verify FIRST availability
+      app.warn('Could not find FSL program fast; '
+               'script will not use fast for cerebellar tissue segmentation')
+  else:
+    app.warn('Environment variable FSLDIR is not set; '
+             'script will run without FSL components')
+  # Verify that FIRST data will be available,
+  #   whether from an input directory or by executing internally
+  if app.ARGS.first_dir:
+    have_first = True
+  else:
     try:
       first_cmd = fsl.exe_name('run_first_all')
     except MRtrixError:
       first_cmd = None
     first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin')
-    have_first = first_cmd and os.path.isdir(first_atlas_path)
-  else:
-    app.warn('Environment variable FSLDIR is not set; '
-             'script will run without FSL components')
+    have_first = fsl_path and first_cmd and os.path.isdir(first_atlas_path)
 
   acpc_string = f'anterior {"& posterior commissures" if ATTEMPT_PC else "commissure"}'
   have_acpcdetect = bool(shutil.which('acpcdetect')) and 'ARTHOME' in os.environ
@@ -302,8 +308,8 @@ def execute(): #pylint: disable=unused-variable
                           f'(candidate images: {hipp_subfield_all_images})')
     elif hippocampi_method == 'first':
       if not have_first:
-        raise MRtrixError('Cannot use "first" method for hippocampi segmentation; '
-                          'check FSL installation')
+        raise MRtrixError('Cannot use "first" method for hippocampi segmentation: '
+                          'FSL installation not found, and -fist_dir not specified')
   else:
     if have_hipp_subfields:
       hippocampi_method = 'subfields'
@@ -313,9 +319,8 @@ def execute(): #pylint: disable=unused-variable
                   ' segmentation')
     elif have_first:
       hippocampi_method = 'first'
-      app.console('No hippocampal subfields module output detected, '
-                  'but FSL FIRST is installed; '
-                  'will utilise latter for hippocampi segmentation')
+      app.console('No hippocampal subfields module output detected; '
+                  'FSL FIRST will be utilised for hippocampi segmentation')
     else:
       hippocampi_method = 'aseg'
       app.console('Neither hippocampal subfields module output nor FSL FIRST detected; '
@@ -337,7 +342,6 @@ def execute(): #pylint: disable=unused-variable
     app.warn('Option -sgm_amyg_hipp ignored '
              '(hsvs algorithm always assigns hippocampi & ampygdalae as sub-cortical grey matter)')
 
-
   # Similar logic for thalami
   thalami_method = app.ARGS.thalami
   if thalami_method:
@@ -346,8 +350,8 @@ def execute(): #pylint: disable=unused-variable
         raise MRtrixError('Could not find thalamic nuclei module output')
     elif thalami_method == 'first':
       if not have_first:
-        raise MRtrixError('Cannot use "first" method for thalami segmentation; '
-                          'check FSL installation')
+        raise MRtrixError('Cannot use "first" method for thalami segmentation: '
+                          'no FSL installation found, and -first_dir not specified')
   else:
     # Not happy with outputs of thalamic nuclei submodule; default to FIRST
     if have_first:
@@ -365,6 +369,24 @@ def execute(): #pylint: disable=unused-variable
       app.console('Neither thalamic nuclei module output nor FSL FIRST detected; '
                   'FreeSurfer aseg will be used for thalami segmentation')
 
+  # Generate the list of structures to be segmented by FIRST
+  from_first = []
+  if have_first:
+    from_first = SGM_FIRST_MAP.copy()
+    if hippocampi_method == 'subfields':
+      from_first = { key: value for key, value in from_first.items() if 'Hippocampus' not in value }
+      if hipp_subfield_has_amyg:
+        from_first = { key: value for key, value in from_first.items() if 'Amygdala' not in value }
+    elif hippocampi_method == 'aseg':
+      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 }
+
+  # If -first_dir has been specified, need to make sure that we can find all requisite files
+  first_input_prefix = None
+  if app.ARGS.first_dir:
+    first_input_prefix = fsl.check_first_input(app.ARGS.first_dir, from_first.keys())
+
 
   ###########################
   # Commencing segmentation #
@@ -549,30 +571,18 @@ def execute(): #pylint: disable=unused-variable
     progress.done()
 
   if have_first:
-    app.console('Running FSL FIRST to segment sub-cortical grey matter structures')
-    from_first = SGM_FIRST_MAP.copy()
-    if hippocampi_method == 'subfields':
-      from_first = { key: value for key, value in from_first.items() if 'Hippocampus' not in value }
-      if hipp_subfield_has_amyg:
-        from_first = { key: value for key, value in from_first.items() if 'Amygdala' not in value }
-    elif hippocampi_method == 'aseg':
-      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 }
-    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')
-      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.*'))
+    first_vtk_files = []
+    if app.ARGS.first_dir:
+      assert first_input_prefix
+      first_vtk_files = [app.ARGS.first_dir / f'{first_input_prefix}{key}_first.vtk' for key in from_first.keys()]
+    else:
+      app.console('Running FSL FIRST to segment sub-cortical grey matter structures')
+      run.command([first_cmd, '-s', ','.join(from_first.keys()), '-i', 'T1.nii', '-b', '-o', 'first'])
+      fsl.check_first_output('first', from_first.keys())
+      first_vtk_files = [f'first-{key}_first-vtk' for key in from_first.keys()]
+      app.cleanup(glob.glob('T1_to_std_sub.*'))
     progress = app.ProgressBar('Mapping FIRST segmentations to image', 2*len(from_first))
-    for key, value in from_first.items():
-      vtk_in_path = f'first-{key}_first.vtk'
+    for (key, value), vtk_in_path in zip(from_first.items(), first_vtk_files):
       vtk_converted_path = f'first-{key}_transformed.vtk'
       run.command(['meshconvert', vtk_in_path, vtk_converted_path, '-transform', 'first2real', 'T1.nii'])
       app.cleanup(vtk_in_path)
diff --git a/python/mrtrix3/commands/labelsgmfirst.py b/python/mrtrix3/commands/labelsgmfirst.py
index db428a85d2..6e60dd4744 100644
--- a/python/mrtrix3/commands/labelsgmfirst.py
+++ b/python/mrtrix3/commands/labelsgmfirst.py
@@ -55,6 +55,7 @@ def usage(cmdline): #pylint: disable=unused-variable
                        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',
+                       type=app.Parser.DirectoryIn(),
                        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')
@@ -71,9 +72,25 @@ def execute(): #pylint: disable=unused-variable
     if utils.is_windows():
       raise MRtrixError('Script cannot run on Windows due to FSL dependency')
 
+  # 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.
+  structure_map = { 'L_Accu':'Left-Accumbens-area',  'R_Accu':'Right-Accumbens-area',
+                    'L_Caud':'Left-Caudate',         'R_Caud':'Right-Caudate',
+                    'L_Pall':'Left-Pallidum',        'R_Pall':'Right-Pallidum',
+                    'L_Puta':'Left-Putamen',         'R_Puta':'Right-Putamen',
+                    'L_Thal':'Left-Thalamus-Proper', 'R_Thal':'Right-Thalamus-Proper' }
+  if app.ARGS.sgm_amyg_hipp:
+    structure_map.update({ 'L_Amyg':'Left-Amygdala',    'R_Amyg':'Right-Amygdala',
+                           'L_Hipp':'Left-Hippocampus', 'R_Hipp':'Right-Hippocampus' })
+
   image.check_3d_nonunity(app.ARGS.t1)
 
-  if not app.ARGS.first_dir:
+  first_cmd = None
+  first_object_files = []
+  if app.ARGS.first_dir:
+    first_prefix = fsl.check_first_input(app.ARGS.first_dir, structure_map.keys())
+    first_object_files = [app.ARGS.first_dir / f'{first_prefix}{struct}_first.vtk' for struct in structure_map.keys()]
+  else:
     fsl_path = os.environ.get('FSLDIR', '')
     if not fsl_path:
       raise MRtrixError('Environment variable FSLDIR is not set; '
@@ -86,21 +103,10 @@ def execute(): #pylint: disable=unused-variable
       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.
-  structure_map = { 'L_Accu':'Left-Accumbens-area',  'R_Accu':'Right-Accumbens-area',
-                    'L_Caud':'Left-Caudate',         'R_Caud':'Right-Caudate',
-                    'L_Pall':'Left-Pallidum',        'R_Pall':'Right-Pallidum',
-                    'L_Puta':'Left-Putamen',         'R_Puta':'Right-Putamen',
-                    'L_Thal':'Left-Thalamus-Proper', 'R_Thal':'Right-Thalamus-Proper' }
-  if app.ARGS.sgm_amyg_hipp:
-    structure_map.update({ 'L_Amyg':'Left-Amygdala',    'R_Amyg':'Right-Amygdala',
-                           'L_Hipp':'Left-Hippocampus', 'R_Hipp':'Right-Hippocampus' })
-
   t1_spacing = image.Header(app.ARGS.t1).spacing()
   upsample_for_first = False
   # If voxel size is 1.25mm or larger, make a guess that the user has erroneously re-gridded their data
-  if math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0/3.0) > 1.225:
+  if not app.ARGS.first_dir and math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0/3.0) > 1.225:
     app.warn(f'Voxel size of input T1 image larger than expected for T1-weighted images ({t1_spacing}); '
              f'image will be resampled to 1mm isotropic in order to maximise chance of '
              f'FSL FIRST script succeeding')
@@ -120,21 +126,13 @@ def execute(): #pylint: disable=unused-variable
                 preserve_pipes=True)
 
   # Run FIRST
-  first_input_is_brain_extracted = ''
-  if app.ARGS.premasked:
-    first_input_is_brain_extracted = ' -b'
   if not app.ARGS.first_dir:
+    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')
-  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())
+    fsl.check_first_output('first', structure_map.keys())
 
   # Generate an empty image that will be used to construct the new SGM nodes
   run.command('mrcalc parc.mif 0 -min sgm.mif')
@@ -155,10 +153,9 @@ def execute(): #pylint: disable=unused-variable
   # In this use case, don't want the PVE images; want to threshold at 0.5
   mask_list = [ ]
   progress = app.ProgressBar('Generating mask images for SGM structures', len(structure_map))
-  for key, value in structure_map.items():
+  for (key, value), vtk_in_path in zip(structure_map.items(), first_object_files):
     image_path = f'{key}_mask.mif'
     mask_list.append(image_path)
-    vtk_in_path = f'first-{key}_first.vtk'
     run.command(f'meshconvert {vtk_in_path} first-{key}_transformed.vtk -transform first2real T1.nii')
     run.command(f'mesh2voxel first-{key}_transformed.vtk parc.mif - | '
                 f'mrthreshold - {image_path} -abs 0.5')
diff --git a/python/mrtrix3/fsl.py b/python/mrtrix3/fsl.py
index 8a57769fba..389aa4b2e1 100644
--- a/python/mrtrix3/fsl.py
+++ b/python/mrtrix3/fsl.py
@@ -24,11 +24,30 @@
 
 
 # Functions that may be useful for scripts that interface with FMRIB FSL tools
+# If user provides directory containing pre-calculated FIRST outputs,
+#   need to:
+#   - Ensure set of files to use is unambiguous
+#   - Check that everything expected to be present is there
+#   - Yield the filename prefix so that files can be loaded easily
+def check_first_input(dirpath, structures):
+  candidate_files = list(dirpath.glob('*_first.vtk'))
+  filename_prefix = candidate_files[0][:-(6+len('_first.vtk'))]
+  if not all(item.startswith(filename_prefix) for item in candidate_files):
+    raise MRtrixError(f'Inconsistency in filename prefixes in FIRST input directory {dirpath}')
+  for struct in structures:
+    filename = f'{filename_prefix}{struct}_first.vtk'
+    inpath = dirpath / filename
+    if not inpath.is_file():
+      raise MRtrixError(f'Unable to find VTK file for structure "{struct}" in FIRST input directory '
+                        f'(expected location: {inpath})')
+  # TODO Also decide on a suitable image to use as the reference for conversion to realspace,
+  #   and check for its presence
+  return filename_prefix
 
 # FSL's run_first_all script can be difficult to wrap, since it does not provide
 #   a meaningful return code, and may run via SGE, which then requires waiting for
 #   the output files to appear.
-def check_first(prefix, structures): #pylint: disable=unused-variable
+def check_first_output(prefix, structures): #pylint: disable=unused-variable
   from mrtrix3 import app, path #pylint: disable=import-outside-toplevel
   vtk_files = [ prefix + '-' + struct + '_first.vtk' for struct in structures ]
   existing_file_count = sum(os.path.exists(filename) for filename in vtk_files)
diff --git a/testing/scripts/CMakeLists.txt b/testing/scripts/CMakeLists.txt
index 9a0b9fad51..d1fbe916a2 100644
--- a/testing/scripts/CMakeLists.txt
+++ b/testing/scripts/CMakeLists.txt
@@ -33,6 +33,8 @@ add_bash_script_test(5ttgen/freesurfer_piping)
 add_bash_script_test(5ttgen/freesurfer_sgmamyghipp)
 add_bash_script_test(5ttgen/freesurfer_whitespace)
 add_bash_script_test(5ttgen/fsl_default)
+add_bash_script_test(5ttgen/fsl_fastdir)
+add_bash_script_test(5ttgen/fsl_firstdir)
 add_bash_script_test(5ttgen/fsl_mask)
 add_bash_script_test(5ttgen/fsl_nocrop)
 add_bash_script_test(5ttgen/fsl_piping)
@@ -42,6 +44,7 @@ add_bash_script_test(5ttgen/fsl_whitespace)
 add_bash_script_test(5ttgen/hsvs_aseg)
 add_bash_script_test(5ttgen/hsvs_default)
 add_bash_script_test(5ttgen/hsvs_first)
+add_bash_script_test(5ttgen/hsvs_firstdir)
 add_bash_script_test(5ttgen/hsvs_modules)
 add_bash_script_test(5ttgen/hsvs_piping)
 add_bash_script_test(5ttgen/hsvs_template)
@@ -228,6 +231,7 @@ add_bash_script_test(for_each/exclude "pythonci")
 add_bash_script_test(for_each/parallel "pythonci")
 
 add_bash_script_test(labelsgmfirst/default)
+add_bash_script_test(labelsgmfirst/firstdir)
 add_bash_script_test(labelsgmfirst/freesurfer)
 add_bash_script_test(labelsgmfirst/piping)
 add_bash_script_test(labelsgmfirst/premasked)
diff --git a/testing/scripts/tests/5ttgen/fsl_fastdir b/testing/scripts/tests/5ttgen/fsl_fastdir
new file mode 100644
index 0000000000..36dc316150
--- /dev/null
+++ b/testing/scripts/tests/5ttgen/fsl_fastdir
@@ -0,0 +1,19 @@
+#!/bin/bash
+# Verify "5ttgen fsl" operation when -fast_dir is used
+# Only ensure successful completion
+# Make sure that 5ttgen fsl doesn't invoke FAST
+
+mkdir tmp_fast
+
+mrconvert BIDS/sub-01/anat/sub-01_T1w.nii.gz tmp_fast/T1w.nii
+
+fast tmp_fast/T1w.nii tmp_fast/prefix
+
+echo "false" > tmp_fast/fast
+chmod 775 tmp_fast/fast
+export PATH=$(pwd)/tmp_fast:$PATH
+
+5ttgen fsl BIDS/sub-01/anat/sub-01_T1w.nii.gz tmp.mif \
+-fast_dir tmp_fast/ \
+-force
+
diff --git a/testing/scripts/tests/5ttgen/fsl_firstdir b/testing/scripts/tests/5ttgen/fsl_firstdir
new file mode 100644
index 0000000000..e1f571080e
--- /dev/null
+++ b/testing/scripts/tests/5ttgen/fsl_firstdir
@@ -0,0 +1,23 @@
+#!/bin/bash
+# Verify "5ttgen fsl" operation when -first_dir is used
+# Only ensure successful completion
+# Make sure that 5ttgen fsl doesn't invoke FIRST
+
+mkdir tmp_first
+
+mrgrid BIDS/sub-01/anat/sub-01_T1w.nii.gz regrid tmp_T1w.nii \
+-scale 2
+
+run_first_all -m none \
+-s L_Accu,R_Accu,L_Caud,R_Caud,L_Pall,R_Pall,L_Puta,R_Puta,L_Thal,R_Thal \
+-i tmp_T1w.nii \
+-o tmp_first/prefix
+
+echo "false" > tmp_first/run_first_all
+chmod 775 tmp_first/run_first_all
+export PATH=$(pwd)/tmp_first:$PATH
+
+5ttgen fsl BIDS/sub-01/anat/sub-01_T1w.nii.gz tmp.mif \
+-first_dir tmp_first/ \
+-force
+
diff --git a/testing/scripts/tests/5ttgen/hsvs_firstdir b/testing/scripts/tests/5ttgen/hsvs_firstdir
new file mode 100644
index 0000000000..c6810c8d68
--- /dev/null
+++ b/testing/scripts/tests/5ttgen/hsvs_firstdir
@@ -0,0 +1,21 @@
+#!/bin/bash
+# Verify "5ttgen hsvs" algorithm when -first_dir is used
+# Make sure that 5ttgen hsvs doesn't invoke FIRST
+
+mkdir tmp_first
+
+mrconvert freesurfer/sub-01/mri/norm.mgz tmp_T1w.nii
+
+run_first_all -m none \
+-s L_Accu,R_Accu,L_Caud,R_Caud,L_Pall,R_Pall,L_Puta,R_Puta,L_Thal,R_Thal \
+-i tmp_T1w.nii \
+-o tmp_first/prefix
+
+echo "false" > tmp_first/run_first_all
+chmod 775 tmp_first/run_first_all
+export PATH=$(pwd)/tmp_first:$PATH
+
+5ttgen hsvs freesurfer/sub-01 tmp.mif \
+-first_dir tmp_first \
+-force
+
diff --git a/testing/scripts/tests/labelsgmfirst/firstdir b/testing/scripts/tests/labelsgmfirst/firstdir
new file mode 100644
index 0000000000..bf534ec6e0
--- /dev/null
+++ b/testing/scripts/tests/labelsgmfirst/firstdir
@@ -0,0 +1,21 @@
+#!/bin/bash
+# Verify successful completion when -first_dir option is used
+# Make sure that labelsgmfirst does not invoke FIRST
+
+mkdir tmp_first
+mrgrid BIDS/sub-01/anat/sub-01_T1w.nii.gz regrid tmp_T1w.nii \
+-scale 2
+
+run_first_all -m none \
+-s L_Accu,R_Accu,L_Caud,R_Caud,L_Pall,R_Pall,L_Puta,R_Puta,L_Thal,R_Thal \
+-i tmp_T1w.nii \
+-o tmp_first/prefix
+
+echo "false" > tmp_first/run_first_all
+chmod 775 tmp_first/run_first_all
+export PATH=$(pwd)/tmp_first:$PATH
+
+labelsgmfirst BIDS/sub-01/anat/sub-01_parc-desikan_indices.nii.gz BIDS/sub-01/anat/sub-01_T1w.nii.gz BIDS/parc-desikan_lookup.txt tmp.mif \
+-first_dir tmp_first/ \
+-force
+