Do thickness

Dockerfile

@@ -1,4 +1,4 @@
-FROM docker.io/fnndsc/pl-gifit:base-1
+FROM docker.io/fnndsc/pl-gifit:base-2
 
 LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
       org.opencontainers.image.title="pl-gifit" \

base/Dockerfile

@@ -14,6 +14,8 @@ RUN microminc.sh -p '&run' \
     print_n_polygons \
     volume_object_evaluate \
     vertstats_math \
+    cortical_thickness \
+    average_surfaces \
         /microminc
 
 # MNI data needs to be copied manually

base/build.sh

@@ -2,4 +2,4 @@
 
 exec docker buildx build --push \
     --platform linux/amd64,linux/arm64,linux/ppc64le \
-    -t docker.io/fnndsc/pl-gifit:base-1 .
+    -t docker.io/fnndsc/pl-gifit:base-2 .

gifit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.1.0'
+__version__ = '0.2.0'
 
 DISPLAY_TITLE = r"""
        _             _  __ _ _   

gifit/__main__.py

@@ -8,7 +8,7 @@
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
-from typing import Optional
+from typing import Optional, Sequence
 
 from chris_plugin import chris_plugin, PathMapper
 from loguru import logger
@@ -25,6 +25,8 @@
                     help='Name of built-in model to use, or a path to a custom CSV model.')
 parser.add_argument('-s', '--size', dest='size', type=int, default=81920,
                     help='Output mesh size')
+parser.add_argument('-t', '--thickness-fwhm', dest='thickness_fwhm', type=str, default='0,10',
+                    help='List of fwhm values in mm to use for calculating thickness between surfaces')
 parser.add_argument('-V', '--version', action='version',
                     version=f'%(prog)s {__version__}')
 parser.add_argument('-J', '--threads', type=int, default=0,
@@ -51,17 +53,20 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     model_file = options.model if os.path.isfile(options.model) else get_builtin_model(options.model)
     model = Model(model_file)
 
+    thickness_fwhm = __parse_thickness_fwhm(options.thickness_fwhm)
+
     mapper = PathMapper.file_mapper(inputdir, outputdir, glob='**/*.mnc', suffix='.obj')
     with ThreadPoolExecutor(max_workers=nproc) as pool:
-        results = pool.map(lambda t, p, s: run_surface_fit(*t, p, s), mapper,
+        results = pool.map(lambda t, p, s, b: run_surface_fit(*t, p, s, b), mapper,
                            itertools.repeat(model),
-                           itertools.repeat(str(options.size)))
+                           itertools.repeat(str(options.size)),
+                           itertools.repeat(thickness_fwhm))
 
     if not options.no_fail and not all(results):
         sys.exit(1)
 
 
-def run_surface_fit(grid: Path, output_surf: Path, model: Model, size: str) -> bool:
+def run_surface_fit(grid: Path, output_surf: Path, model: Model, size: str, thickness_fwhm: Sequence[int]) -> bool:
     """
     :return: True if successful
     """
@@ -93,12 +98,23 @@ def run_surface_fit(grid: Path, output_surf: Path, model: Model, size: str) -> b
     rc_file = log_file.with_suffix('.rc')
     rc_file.write_text(str(job.returncode))
 
-    if job.returncode == 0:
-        logger.info('Finished: {} -> {}', starting_surface, output_surf)
-        return True
+    if job.returncode != 0:
+        logger.error('FAILED -- check log file for details: {}', log_file)
+        return False
+
+    thickness_commands_worked = True
+    for f in thickness_fwhm:
+        output_file = output_surf.with_suffix(f'.tlink_{f}mm.txt')
+        log_file = output_file.with_suffix('.log')
+        cmd = ['cortical_thickness', '-tlink', '-fwhm', str(f), output_surf, starting_surface, output_file]
+        with log_file.open('wb') as log_handle:
+            proc = sp.run(cmd, stdout=log_handle, stderr=log_handle)
+        if proc.returncode != 0:
+            logger.error('Command failed: {}', shlex.join(map(str, cmd)))
+            thickness_commands_worked = False
 
-    logger.error('FAILED -- check log file for details: {}', log_file)
-    return False
+    logger.info('Finished: {} -> {}', starting_surface, output_surf)
+    return thickness_commands_worked
 
 
 def locate_surface_for(mask: Path) -> Optional[Path]:
@@ -116,5 +132,13 @@ def get_builtin_model(name: str) -> str:
     return str(model_file)
 
 
+def __parse_thickness_fwhm(value) -> Sequence[int]:
+    try:
+        return [int(x) for x in value.split(',')]
+    except ValueError:
+        logger.error(f'"{value}" is not a comma-separated list of numbers')
+        sys.exit(1)
+
+
 if __name__ == '__main__':
     main()