tutorial issue fix

docs/guides/install.md

@@ -2,10 +2,10 @@
 
 PyALFE supports Linux x86-64, Mac x86-64, and Mac arm64 and requires python >= 3.9.
 
-### Image registration and processing
-PyALFE can be configured to use either [Greedy](https://greedy.readthedocs.io/en/latest/) or [AntsPy](https://antspy.readthedocs.io/en/latest/registration.html) registration tools.
-Similarly, PyALFE can be configured to use [Convert3D](https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md) or python native library [Nilearn](https://nilearn.github.io/stable/index.html) for image processing tasks.
-To use Greedy and Convert3d, these command line tools should be downloaded using the [download command](#download-models-and-tools).
+### Prerquisite
+PyALFE uses [Greedy](https://greedy.readthedocs.io/en/latest/) registration tool by default. The instruction for installing Greedy can be found [here](https://greedy.readthedocs.io/en/latest/install.html#using-pre-compiled-binaries).
+
+Alternatively, PyALFE can be configured to use [AntsPy](https://antspy.readthedocs.io/en/latest/registration.html) registration tool. To use AntsPy, you can install PyALFE with [ants support](#extras).
 
 ### Option 1: PyPI
 
@@ -72,7 +72,7 @@ when performing a build and install
 pip install 'dist/pyalfe-0.1.0-py3-none-any.whl[radiomics]'
 ```
 
-If you want to use ant registration tool, you can install pyalfe with ants support:
+If you want to use ants registration tool, you can install pyalfe with ants support:
 ```bash
 pip install 'pyalfe[ants]'
 ```

docs/guides/tutorial.md

@@ -39,7 +39,7 @@ pyalfe download models
 
 Configure pyalfe by running
 ```bash
-pyalfe configrue
+pyalfe configure
 ```
 and simply pressing enter for all the prompts for default values.
 

pyalfe/interfaces/c3d.py

@@ -1,11 +1,15 @@
-import subprocess
+import io
 
-from pyalfe.tools import C3D_PATH
+from picsl_c3d import Convert3D
 
 
 class C3D:
-    def __init__(self, c3d_path=C3D_PATH):
-        self.cmd = [c3d_path]
+    def __init__(self):
+        self.cmd = []
+        self.c = Convert3D()
+
+    def __repr__(self):
+        return ' '.join([str(part) for part in self.cmd])
 
     def assign(self, var):
         self.cmd.append('-as')
@@ -97,7 +101,9 @@ def sdt(self):
         return self
 
     def run(self):
-        return subprocess.run(self.cmd, capture_output=True).stdout.decode("utf-8")
+        return self.c.execute(self.__repr__())
 
     def check_output(self):
-        return subprocess.check_output(self.cmd).decode("utf-8")
+        cmd_output = io.StringIO()
+        self.c.execute(self.__repr__(), out=cmd_output)
+        return cmd_output.getvalue()

pyalfe/interfaces/freesurfer.py

@@ -1,12 +1,23 @@
 import subprocess
+from shutil import which
 
 
 class FreeSurfer:
     def __init__(self):
         self.cmd = []
 
     def mri_synthseg(self, input, output):
-        self.cmd += ['mri_synthseg', '--i', input, '--o', output]
+        synthseg_cmd = 'mri_synthseg'
+        if which(synthseg_cmd) is None:
+            raise RuntimeError(
+                f'{synthseg_cmd} executable was not found in your system. '
+                'To download and install FreeSurfer version 7, visit:\n '
+                'https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall \n'
+                'To configure FreeSurfer, visit:\n'
+                'https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux \n'
+                'https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac'
+            )
+        self.cmd += [synthseg_cmd, '--i', input, '--o', output]
         return self
 
     def run(self):

pyalfe/interfaces/greedy.py

@@ -1,11 +1,22 @@
 import subprocess
+from shutil import which
 
-from pyalfe.tools import GREEDY_PATH
+from pyalfe.tools import GREEDY_PATH, greedy_url
 
 
 class Greedy:
     def __init__(self, greedy_path=GREEDY_PATH):
         self.cmd = [greedy_path]
+        if which(greedy_path) is None:
+            msg = (
+                f'{greedy_path} executable was not found in your system. '
+                'To download and install greedy, visit:\n '
+                'https://greedy.readthedocs.io/en/latest/install.html#using-pre-compiled-binaries'
+            )
+            if greedy_url:
+                msg += f'\n or {greedy_url} \n'
+
+            raise RuntimeError(msg)
 
     def dim(self, d):
         self.cmd += ['-d', str(d)]

pyalfe/tools/__init__.py

@@ -1,42 +1,62 @@
 import os
+from collections import defaultdict
 
-greedy_url = {
-    'Linux': {
-        'x86_64': (
-            'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
-            'greedy-nightly-Linux-gcc64.tar.gz'
-        )
-    },
-    'Darwin': {
-        'x86_64': (
-            'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
-            'greedy-nightly-MacOS-x86_64.dmg'
+greedy_url = defaultdict(
+    lambda: defaultdict(str),
+    {
+        'Linux': defaultdict(
+            str,
+            {
+                'x86_64': (
+                    'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
+                    'greedy-nightly-Linux-gcc64.tar.gz'
+                )
+            },
         ),
-        'arm64': (
-            'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
-            'greedy-nightly-MacOS-arm64.dmg'
+        'Darwin': defaultdict(
+            str,
+            {
+                'x86_64': (
+                    'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
+                    'greedy-nightly-MacOS-x86_64.dmg'
+                ),
+                'arm64': (
+                    'https://sourceforge.net/projects/greedy-reg/files/Nightly/'
+                    'greedy-nightly-MacOS-arm64.dmg'
+                ),
+            },
         ),
     },
-}[os.uname()[0]][os.uname()[-1]]
+)[os.uname()[0]][os.uname()[-1]]
 
-c3d_url = {
-    'Linux': {
-        'x86_64': (
-            'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
-            'c3d-nightly-Linux-gcc64.tar.gz'
-        )
-    },
-    'Darwin': {
-        'x86_64': (
-            'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
-            'c3d-nightly-MacOS-x86_64.dmg'
+
+c3d_url = defaultdict(
+    lambda: defaultdict(str),
+    {
+        'Linux': defaultdict(
+            str,
+            {
+                'x86_64': (
+                    'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
+                    'c3d-nightly-Linux-gcc64.tar.gz'
+                )
+            },
         ),
-        'arm64': (
-            'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
-            'c3d-nightly-MacOS-arm64.dmg'
+        'Darwin': defaultdict(
+            str,
+            {
+                'x86_64': (
+                    'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
+                    'c3d-nightly-MacOS-x86_64.dmg'
+                ),
+                'arm64': (
+                    'https://sourceforge.net/projects/c3d/files/c3d/Nightly/'
+                    'c3d-nightly-MacOS-arm64.dmg'
+                ),
+            },
         ),
     },
-}[os.uname()[0]][os.uname()[-1]]
+)[os.uname()[0]][os.uname()[-1]]
 
 GREEDY_PATH = 'greedy'  # importlib.resources.files('pyalfe.tools').joinpath('greedy')
 C3D_PATH = 'c3d'  # importlib.resources.files('pyalfe.tools').joinpath('c3d')

pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     "huggingface_hub",
     "torch",
     "pandas",
+    "picsl_c3d",
     "pybids",
     "nibabel",
     "nilearn",