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docs/source/user_section/installation/install_on_windows.rst

@@ -62,6 +62,9 @@ Dependencies
 Installation Procedure for Windows
 ----------------------------------
 
+Conda requires an installation path that does not contain spaces. Your username should not contain spaces to avoid this issue.
+If your username contains spaces, you can create a new user account with no spaces in the username or use a different OS.
+
 .. Note::
 
     The installer will install ``Shimming Toolbox`` and ``dcm2niix`` into an isolated environment. It will not interfere if you already have ``dcm2niix`` installed.

shimmingtoolbox/cli/check_env.py

@@ -83,10 +83,11 @@ def check_prelude_installation():
         bool: True if prelude is installed, False if not.
     """
     try:
-        if sys.platform != 'win32':
-            subprocess.check_call(['which', 'prelude'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
-        else:
+        if sys.platform == 'win32':
             subprocess.check_call(['where', 'prelude'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+        else:
+            subprocess.check_call(['which', 'prelude'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
     except subprocess.CalledProcessError as error:
         print_fail()
         print(f"Error {error.returncode}: prelude is not installed or not in your PATH.")
@@ -106,10 +107,10 @@ def check_dcm2niix_installation():
         bool: True if dcm2niix is installed, False if not.
     """
     try:
-        if sys.platform != 'win32':
-            subprocess.check_call(['which', 'dcm2niix'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
-        else:
+        if sys.platform == 'win32':
             subprocess.check_call(['where', 'dcm2niix'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+        else:
+            subprocess.check_call(['which', 'dcm2niix'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
     except subprocess.CalledProcessError as error:
         print(error)
         print_fail()

shimmingtoolbox/unwrap/skimage_unwrap.py

@@ -60,18 +60,14 @@ def skimage_unwrap(nii_wrapped_phase, mag=None, mask=None, threshold=None, fname
     # Mask the wrapped phase
     ma_wrapped_phase = ma.array(wrapped_phase, mask=~unwrap_mask.astype(bool))
 
-    singleton = False
     if ma_wrapped_phase.ndim == 3 and ma_wrapped_phase.shape[2] == 1:
-        # If the phase is 3D with a single slice, remove the last dimension
-        ma_wrapped_phase = ma_wrapped_phase[:, :, 0]
-        singleton = True
-
-    # Unwrap the masked phase
-    ma_unwrapped_phase = unwrap_phase(ma_wrapped_phase, rng=0)
-
-    if singleton:
-        # If the phase was 3D with a single slice, add the last dimension back
+        # If the phase is 3D with a single slice, pass the array as 2D and unwrap
+        ma_unwrapped_phase = unwrap_phase(ma_wrapped_phase[:, :, 0], rng=0)
+        # Add the 3rd dimension back
         ma_unwrapped_phase = ma_unwrapped_phase[:, :, np.newaxis]
+    else:
+        # Normal 3D case: Unwrap the phase
+        ma_unwrapped_phase = unwrap_phase(ma_wrapped_phase, rng=0)
 
     # Fill the masked values with 0
     unwrapped_phase = ma_unwrapped_phase.filled(0)