Documentation/Nightly/Modules/DTI ALPSIndex - Revision history

Acsenrafilho at 17:11, 24 May 2024

2024-05-24T17:11:33Z

Acsenrafilho at 13:15, 17 April 2024

2024-04-17T13:15:05Z

Acsenrafilho: Add information about the runDTIALPS.py script

2024-04-17T13:08:38Z

Add information about the runDTIALPS.py script

Acsenrafilho: Created page with "{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 39: / Line 39: @@
 <code>./Slicer --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd</code>
-Assuming that Slicer is installed on Linux/Mac machines:
+Assuming that Slicer is installed on Windows machines:
 <code>Slicer.exe --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd</code>

@@ Line 45: / Line 45: @@
 The <code>runDTIALPS.py</code> has some options that can be used:
-. <code>--MNISpace</code>: Informs whether the input DTI image is already in the MNI space (2 mm resolution). If yes, the input Proj/Assoc paths are changed for the standar MNI labels instead.
+. <code>--MNISpace</code>: Informs whether the input DTI image is already in the MNI space (2 mm resolution). If yes, the input Proj/Assoc paths are changed for the standard MNI labels instead.
 . <code>--verbose</code>: Show more details thoughout the processing.
 <!-- ---------------------------- -->

← Older revision		Revision as of 13:08, 17 April 2024
Line 27:		Line 27:
	* Use Case 1: Obtain the DTI-ALPS index calculation from standard DTI image and propers anatomical labels (see details at Taoka et al. 2017 paper <ref>https://pubmed.ncbi.nlm.nih.gov/28197821/</ref>)		* Use Case 1: Obtain the DTI-ALPS index calculation from standard DTI image and propers anatomical labels (see details at Taoka et al. 2017 paper <ref>https://pubmed.ncbi.nlm.nih.gov/28197821/</ref>)
	**The DTI-ALPS index is a scalar value that represents the activity of the glymphatic system, which may be evaluated with diffusion images. Lower diffusivity along the perivascular space on DTI-APLS seems to reflect impairment of the glymphatic system.		**The DTI-ALPS index is a scalar value that represents the activity of the glymphatic system, which may be evaluated with diffusion images. Lower diffusivity along the perivascular space on DTI-APLS seems to reflect impairment of the glymphatic system.
		+
		+	<!-- ---------------------------- -->
		+	{{documentation/{{documentation/version}}/module-section\|Usage Tips}}
		+	* Tip 1: Call the DTI-ALPS calculation using GUI interface
		+	**The DTI-ALPS index can be calculated using the direct GUI interface provided in the Slicer Module. See the User Interface section below.
		+	* Tip 2: Call the DTI-ALPS calculation using command line Python script
		+	**This Slicer Module provides a Python script to be called in the Slicer execution model, using command line. This can be useful when the user want to call a series of calculation without the use of GUI interface or by a server. See some ways to call the Python script <code>runDTIALPS.py</code>:
		+
		+	Assuming that Slicer is installed on Linux/Mac machines:
		+
		+	<code>./Slicer --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd</code>
		+
		+	Assuming that Slicer is installed on Linux/Mac machines:
		+
		+	<code>Slicer.exe --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd</code>
		+
		+	The <code>runDTIALPS.py</code> has some options that can be used:
		+
		+	1. <code>--MNISpace</code>: Informs whether the input DTI image is already in the MNI space (2 mm resolution). If yes, the input Proj/Assoc paths are changed for the standar MNI labels instead.
		+
		+	2. <code>--verbose</code>: Show more details thoughout the processing.