Slicer3:Slicer Daemon - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:35:19Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna: Unprotected "Slicer3:Slicer Daemon"

2008-05-20T17:33:32Z

Marianna: Replacing page with ''''Note:''' We are migrating this content to the slicer.org domain - The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Slicer_Daem...'

2008-05-20T17:33:24Z

Replacing page with '<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Slicer_Daem...'

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Kquintus: /* Slicer-Matlab interface and tensor data */

2008-02-08T22:58:36Z

Slicer-Matlab interface and tensor data

Kquintus: /* Slicer-Matlab interface and tensor data */

2008-02-08T20:17:17Z

Slicer-Matlab interface and tensor data

Kquintus: /* Basic Slicer-Matlab tutorial */

2008-02-08T20:00:58Z

Basic Slicer-Matlab tutorial

Kquintus at 19:59, 8 February 2008

2008-02-08T19:59:44Z

Pieper: /* Tcl */

2007-12-14T01:15:52Z

Tcl

Kquintus: /* Convert tensor data between gradient space and ijk space */

2007-08-07T16:08:53Z

Convert tensor data between gradient space and ijk space

Kquintus: /* Convert tensor data between gradient space and ijk space */

2007-08-07T16:06:57Z

Convert tensor data between gradient space and ijk space

← Older revision		Revision as of 17:35, 10 July 2017
Line 1:		Line 1:
−	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Slicer3:Slicer_Daemon here]</font></big>	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Slicer_Daemon here]</font></big>

@@ Line 249: / Line 249: @@
 The transformation function needs the original measurement frame matrix, otherwise the transformation obviously can't be done.
-Such transformations incur numerical errors. After both transformations the data is back in original gradient space and should be exactly the same as the data originally loaded, but this is not quite the case. In part this is due to matrix inversions, especially when the measurement frame is non trivial and tensor elements are very small. To give you an idea how big this numerical error can be, the following inital test can be performed with the original file-loaded nrrd structure:
+Such transformations incur numerical errors. After both transformations the data is back in original gradient space and should be exactly the same as the data originally loaded, but this is not quite the case. In part this is due to matrix inversions, especially when the measurement frame is non trivial and tensor elements are very small. To give you an idea how big this numerical error can be, the following initial test can be performed with the original file-loaded nrrd structure:
   tensor_first_to_ijk_then_back_to_gradient = transformationTestLoop(tensor_gradient_space);
-This script compares tensors element by element. This is not a necessarliy a good measure for tensor integrity. Even though the element-wise relative difference might be very big, measures like trace of FA might still be very alike.
+This script compares tensors element by element. This is not a neccessarliy a good measure for tensor integrity. Even though the element-wise relative difference might be very big, measures like trace of FA might still be very alike.
 ==== TODO ====

← Older revision		Revision as of 20:17, 8 February 2008
Line 252:		Line 252:
	tensor_first_to_ijk_then_back_to_gradient = transformationTestLoop(tensor_gradient_space);		tensor_first_to_ijk_then_back_to_gradient = transformationTestLoop(tensor_gradient_space);
	This script compares tensors element by element. This is not a necessarliy a good measure for tensor integrity. Even though the element-wise relative difference might be very big, measures like trace of FA might still be very alike.		This script compares tensors element by element. This is not a necessarliy a good measure for tensor integrity. Even though the element-wise relative difference might be very big, measures like trace of FA might still be very alike.
		+
		+	==== TODO ====
		+
		+	* the scripts need some adjustments for sending labelmaps back to Slicer (the labelmap flag needs to be set for the volume).
		+	* Sending tensor data back to Slicer crashes Slicer. This has worked before but something in Slicer has changed. One idea is that a display node needs to be created now when creating the volume in Slicer.

@@ Line 147: / Line 147: @@
 * Typing the following command in Matlab, the Slicer volume named "wcase1.nhdr" will be piped into a Matlab structure called "slicer_volume":
   slicer_volume = getSlicerVolume('wcase1.nhdr')
-Instead of stating the name of the volume in Slicer you can also state the id (first volume loaded gets assigned number "0", ascending numbers from there):
 All volumes that come out of Slicer are in 'right-anterior-superior' orientation, have 'raw' encoding, and 'little' endian. Even if the original file loaded into Slicer had other header parameters.

@@ Line 147: / Line 147: @@
 * Typing the following command in Matlab, the Slicer volume named "wcase1.nhdr" will be piped into a Matlab structure called "slicer_volume":
   slicer_volume = getSlicerVolume('wcase1.nhdr')
+Instead of stating the name of the volume in Slicer you can also state the id (first volume loaded gets assigned number "0", ascending numbers from there):
 All volumes that come out of Slicer are in 'right-anterior-superior' orientation, have 'raw' encoding, and 'little' endian. Even if the original file loaded into Slicer had other header parameters.

← Older revision	Revision as of 17:33, 20 May 2008
(No difference)

@@ Line 13: / Line 13: @@
 == Tcl ==
 Two utilities are provided:
@@ Line 30: / Line 32: @@
   # run an external command and put the data back into slicer
   slicerget.tcl 1 | unu 1op abs -i - slicerput.tcl abs
 == Python ==