Slicer3:XCEDE use cases - Revision history

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

2017-07-10T17:04:02Z

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

Marianna: Protected "Slicer3:XCEDE use cases" [edit=sysop:move=sysop]

2008-05-20T20:01:24Z

Protected "Slicer3:XCEDE use cases" [edit=sysop:move=sysop]

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:XCEDE_use_c...'

2008-05-20T20:01:09Z

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:XCEDE_use_c...'

Pieper: /* Qdec Module */

2007-11-12T20:19:11Z

Qdec Module

Pieper: /* Qdec Module */

2007-11-12T20:15:21Z

Qdec Module

Wjp: /* Query Atlas Module */

2007-09-27T14:25:20Z

Query Atlas Module

Wjp: /* Query Atlas Module */

2007-09-27T14:25:12Z

Query Atlas Module

Wjp: /* Query Atlas Module */

2007-09-27T14:24:48Z

Query Atlas Module

Wjp: /* Query Atlas Module */

2007-09-26T14:18:36Z

Query Atlas Module

Wjp: /* Query Atlas Module */

2007-09-26T14:18:02Z

Query Atlas Module

← Older revision		Revision as of 17:04, 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:XCEDE_use_cases 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:XCEDE_use_cases here]</font></big>

← Older revision		Revision as of 20:01, 20 May 2008
Line 1:		Line 1:
−	~~== Slicer3 use cases for XCEDE ==~~	+	<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:XCEDE_use_cases here]</font></big>
−
−	~~=== Query Atlas Module ===~~
−
−	'''~~Contents~~:'''
−
−	~~This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:~~
−
−	* One FreeSurfer "lh" model and one FreeSurfer "rh" model at most
−	* the FreeSurfer structural brain.mgz image volume
−	* the FreeSurfer example functional example_func.nii
−	* some FIPS-generated Statistical volumes
−	* the FreeSurfer aparc+aseg.mgz label map volume
−	* the FreeSurfer lh.aparc.annot annotation file
−	* the matrix to align the example_func + statistics to the brain.mgz: anat2exf.register.dat
−
−	~~'''Assumptions:'''~~
−	* we are assuming a single lh or rh model (or one of each) is in the catalog. (Reason: Slicer will load the lh.aparc.annot file as a scalar overlay onto a model; so the overlay needs to be associated with a model automatically during load. Since the catalog attribute list contains no references to other datasets, the only way to associate the lh.aparc.annot to the lh.pial surface is by matching on the "lh." and "rh." in the model and annotation names.)
−
−	* we are detecting whether a matrix with the name "anat2efx" is in the catalog (we should probably check the uri instead) -- and if so, we are wrapping the list of all FIPS-generated statistical volumes and the example_func(noted above) in a derived transform in the load routine. We recognize files with the string "brain.mgz" "example_func" and "anat2exf" in them, in order to do some automatic calculation of the Slicer transform that does the Slicer ras2ras registration. Then we stuff volumes with "example_func" or "stat" in their name into the derived transform.
−	** the tests to detect these files are weak -- need a better test: now, a structural volume with the string 'stat' embedded in it will be stuffed into the transform by mistake.
−	** no registration transform is computed if volumes matching the brain.mgz, example_func and an anat2exf.register.dat file are ~~not detected.~~
−
−	~~'''New value inventions for attributes:'''~~
−	* Freesurfer:matrix-1 (this ~~gives us a clue about file format).~~
−	* Freesurfer:overlay-1 (for files that need to be associated with a model in order to load in Slicer)
−	* Freesurfer:label-1 (for mgz files that are label maps) This gives us a hint about what kind of color map to ~~use to display~~ the ~~image data~~. ~~The default colormap for volume data is greyscale.~~
−
−	~~'''Validation:'''~~
−
−	~~=== Qdec Module ===~~
−
−	~~Description needed...~~
−
−	~~=== Prototype XCAT Files ===~~
−	~~<pre>~~
−	~~<XCEDE>~~
−	~~<catalog ID="ID0">~~
−
−	~~<catalogList>~~
−
−	~~<catalog ID="ID1">~~
−	~~<entryList>~~
−
−	~~<entry ID="ID2" name="anat2exf" description="matrix that registers anatomical information to functional datasets" format="FreeSurfer:matrix~~-~~1" content="anat2exf" cachePath="" modelID="ID2" uri="./anat2exf.register.dat"/>~~
−
−	<~~entry ID="ID3" name="lh.pial" description="pial surface of left hemisphere" format="FreeSurfer:surface-1" content~~="~~lh.pial~~" ~~cachePath="" uri="./lh.pial"/~~>
−
−	~~<entry ID="ID4" name="rh.pial" description="pial surface of right hemisphere" format="FreeSurfer~~:~~surface-1" content="rh.pial" cachePath="" uri=".~~/~~rh.pial"~~/>
−
−	~~<entry ID="ID5" name="brain" description="extracted brain mri" format="FreeSurfer:mgz-1" content="brain" cachePath="" uri="~~.~~/brain~~.~~mgz"~~/>
−
−	~~<entry ID="ID6" name="exf" description="example functional dataset" format="nifti:nii-1" content="example_func" cachePath="" uri=".~~/~~example_func~~.~~nii"~~/>
−
−	~~<entry ID="ID7" name="zstat7" description="7th zstatisic contrast E1+E3+E5>Fix" format="nifti:nii-1" content="zstat7" cachePath="" uri="./zstat7.nii"/>~~
−
−	~~<entry ID="ID8" name="zstat14" description="14th zstatisic contrast P1+P3+P5>Fix" format="nifti:nii-1" content="zstat14" cachePath="" uri="./zstat14.nii"/>~~
−
−	~~<entry ID="ID9" name="zstat17" description="17th zstatisic contrast Learn>Fix" format="nifti~~:~~nii-1" content="zstat17" cachePath="" uri="./zstat17.nii"/>~~
−
−	~~<entry ID="ID10" name="aparc+aseg" description="parcellation and segmentation label map" labelmap="true" format="FreeSurfer:mgz-1" content="aparc+aseg" cachePath="" uri="./aparc+aseg.mgz"/>~~
−
−	~~<entry ID="ID11" name="lh.aparc.annot" description="annotations for surface of left hemisphere" format="FreeSurfer:overlay-1" content="lh.aparc.annot" cachePath="" uri="./lh.aparc.annot"/>~~
−
−	~~<entry ID="ID12" name="rh.aparc.annot" description="annotations for surface of right hemisphere" format="FreeSurfer:overlay-1" content="rh.aparc.annot" cachePath="" uri="./rh.aparc.annot"/>~~
−
−	~~</entryList>~~
−	~~</catalog>~~
−
−	~~</catalogList>~~
−
−	~~</catalog>~~
−	</~~XCEDE~~>
−
−	</~~pre~~>

← Older revision		Revision as of 20:19, 12 November 2007
Line 31:		Line 31:
	=== Qdec Module ===		=== Qdec Module ===

		+	Description needed...

	=== Prototype XCAT Files ===		=== Prototype XCAT Files ===

← Older revision		Revision as of 20:15, 12 November 2007
Line 30:		Line 30:

	=== Qdec Module ===		=== Qdec Module ===
		+
		+
		+	=== Prototype XCAT Files ===
		+	<pre>
		+	<XCEDE>
		+	<catalog ID="ID0">
		+
		+	<catalogList>
		+
		+	<catalog ID="ID1">
		+	<entryList>
		+
		+	<entry ID="ID2" name="anat2exf" description="matrix that registers anatomical information to functional datasets" format="FreeSurfer:matrix-1" content="anat2exf" cachePath="" modelID="ID2" uri="./anat2exf.register.dat"/>
		+
		+	<entry ID="ID3" name="lh.pial" description="pial surface of left hemisphere" format="FreeSurfer:surface-1" content="lh.pial" cachePath="" uri="./lh.pial"/>
		+
		+	<entry ID="ID4" name="rh.pial" description="pial surface of right hemisphere" format="FreeSurfer:surface-1" content="rh.pial" cachePath="" uri="./rh.pial"/>
		+
		+	<entry ID="ID5" name="brain" description="extracted brain mri" format="FreeSurfer:mgz-1" content="brain" cachePath="" uri="./brain.mgz"/>
		+
		+	<entry ID="ID6" name="exf" description="example functional dataset" format="nifti:nii-1" content="example_func" cachePath="" uri="./example_func.nii"/>
		+
		+	<entry ID="ID7" name="zstat7" description="7th zstatisic contrast E1+E3+E5>Fix" format="nifti:nii-1" content="zstat7" cachePath="" uri="./zstat7.nii"/>
		+
		+	<entry ID="ID8" name="zstat14" description="14th zstatisic contrast P1+P3+P5>Fix" format="nifti:nii-1" content="zstat14" cachePath="" uri="./zstat14.nii"/>
		+
		+	<entry ID="ID9" name="zstat17" description="17th zstatisic contrast Learn>Fix" format="nifti:nii-1" content="zstat17" cachePath="" uri="./zstat17.nii"/>
		+
		+	<entry ID="ID10" name="aparc+aseg" description="parcellation and segmentation label map" labelmap="true" format="FreeSurfer:mgz-1" content="aparc+aseg" cachePath="" uri="./aparc+aseg.mgz"/>
		+
		+	<entry ID="ID11" name="lh.aparc.annot" description="annotations for surface of left hemisphere" format="FreeSurfer:overlay-1" content="lh.aparc.annot" cachePath="" uri="./lh.aparc.annot"/>
		+
		+	<entry ID="ID12" name="rh.aparc.annot" description="annotations for surface of right hemisphere" format="FreeSurfer:overlay-1" content="rh.aparc.annot" cachePath="" uri="./rh.aparc.annot"/>
		+
		+	</entryList>
		+	</catalog>
		+
		+	</catalogList>
		+
		+	</catalog>
		+	</XCEDE>
		+
		+	</pre>

← Older revision		Revision as of 14:25, 27 September 2007
Line 4:		Line 4:

	'''Contents:'''		'''Contents:'''
		+
	This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:		This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:

← Older revision	Revision as of 20:01, 20 May 2008
(No difference)

← Older revision		Revision as of 14:25, 27 September 2007
Line 3:		Line 3:
	=== Query Atlas Module ===		=== Query Atlas Module ===

		+	'''Contents:'''
	This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:		This is a record of the way we're using the xcede2.0 catalog in order to load in a query atlas scene that contains:

@@ Line 13: / Line 13: @@
 * the matrix to align the example_func + statistics to the brain.mgz: anat2exf.register.dat
-Assumptions:
+'''Assumptions:'''
 * we are assuming a single lh or rh model (or one of each) is in the catalog. (Reason: Slicer will load the lh.aparc.annot file as a scalar overlay onto a model; so the overlay needs to be associated with a model automatically during load. Since the catalog attribute list contains no references to other datasets, the only way to associate the lh.aparc.annot to the lh.pial surface is by matching on the "lh." and "rh." in the model and annotation names.)
@@ Line 20: / Line 20: @@
 ** no registration transform is computed if volumes matching the brain.mgz, example_func and an anat2exf.register.dat file are not detected.
-New value inventions for attributes:
+'''New value inventions for attributes:'''
 * Freesurfer:matrix-1 (this gives us a clue about file format).
 * Freesurfer:overlay-1 (for files that need to be associated with a model in order to load in Slicer)
 * Freesurfer:label-1 (for mgz files that are label maps) This gives us a hint about what kind of color map to use to display the image data. The default colormap for volume data is greyscale.
 === Qdec Module ===

@@ Line 16: / Line 16: @@
 * we are assuming a single lh or rh model (or one of each) is in the catalog. (Reason: Slicer will load the lh.aparc.annot file as a scalar overlay onto a model; so the overlay needs to be associated with a model automatically during load. Since the catalog attribute list contains no references to other datasets, the only way to associate the lh.aparc.annot to the lh.pial surface is by matching on the "lh." and "rh." in the model and annotation names.)
-* we are detecting whether a matrix with the name "anat2efx" is in the catalog (we should probably check the uri instead) -- and if so, we are wrapping the list of all FIPS-generated statistical volumes and the example_func(noted above) in a derived transform in the load routine. We recognize files with the string "brain.mgz" "example_func" and "anat2exf" in them, in order to do some automatic calculation of the Slicer transform that does the Slicer ras2ras registration of example_func and statistics to high-res anatomical. Then we stuff volumes with "example_func" or "stat" in their name into the derived transform.
+* we are detecting whether a matrix with the name "anat2efx" is in the catalog (we should probably check the uri instead) -- and if so, we are wrapping the list of all FIPS-generated statistical volumes and the example_func(noted above) in a derived transform in the load routine. We recognize files with the string "brain.mgz" "example_func" and "anat2exf" in them, in order to do some automatic calculation of the Slicer transform that does the Slicer ras2ras registration. Then we stuff volumes with "example_func" or "stat" in their name into the derived transform.
 ** the tests to detect these files are weak -- need a better test: now, a structural volume with the string 'stat' embedded in it will be stuffed into the transform by mistake.
 ** no registration transform is computed if volumes matching the brain.mgz, example_func and an anat2exf.register.dat file are not detected.