Head Localization and MRI Coregistration - Revision history

Nugenta at 19:23, 19 March 2019

2019-03-19T19:23:44Z

← Older revision		Revision as of 15:23, 19 March 2019
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	* The tool [[orthohull.py\|orthohull.py]] is used to create the headmodel needed for further processing from the AFNI anatomical MRI with fiducial points "Nation," "Left Ear," and "Right Ear" saved as tags in the header. It is assumed that the MRI has not been skull-stripped. The -t and -m options perform a normalization to Talairach or MNI space, respectively. Additional options available, execute command with no arguments to see usage information.		* The tool [[orthohull.py\|orthohull.py]] is used to create the headmodel needed for further processing from the AFNI anatomical MRI with fiducial points "Nation," "Left Ear," and "Right Ear" saved as tags in the header. It is assumed that the MRI has not been skull-stripped. The -t and -m options perform a normalization to Talairach or MNI space, respectively. Additional options available, execute command with no arguments to see usage information.
	: {\| width=600 style="border: 1px solid lightgrey;"		: {\| width=600 style="border: 1px solid lightgrey;"
	\|~~Usage~~: orthohull ~~[-t][-m] brain~~+orig.HEAD		\|Minimal usage: orthohull.py anat+orig.HEAD
	\|}		\|}
	: You can additionally use SUMA to visualize the output surface, which defaults to ortho_brainhull.ply		: You can additionally use SUMA to visualize the output surface, which defaults to ortho_brainhull.ply

Nugenta at 19:22, 19 March 2019

2019-03-19T19:22:21Z

← Older revision		Revision as of 15:22, 19 March 2019
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	#Digitizer Method: At the time of the MEG, digitize the location of the head coils on the subject's head, along with either additional digitizer points covering the head or a 3d scan of the head shape (with a Polhemus device, Kinect, or Structure sensor). The headshape point cloud can then be aligned with the MRI in a semi-automated fashion; a detailed tutorial for this method is forthcoming.		#Digitizer Method: At the time of the MEG, digitize the location of the head coils on the subject's head, along with either additional digitizer points covering the head or a 3d scan of the head shape (with a Polhemus device, Kinect, or Structure sensor). The headshape point cloud can then be aligned with the MRI in a semi-automated fashion; a detailed tutorial for this method is forthcoming.

	* The tool [[~~local:/web/~~orthohull\|orthohull]] is used to create the headmodel needed for further processing from the AFNI anatomical MRI with fiducial points "Nation," "Left Ear," and "Right Ear" saved as tags in the header. It is assumed that the MRI has not been skull-stripped. The -t and -m options perform a normalization to Talairach or MNI space, respectively. Additional options available, execute command with no arguments to see usage information.		* The tool [[orthohull.py\|orthohull.py]] is used to create the headmodel needed for further processing from the AFNI anatomical MRI with fiducial points "Nation," "Left Ear," and "Right Ear" saved as tags in the header. It is assumed that the MRI has not been skull-stripped. The -t and -m options perform a normalization to Talairach or MNI space, respectively. Additional options available, execute command with no arguments to see usage information.
	: {\| width=600 style="border: 1px solid lightgrey;"		: {\| width=600 style="border: 1px solid lightgrey;"
	\|Usage: orthohull [-t][-m] brain+orig.HEAD		\|Usage: orthohull [-t][-m] brain+orig.HEAD

Nugenta: Nugenta moved page HeadLocMRICoreg to Head Localization and MRI Coregistration

2018-02-20T20:57:29Z

Nugenta moved page HeadLocMRICoreg to Head Localization and MRI Coregistration

← Older revision	Revision as of 16:57, 20 February 2018
(No difference)

Nugenta at 20:24, 20 February 2018

2018-02-20T20:24:38Z

@@ Line 3: / Line 3: @@
 The first step in any analysis pipeline is to localize the MEG data to anatomical space, which is generally done using a structural MRI. When doing this localization, it is important to know if the subject moved during the recording.
-* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)
+* Use [[local:/meg/headMotionDetect|headMotionDetect]] to determine epochs with head motion over a given threshold (in cm)
-{| width=600 style="border: 1px solid black;"
+: {| width=600 style="border: 1px solid lightgrey;"
 |Usage: headMotionDetect -th 0.25 dataset.ds
 |}

Nugenta at 19:09, 20 February 2018

2018-02-20T19:09:32Z

← Older revision		Revision as of 15:09, 20 February 2018
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	* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)		* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)

	{\| width=600 ~~align=center~~ style="border: 1px solid black;"		{\| width=600 style="border: 1px solid black;"
	\|Usage: headMotionDetect -th 0.25 dataset.ds		\|Usage: headMotionDetect -th 0.25 dataset.ds
	\|}		\|}

Nugenta at 19:08, 20 February 2018

2018-02-20T19:08:51Z

← Older revision		Revision as of 15:08, 20 February 2018
Line 5:		Line 5:
	* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)		* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)

	{\| width=600 align=center style="border: 1px;"		{\| width=600 align=center style="border: 1px solid black;"
	\|headMotionDetect -th 0.25 dataset.ds		\|Usage: headMotionDetect -th 0.25 dataset.ds
	\|}		\|}

Nugenta at 19:08, 20 February 2018

2018-02-20T19:08:29Z

← Older revision		Revision as of 15:08, 20 February 2018
Line 5:		Line 5:
	* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)		* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)

	{\| ~~class=wikitable~~ width=600 align=center		{\| width=600 align=center style="border: 1px;"
	\|headMotionDetect -th 0.25 dataset.ds		\|headMotionDetect -th 0.25 dataset.ds
	\|}		\|}

Nugenta at 19:02, 20 February 2018

2018-02-20T19:02:44Z

← Older revision		Revision as of 15:02, 20 February 2018
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	\|headMotionDetect -th 0.25 dataset.ds		\|headMotionDetect -th 0.25 dataset.ds
	\|}		\|}

			*

Nugenta: Created page with "===== Head Localization and MRI Co-Registration ===== The first step in any analysis pipeline is to localize the MEG data to anatomical space, which is generally done using a..."

2018-02-20T19:02:17Z

Created page with "===== Head Localization and MRI Co-Registration ===== The first step in any analysis pipeline is to localize the MEG data to anatomical space, which is generally done using a..."

New page

===== Head Localization and MRI Co-Registration =====

The first step in any analysis pipeline is to localize the MEG data to anatomical space, which is generally done using a structural MRI. When doing this localization, it is important to know if the subject moved during the recording.

* Use headMotionDetect to determine epochs with head motion over a given threshold (in cm)

{| class=wikitable width=600 align=center
|headMotionDetect -th 0.25 dataset.ds
|}