Tunable Parameters - Revision history

Tomh: /* Unconstrained */

2019-05-07T20:45:41Z

Unconstrained

← Older revision		Revision as of 16:45, 7 May 2019
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	==Unconstrained==		==Unconstrained==
	Unconstrained		Unconstrained
	Instead of using surface normals generated by FreeSurfer, when Unconstrained is specified, the dipole moment is calculated the usual way using the OrientBand covariance.		Only applicable to [[roi_wts]]. Instead of using surface normals generated by FreeSurfer, when Unconstrained is specified, the dipole moment is calculated the usual way using the OrientBand covariance.

	=Frequency Specification=		=Frequency Specification=

Tomh: /* Extent */

2019-05-07T20:42:56Z

Extent

← Older revision		Revision as of 16:42, 7 May 2019
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	==Extent==		==Extent==
	Extent EXT		Extent EXT
	The primary purpose of Extent is to give an extent to the ROI centroids listed in a Target file for use by [[patch_wts~~\|patch_wts~~]]. Extent can also be used by [[sam_wts\|sam_wts]] to add interpolation around each voxel or target. Units are in mm.		The primary purpose of Extent is to give an extent to the ROI centroids listed in a Target file for use by [[patch_wts]] or [[roi_wts]]. Extent can also be used by [[sam_wts\|sam_wts]] to add interpolation around each voxel or target. Units are in mm.

	==ROIList==		==ROIList==

Tomh: unconstrained

2019-05-07T20:28:41Z

unconstrained

← Older revision		Revision as of 16:28, 7 May 2019
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	ROIList ROILISTFILE		ROIList ROILISTFILE
	After running FSNormals.py, the result is a .norm file that gives the list of vertices for each ROI in the selected FreeSurfer parcellation (generally, the Desikan or Destrieux). However, the user may not want to estimate the beamformer for all ROIs in the parcellation, in order to save computational time and reduce the multiple comparisons problem. Standard ROIList files are distributed with SAMsrcV5 for both Desikan and Destrieux parcellations. The user may copy these files and comment out ROIs that are of no interest using the # character.		After running FSNormals.py, the result is a .norm file that gives the list of vertices for each ROI in the selected FreeSurfer parcellation (generally, the Desikan or Destrieux). However, the user may not want to estimate the beamformer for all ROIs in the parcellation, in order to save computational time and reduce the multiple comparisons problem. Standard ROIList files are distributed with SAMsrcV5 for both Desikan and Destrieux parcellations. The user may copy these files and comment out ROIs that are of no interest using the # character.

			==Unconstrained==
			Unconstrained
			Instead of using surface normals generated by FreeSurfer, when Unconstrained is specified, the dipole moment is calculated the usual way using the OrientBand covariance.

	=Frequency Specification=		=Frequency Specification=

Tomh: /* Transform */

2019-05-07T20:01:36Z

Transform

← Older revision		Revision as of 16:01, 7 May 2019
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	==Transform==		==Transform==
	Transform ~~XFORMFILE~~		Transform
	This parameter is only used if sam_coreg is used. sam_coreg will use the FreeSurfer normals and the MEG data to determine the best fit coregistration of the MRI and MEG. The result will be a transform, the name of which defaults to ~~Transform~~.xfm. The given transform defines a translation and rotation to be applied to MEG sensors.		This parameter is only used if sam_coreg is used. sam_coreg will use the FreeSurfer normals and the MEG data to determine the best fit coregistration of the MRI and MEG. The result will be a transform, the name of which defaults to <surface>.xfm where <surface> is the FreeSurfer surface used (see the [[Tunable_Parameters#Surface\|Surface]] parameter). The given transform defines a translation and rotation to be applied to the MEG sensors. By default no transform is applied, you must specify Transform (no arguments) to use the transform.

	==TargetName==		==TargetName==

Tomh: /* Surface */

2019-05-07T19:54:45Z

Surface

← Older revision		Revision as of 15:54, 7 May 2019
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	==Surface==		==Surface==
	Surface ~~WHITE~~\|~~SM_WHITE~~\|~~PIAL~~		Surface white\|smoothwm\|pial
	Specifies which surface was used to create the cortical normals contained in the Atlas file.		Specifies which surface was used to create the cortical normals contained in the Atlas file.

	==Transform==		==Transform==

Nugenta at 19:19, 19 March 2019

2019-03-19T19:19:42Z

← Older revision		Revision as of 15:19, 19 March 2019
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	==SegFile==		==SegFile==
	SegFile MARKNAME FILE TRUE\|FALSE		SegFile MARKNAME FILE TRUE\|FALSE
	Specifies a Marker using a file. The lines of the file must contain three columns, "trial T0 T1", where the first trial is 0, and T0 and T1 are in seconds. Not applicable with analyses which assume constant length segments (everything except sam_3d).		Specifies a Marker using a file. The lines of the file must contain three columns, "trial T0 T1", where the first trial is 0, and T0 and T1 are in seconds. Not applicable with analyses which assume constant length segments (everything except [[sam_3d\|sam_3d]]).
	Incompatible with DataSegment.		Incompatible with DataSegment.

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	TargetName TARGETFILE		TargetName TARGETFILE
	Instead of estimating beamformer weights at every point within a rectilinear grid, or on a surface, you can instead request beamformer weights only for a discrete list of coordinates. The Target file is a simple text file which gives x, y, and z coordinates (in centimeters), with one set of coordinates per line. SAM routines will look for the target file in the MRI directory of the designated participant (or, if PrefixLength is set to 0, the directory designated by MRIDirectory).		Instead of estimating beamformer weights at every point within a rectilinear grid, or on a surface, you can instead request beamformer weights only for a discrete list of coordinates. The Target file is a simple text file which gives x, y, and z coordinates (in centimeters), with one set of coordinates per line. SAM routines will look for the target file in the MRI directory of the designated participant (or, if PrefixLength is set to 0, the directory designated by MRIDirectory).

			==Extent==
			Extent EXT
			The primary purpose of Extent is to give an extent to the ROI centroids listed in a Target file for use by [[patch_wts\|patch_wts]]. Extent can also be used by [[sam_wts\|sam_wts]] to add interpolation around each voxel or target. Units are in mm.

	==ROIList==		==ROIList==

Nugenta: /* Image Coordinate Space Specification */

2019-03-08T21:56:22Z

Image Coordinate Space Specification

← Older revision		Revision as of 17:56, 8 March 2019
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	ImageFormat ORIG\|TLRC RES		ImageFormat ORIG\|TLRC RES
	This parameter controls how the SAM beamformer coefficients (weights) are generated. The default is ORIG in which the weights correspond precisely to the ROI and grid spacing specified by XBounds, YBounds, ZBounds and ImageStep. The beamformer weights are written as a NIFTI file. Designating the ImageFormat as TLRC will apply the AFNI program @auto_tlrc to the beamformer weight file, transforming the weights into the common Talairach space according to the Talairach transform included in the ortho+tlrc MRI image. The transform is applied to each SAM coefficient file. The original weight files are retained and the new transformed file names are appended with _at.nii. The resolution of the transform is specified in millimeters. It is recommended that the original ROI grid spacing (specified by ImageStep) be smaller than the Talairach grid spacing because the transform uses nearest neighbor to move the ortho grid to Talairach grid. The Talairach transform can also be applied to weights derived from an atlas. This parameter cannot be specified on the command line.		This parameter controls how the SAM beamformer coefficients (weights) are generated. The default is ORIG in which the weights correspond precisely to the ROI and grid spacing specified by XBounds, YBounds, ZBounds and ImageStep. The beamformer weights are written as a NIFTI file. Designating the ImageFormat as TLRC will apply the AFNI program @auto_tlrc to the beamformer weight file, transforming the weights into the common Talairach space according to the Talairach transform included in the ortho+tlrc MRI image. The transform is applied to each SAM coefficient file. The original weight files are retained and the new transformed file names are appended with _at.nii. The resolution of the transform is specified in millimeters. It is recommended that the original ROI grid spacing (specified by ImageStep) be smaller than the Talairach grid spacing because the transform uses nearest neighbor to move the ortho grid to Talairach grid. The Talairach transform can also be applied to weights derived from an atlas. This parameter cannot be specified on the command line.

			==Mask==
			Mask MASKFILE
			Mask file name required when ImageFormat TLRC is used. The mask file resolution must agree with the resolution (RES) specified in ImageFormat.

	==Atlas==		==Atlas==
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	==ROIList==		==ROIList==
	ROIList ROILISTFILE		ROIList ROILISTFILE
	After running FSNormals.py, the result is a .norm file that gives the list of vertices for each ROI in the selected FreeSurfer parcellation (generally, the Desikan or Destrieux). However, the user may not want to estimate the beamformer for all ROIs in the parcellation, in order to save computational time and reduce the multiple comparisons problem. Standard ROIList files are distributed with SAMsrcV5 for both Desikan and Destrieux parcellations. The user may copy these files and comment out ROIs that are of no interest using the # character.		After running FSNormals.py, the result is a .norm file that gives the list of vertices for each ROI in the selected FreeSurfer parcellation (generally, the Desikan or Destrieux). However, the user may not want to estimate the beamformer for all ROIs in the parcellation, in order to save computational time and reduce the multiple comparisons problem. Standard ROIList files are distributed with SAMsrcV5 for both Desikan and Destrieux parcellations. The user may copy these files and comment out ROIs that are of no interest using the # character.

	=Frequency Specification=		=Frequency Specification=

Nugenta at 19:39, 8 March 2019

2019-03-08T19:39:40Z

← Older revision		Revision as of 15:39, 8 March 2019
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	Atlas ATLASFILE		Atlas ATLASFILE
	Instead of using a rectilinear space of voxels, beam former weights can be calculated for each "voxel" or greyordinate on a cortical surface derived from the MRI using FreeSurfer. The atlas file contains the coordinates and orientation vector for each neocortical location. An atlas may be generated by applying [[FSnormals.py\|FSnormals.py]] and [[reduce_surface.py\|reduce_surface.py]] to the subject’s surface data obtained from FreeSurfer. If present, it overrides the XBounds, YBounds, ZBounds, and ImageStep parameters. The default location of the atlas is set using the MRIDirectory, PrefixLength, and MRIPattern parameters.		Instead of using a rectilinear space of voxels, beam former weights can be calculated for each "voxel" or greyordinate on a cortical surface derived from the MRI using FreeSurfer. The atlas file contains the coordinates and orientation vector for each neocortical location. An atlas may be generated by applying [[FSnormals.py\|FSnormals.py]] and [[reduce_surface.py\|reduce_surface.py]] to the subject’s surface data obtained from FreeSurfer. If present, it overrides the XBounds, YBounds, ZBounds, and ImageStep parameters. The default location of the atlas is set using the MRIDirectory, PrefixLength, and MRIPattern parameters.

			==Surface==
			Surface WHITE\|SM_WHITE\|PIAL
			Specifies which surface was used to create the cortical normals contained in the Atlas file.

	==Transform==		==Transform==

Nugenta at 15:51, 7 March 2019

2019-03-07T15:51:49Z

← Older revision		Revision as of 11:51, 7 March 2019
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	==PrefixLength==		==PrefixLength==
	PrefixLength N		PrefixLength N
	This parameter controls the number of characters at the beginning of the MEG dataset that are used to find the required MRI files, and to name the output files. The default is 8, according to the NIH convention for naming MEG datasets with an 8 digit hash code. For sites having a different number of characters for identifying datasets and participants, PrefixLength can be used.		This parameter controls the number of characters at the beginning of the MEG dataset that are used to find the required MRI files, and to name the output files. The default is 8, according to the NIH convention for naming MEG datasets with an 8 digit hash code. For sites having a different number of characters for identifying datasets and participants, PrefixLength can be used. Note that setting PrefixLength to 0 will assume that all MRI files are in the MRIDirectory without subject-specific subdirectories.

	==ImageDirectory==		==ImageDirectory==
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	==Atlas==		==Atlas==
	Atlas ATLASFILE		Atlas ATLASFILE
	Instead of using a rectilinear space of voxels, beam former weights can be calculated for each "voxel" or greyordinate on a cortical surface derived from the MRI using FreeSurfer. The atlas file contains the coordinates and orientation vector for each neocortical location. An atlas may be generated by applying [[FSnormals.py\|FSnormals.py]] and [[reduce_surface.py\|reduce_surface.py]] to the subject’s surface data obtained from FreeSurfer. If present, it overrides the XBounds, YBounds, ZBounds, and ImageStep parameters. The default location of the atlas is set using the MRIDirectory and MRIPattern parameters.		Instead of using a rectilinear space of voxels, beam former weights can be calculated for each "voxel" or greyordinate on a cortical surface derived from the MRI using FreeSurfer. The atlas file contains the coordinates and orientation vector for each neocortical location. An atlas may be generated by applying [[FSnormals.py\|FSnormals.py]] and [[reduce_surface.py\|reduce_surface.py]] to the subject’s surface data obtained from FreeSurfer. If present, it overrides the XBounds, YBounds, ZBounds, and ImageStep parameters. The default location of the atlas is set using the MRIDirectory, PrefixLength, and MRIPattern parameters.

	==Transform==		==Transform==
	Transform XFORMFILE		Transform XFORMFILE
	This parameter is only used if sam_coreg is used. sam_coreg will use the FreeSurfer normals and the MEG data to determine the best fit coregistration of the MRI and MEG. The result will be a transform, the name of which defaults to Transform.xfm. The given transform defines a translation and rotation to be applied to MEG sensors.		This parameter is only used if sam_coreg is used. sam_coreg will use the FreeSurfer normals and the MEG data to determine the best fit coregistration of the MRI and MEG. The result will be a transform, the name of which defaults to Transform.xfm. The given transform defines a translation and rotation to be applied to MEG sensors.

			==TargetName==
			TargetName TARGETFILE
			Instead of estimating beamformer weights at every point within a rectilinear grid, or on a surface, you can instead request beamformer weights only for a discrete list of coordinates. The Target file is a simple text file which gives x, y, and z coordinates (in centimeters), with one set of coordinates per line. SAM routines will look for the target file in the MRI directory of the designated participant (or, if PrefixLength is set to 0, the directory designated by MRIDirectory).

			==ROIList==
			ROIList ROILISTFILE
			After running FSNormals.py, the result is a .norm file that gives the list of vertices for each ROI in the selected FreeSurfer parcellation (generally, the Desikan or Destrieux). However, the user may not want to estimate the beamformer for all ROIs in the parcellation, in order to save computational time and reduce the multiple comparisons problem. Standard ROIList files are distributed with SAMsrcV5 for both Desikan and Destrieux parcellations. The user may copy these files and comment out ROIs that are of no interest using the # character.

	=Frequency Specification=		=Frequency Specification=

Nugenta at 20:28, 5 March 2019

2019-03-05T20:28:37Z

← Older revision		Revision as of 16:28, 5 March 2019
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	==Transform==		==Transform==
	Transform XFORMFILE		Transform XFORMFILE
	This parameter is only used if ~~Atlas~~ is ~~specified~~. ~~The~~ ~~given~~ ~~transform~~ ~~defines~~ a ~~translation~~ and ~~rotation~~ to be ~~applied~~ to the ~~Atlas,~~ in ~~order~~ to ~~improve~~ ~~the~~ ~~fit~~ to ~~the~~ ~~true~~ ~~frame~~ of ~~reference~~. ~~This~~ ~~parameter~~ is ~~currently~~ ~~experimental~~ and ~~should~~ ~~not~~ be ~~used~~ ~~lightly~~.		This parameter is only used if sam_coreg is used. sam_coreg will use the FreeSurfer normals and the MEG data to determine the best fit coregistration of the MRI and MEG. The result will be a transform, the name of which defaults to Transform.xfm. The given transform defines a translation and rotation to be applied to MEG sensors.

	=Frequency Specification=		=Frequency Specification=