Source Localization - SAM - Revision history

Tomh: add 3dNormalize documentation

2020-09-30T19:52:21Z

add 3dNormalize documentation

← Older revision		Revision as of 15:52, 30 September 2020
Line 36:		Line 36:
	** [[FSnormals.py \| FSnormals.py]]		** [[FSnormals.py \| FSnormals.py]]
	** [[NIFTIPeak \| NIFTIPeak]]		** [[NIFTIPeak \| NIFTIPeak]]
			** [[3dNormalize \| 3dNormalize]]

Nugenta at 13:46, 18 March 2019

2019-03-18T13:46:24Z

← Older revision		Revision as of 09:46, 18 March 2019
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	** [[mut_img \| mut_img]]		** [[mut_img \| mut_img]]
	* SAM Utility Program Reference Pages		* SAM Utility Program Reference Pages
	** [[orthohull \| orthohull]]		** [[orthohull.py \| orthohull.py]]
	** [[FSnormals.py \| FSnormals.py]]		** [[FSnormals.py \| FSnormals.py]]
	** [[NIFTIPeak \| NIFTIPeak]]		** [[NIFTIPeak \| NIFTIPeak]]

Nugenta at 21:15, 12 March 2019

2019-03-12T21:15:15Z

← Older revision		Revision as of 17:15, 12 March 2019
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	** [[sam_power \| sam_power]]		** [[sam_power \| sam_power]]
	** [[sam_epi \| sam_epi]]		** [[sam_epi \| sam_epi]]
	** [[sam_hfo \| sam_hfo]]
	** [[patch_wts \| patch_wts]]		** [[patch_wts \| patch_wts]]
	** [[roi_wts \| roi_wts]]		** [[roi_wts \| roi_wts]]

Nugenta at 21:07, 12 March 2019

2019-03-12T21:07:34Z

← Older revision		Revision as of 17:07, 12 March 2019
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	** [[patch_wts \| patch_wts]]		** [[patch_wts \| patch_wts]]
	** [[roi_wts \| roi_wts]]		** [[roi_wts \| roi_wts]]
	** [[sam_roi \| sam_roi]]
	** [[sam_entropy \| sam_entropy]]		** [[sam_entropy \| sam_entropy]]
	** [[mut_img \| mut_img]]		** [[mut_img \| mut_img]]

Nugenta at 18:09, 7 March 2019

2019-03-07T18:09:11Z

← Older revision		Revision as of 14:09, 7 March 2019
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	** [[sam_wts \| sam_wts]]		** [[sam_wts \| sam_wts]]
	** [[sam_nwts \| sam_nwts]]		** [[sam_nwts \| sam_nwts]]
	** [[sam_3d \| sam_3d]]		** [[sam_3d and sam_3dc \| sam_3d and sam_3dc]]
	** [[~~sam_3dc~~ \| ~~sam_3dc~~]]		** [[sam_4d and sam_4dc \| sam_4d and sam_4dc]]
		⚫	** [[sam_ers and sam_ersc \| sam_ers and sam_ersc]]
	** [[sam_4d \| sam_4d]]
	** [[sam_4dc \| sam_4dc]]
	** [[sam_ers \| sam_ers]]
⚫	** [[sam_ersc \| sam_ersc]]
	** [[sam_power \| sam_power]]		** [[sam_power \| sam_power]]
	** [[sam_epi \| sam_epi]]		** [[sam_epi \| sam_epi]]

Nugenta at 17:42, 5 March 2019

2019-03-05T17:42:10Z

@@ Line 18: / Line 18: @@
 * [[Suggested Pipelines | Suggested Pipelines]]
 * [[Tunable Parameters | Tunable Parameters]]
-* Program Reference Pages
+* SAM Program Reference Pages
 ** [[sam_cov | sam_cov]]
 ** [[sam_wts | sam_wts]]
 ** [[sam_nwts | sam_nwts]]

Nugenta: /* Documentation: */

2019-03-01T20:49:43Z

Documentation:

← Older revision		Revision as of 16:49, 1 March 2019
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	* [[Installation Instructions \| Installation Instructions]]		* [[Installation Instructions \| Installation Instructions]]
	* [[Suggested Pipelines \| Suggested Pipelines]]		* [[Suggested Pipelines \| Suggested Pipelines]]
			* [[Tunable Parameters \| Tunable Parameters]]
	* Program Reference Pages		* Program Reference Pages
	** [[sam_cov \| sam_cov]]		** [[sam_cov \| sam_cov]]

Nugenta at 20:27, 1 March 2019

2019-03-01T20:27:56Z

← Older revision		Revision as of 16:27, 1 March 2019
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	=== Documentation: ===		=== Documentation: ===

			* [[SAMsrcV3 overview \| SAMsrcV3 overview]]
	* [[Installation Instructions \| Installation Instructions]]		* [[Installation Instructions \| Installation Instructions]]
	* [[Suggested Pipelines \| Suggested Pipelines]]		* [[Suggested Pipelines \| Suggested Pipelines]]

Nugenta at 19:42, 1 March 2019

2019-03-01T19:42:35Z

← Older revision		Revision as of 15:42, 1 March 2019
Line 15:		Line 15:

	* [[Installation Instructions \| Installation Instructions]]		* [[Installation Instructions \| Installation Instructions]]
			* [[Suggested Pipelines \| Suggested Pipelines]]
			* Program Reference Pages
			** [[sam_cov \| sam_cov]]
			** [[sam_wts \| sam_wts]]
			** [[sam_nwts \| sam_nwts]]

Nugenta at 18:16, 1 March 2019

2019-03-01T18:16:24Z

← Older revision		Revision as of 14:16, 1 March 2019
Line 1:		Line 1:
	== The SAMsrcV3 ~~MEG~~ Analysis Suite ==		=== Synthetic Magnetometry: The SAMsrcV3 Analysis Suite ===

			The programs documented here implement the latest advances in MEG source localization. Compared with the older CTF tools, there are many new features (some of them experimental).
	=== Synthetic Aperture Magnetometry ===

			Features include:
	The programs documented here implement the latest advances in MEG source localization. Compared with the older CTF tools, there are many new features (some of them experimental). True within-subject statistics are now available, including a non-parametric test in addition to the usual t and F tests. There is much better handling of shorter time windows, a more flexible control over active, control, and noise covariance matrices, dual-state ERF imaging, realistic head models, and several flavors of multipole source imaging that are available, though some of these latter features are still considered experimental.
			* Flexible control over active, control, and noise covariance matrices
			* Dual-state ERF imaging
			* Realistic head models
			* Hilbert envelope time series computation for connectivity
			* Experimental refinement of MRI coregistration based on Freesurfer normals
			* More efficient workflow
			* Command-line interface for maximal flexibility

			=== Documentation: ===
	There is also a new work flow resulting from a more efficient separation of functionality. For example, the old SAMsrc program has been replaced by a set of several new programs with a modern command-line interface. The old CTF tools were normally installed in /opt/ctf. The new set of programs will generally be copied into a user’s $HOME/bin directory. Many of the old tools are still useful and necessary.

			* [[Installation Instructions \| Installation Instructions]]
	A wiki containing documentation for the SAM suite is [https://kurage.nimh.nih.gov/samdoc/ here]. It's still a work in progress.

	'''Installation instructions:'''

	Linux system (tested under CentOS 6.x, CentOS 7.x, Ubuntu 14.04 LTS, Ubuntu 16.04 LTS, Fedora 27)
	The latest source tarball is available here: [[:Media:SAMsrcV3-20170205.tgz\|SAMsrcV3-20170205.tgz]].
	Download and unpack with:
	tar -xzvf SAMsrcV3-20170205.tgz

	MacOS Users using the '''clang''' compiler (tested under macOS 10.13.x)
	The latest source tarball is available here: [[:Media:SAMsrcV3-20170205_clang.tgz\|SAMsrcV3-20170205_clang.tgz]].
	Download and unpack with:
	tar -xzvf SAMsrcV3-20170205_clang.tgz

	MacOS Users using the '''gcc-7''' compiler (tested under macOS 10.13.x)
	The latest source tarball is available here: [[:Media:SAMsrcV3-20170205_gcc-7.tgz\|SAMsrcV3-20170205_gcc-7.tgz]].
	Download and unpack with:
	tar -xzvf SAMsrcV3-20170205_gcc-7.tgz

	This will create a directory called SAMsrcV3.

← Older revision		Revision as of 15:52, 30 September 2020
Line 36:		Line 36:
	** [[FSnormals.py \| FSnormals.py]]		** [[FSnormals.py \| FSnormals.py]]
	** [[NIFTIPeak \| NIFTIPeak]]		** [[NIFTIPeak \| NIFTIPeak]]
			** [[3dNormalize \| 3dNormalize]]

← Older revision		Revision as of 09:46, 18 March 2019
Line 33:		Line 33:
	** [[mut_img \| mut_img]]		** [[mut_img \| mut_img]]
	* SAM Utility Program Reference Pages		* SAM Utility Program Reference Pages
	** [[orthohull \| orthohull]]		** [[orthohull.py \| orthohull.py]]
	** [[FSnormals.py \| FSnormals.py]]		** [[FSnormals.py \| FSnormals.py]]
	** [[NIFTIPeak \| NIFTIPeak]]		** [[NIFTIPeak \| NIFTIPeak]]

← Older revision		Revision as of 17:15, 12 March 2019
Line 28:		Line 28:
	** [[sam_power \| sam_power]]		** [[sam_power \| sam_power]]
	** [[sam_epi \| sam_epi]]		** [[sam_epi \| sam_epi]]
	** [[sam_hfo \| sam_hfo]]
	** [[patch_wts \| patch_wts]]		** [[patch_wts \| patch_wts]]
	** [[roi_wts \| roi_wts]]		** [[roi_wts \| roi_wts]]

← Older revision		Revision as of 17:07, 12 March 2019
Line 31:		Line 31:
	** [[patch_wts \| patch_wts]]		** [[patch_wts \| patch_wts]]
	** [[roi_wts \| roi_wts]]		** [[roi_wts \| roi_wts]]
	** [[sam_roi \| sam_roi]]
	** [[sam_entropy \| sam_entropy]]		** [[sam_entropy \| sam_entropy]]
	** [[mut_img \| mut_img]]		** [[mut_img \| mut_img]]

← Older revision		Revision as of 14:09, 7 March 2019
Line 23:		Line 23:
	** [[sam_wts \| sam_wts]]		** [[sam_wts \| sam_wts]]
	** [[sam_nwts \| sam_nwts]]		** [[sam_nwts \| sam_nwts]]
	** [[sam_3d \| sam_3d]]		** [[sam_3d and sam_3dc \| sam_3d and sam_3dc]]
	** [[~~sam_3dc~~ \| ~~sam_3dc~~]]		** [[sam_4d and sam_4dc \| sam_4d and sam_4dc]]
		⚫	** [[sam_ers and sam_ersc \| sam_ers and sam_ersc]]
	** [[sam_4d \| sam_4d]]
	** [[sam_4dc \| sam_4dc]]
	** [[sam_ers \| sam_ers]]
⚫	** [[sam_ersc \| sam_ersc]]
	** [[sam_power \| sam_power]]		** [[sam_power \| sam_power]]
	** [[sam_epi \| sam_epi]]		** [[sam_epi \| sam_epi]]