Orthohull.py - Revision history

Nugenta at 16:34, 18 March 2019

2019-03-18T16:34:53Z

← Older revision		Revision as of 12:34, 18 March 2019
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	3dSkullStrip: produces mask+orig.HEAD and mask+orig.BRIK, also surfaces anat.ply, anat_brainhull.ply, anat_innerskull.ply and anat_outerskull.ply		3dSkullStrip: produces mask+orig.HEAD and mask+orig.BRIK, also surfaces anat.ply, anat_brainhull.ply, anat_innerskull.ply and anat_outerskull.ply

	3dCalc: Uses the mask and the original anat file to produce brain+orig.HEAD and brain+orig.BRIK		3dCalc: Uses the mask and the original anat file to produce brain+orig.HEAD and brain+orig.BRIK

	3dTagAlign: Produces tagalong_xform.1D, ortho+orig.HEAD, and ortho+orig.BRIK		3dTagAlign: Produces tagalong_xform.1D, ortho+orig.HEAD, and ortho+orig.BRIK

	ConvertSurface: Produces ortho_brainhull.ply (or a transform to ortho space of whatever surface was specified by -p		ConvertSurface: Produces ortho_brainhull.ply (or a transform to ortho space of whatever surface was specified by -p

	SpharmDeco: Produces smooth_ortho_brainhull.ply		SpharmDeco: Produces smooth_ortho_brainhull.ply

	meshnorm: Produces hull.shape		meshnorm: Produces hull.shape

	ply2fid: Produces multisphere.shape and multisphere.shape_info		ply2fid: Produces multisphere.shape and multisphere.shape_info

	@auto_tlrc: Produces (if requested) ortho+tlrc.HEAD and ortho+tlrc.BRIK, as well as ortho_WarpDrive.log, ortho.Xaff12.1D and ortho.Xat.1D. Note that with the -o option, instead of "ortho", Talairached "brain" files will be created, along with ORTHO_to_TLRC.1D		@auto_tlrc: Produces (if requested) ortho+tlrc.HEAD and ortho+tlrc.BRIK, as well as ortho_WarpDrive.log, ortho.Xaff12.1D and ortho.Xat.1D. Note that with the -o option, instead of "ortho", Talairached "brain" files will be created, along with ORTHO_to_TLRC.1D

Nugenta at 16:34, 18 March 2019

2019-03-18T16:34:23Z

@@ Line 3: / Line 3: @@
 ==Description==
-The program orthohull.py takes a T1 weighted anatomical MRI, with tags placed for the three fiducial points (nasion, and left and right preauricular), and creates a headmodel for use with the SAM software. This program will not function if afni is not installed.
+The program orthohull.py takes a T1 weighted anatomical MRI, with tags placed for the three fiducial points (nasion, and left and right preauricular), and creates a headmodel for use with the SAM software. This program will not function if afni is not installed. In addition, python and numpy must also be available.
 ==Usage==
@@ Line 26: / Line 26: @@
 |  -q          || Forces the output of the hull to be convex (only strictly necessary for problem surfaces)
 |}

Nugenta at 14:59, 18 March 2019

2019-03-18T14:59:24Z

← Older revision		Revision as of 10:59, 18 March 2019
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	{\|		{\|
	\|- valign="top"		\|- valign="top"
	\| style="width: ~~12em~~" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width: 10em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|- valign="top"		\|- valign="top"
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.

Nugenta at 14:59, 18 March 2019

2019-03-18T14:59:13Z

← Older revision		Revision as of 10:59, 18 March 2019
Line 11:		Line 11:
	Other options:		Other options:
	{\|		{\|
			\|- valign="top"
	\|-
	\| style="width: ~~16em~~" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width: 12em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
			\|- valign="top"
	\|-
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.
	\|- valign="top"		\|- valign="top"

Nugenta at 14:58, 18 March 2019

2019-03-18T14:58:56Z

← Older revision		Revision as of 10:58, 18 March 2019
Line 12:		Line 12:
	{\|		{\|
	\|-		\|-
	\| style="width=16em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width: 16em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|-		\|-
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.

Nugenta at 14:58, 18 March 2019

2019-03-18T14:58:17Z

← Older revision		Revision as of 10:58, 18 March 2019
Line 12:		Line 12:
	{\|		{\|
	\|-		\|-
	\| style="width 16em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width=16em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|-		\|-
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.

Nugenta at 14:57, 18 March 2019

2019-03-18T14:57:50Z

← Older revision		Revision as of 10:57, 18 March 2019
Line 12:		Line 12:
	{\|		{\|
	\|-		\|-
	\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width 16em" \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|-		\|-
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.

Nugenta at 14:57, 18 March 2019

2019-03-18T14:57:29Z

← Older revision		Revision as of 10:57, 18 March 2019
Line 13:		Line 13:
	\|-		\|-
	\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
			\|-
	\|- valign="top"
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.
	\|- valign="top"		\|- valign="top"

Nugenta at 14:57, 18 March 2019

2019-03-18T14:57:06Z

← Older revision		Revision as of 10:57, 18 March 2019
Line 11:		Line 11:
	Other options:		Other options:
	{\|		{\|
			\|-
	\|- valign="top"
	\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|- valign="top"		\|- valign="top"

Nugenta at 14:56, 18 March 2019

2019-03-18T14:56:27Z

← Older revision		Revision as of 10:56, 18 March 2019
Line 11:		Line 11:
	Other options:		Other options:
	{\|		{\|
	\|-		\|- valign="top"
	\| style="width 16em;~~valign="top"~~ \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply		\| style="width 16em"; \| -p surfacename \|\| specifies the surface to use to create the headmodel. The default is the brainhull.ply produced by AFNI's 3dSkullStrip routine. Other options include innerskull.ply or outerskull.ply
	\|- valign="top"		\|- valign="top"
	\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.		\| -x prefix \|\| Used to specify a prefix for all output files, this defaults to no prefix.