Difference between revisions of "Orthohull.py"

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==Description==
 
==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.
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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==
 
==Usage==
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Other options:
 
Other options:
 
{|
 
{|
|- " valign="top"
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|- valign="top"
| 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
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| 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
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|- valign="top"
|-
 
| -x prefix: || Used to specify a prefix for all output files, this defaults to no prefix.
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| -x prefix || Used to specify a prefix for all output files, this defaults to no prefix.
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|- valign="top"
|-
 
| -i <inf>: || Used to specify the amount by which the brainhull.ply surface is inflated for the final headmodel. Defaults to 0.005, which inflates the surface by 0.5cm, preventing clipping. use -i0 for no inflation.
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| -i <inf> || Used to specify the amount by which the brainhull.ply surface is inflated for the final headmodel. Defaults to 0.005, which inflates the surface by 0.5cm, preventing clipping. use -i0 for no inflation.
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|- valign="top"
|-
 
 
| -t || Do the Talairach transform as part of the preprocessing (recommended). This will be performed using the AFNI program @auto_tlrc. The Talairach transform will be stored in the header of the ortho+tlrc image.
 
| -t || Do the Talairach transform as part of the preprocessing (recommended). This will be performed using the AFNI program @auto_tlrc. The Talairach transform will be stored in the header of the ortho+tlrc image.
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|- valign="top"
|-
 
 
| -m || Same as -t, but instead of TT_N27+tlrc, use MNI_caez_N27+tlrc as the template.
 
| -m || Same as -t, but instead of TT_N27+tlrc, use MNI_caez_N27+tlrc as the template.
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|- valign="top"
|-
 
 
| -o || By default, the Talairach transform is performed on the ortho/MEG space image, which has been rotated such that all three fiducial points lie in a horizontal plane. Sometimes the Talairach transform will fail, because of the large initial mismatch between the ortho image and the template. This option requests that the Talairach transform be derived using the original space skull stripped image. In this case, the transform will be stored in the file ORTHO_to_TLRC.1D, and can be applied to MEG images using 3dWarp matvec_in2out.
 
| -o || By default, the Talairach transform is performed on the ortho/MEG space image, which has been rotated such that all three fiducial points lie in a horizontal plane. Sometimes the Talairach transform will fail, because of the large initial mismatch between the ortho image and the template. This option requests that the Talairach transform be derived using the original space skull stripped image. In this case, the transform will be stored in the file ORTHO_to_TLRC.1D, and can be applied to MEG images using 3dWarp matvec_in2out.
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|- "valign="top"
|-
 
 
| -q || Forces the output of the hull to be convex (only strictly necessary for problem surfaces)
 
| -q || Forces the output of the hull to be convex (only strictly necessary for problem surfaces)
 
|}
 
|}
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==Output Files==
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orthohull.py essentially runs a series of mostly AFNI commands. Output files are detailed below, grouped according to the routine that generated them. These are for the default implementation, with no prefix specified.
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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
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3dCalc: Uses the mask and the original anat file to produce brain+orig.HEAD and brain+orig.BRIK
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3dTagAlign: Produces tagalong_xform.1D, ortho+orig.HEAD, and ortho+orig.BRIK
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ConvertSurface: Produces ortho_brainhull.ply (or a transform to ortho space of whatever surface was specified by -p
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SpharmDeco: Produces smooth_ortho_brainhull.ply
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meshnorm: Produces hull.shape
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ply2fid: Produces multisphere.shape and multisphere.shape_info
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@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

Latest revision as of 12:34, 18 March 2019

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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. In addition, python and numpy must also be available.

Usage

orthohull.py anat+orig

Other options:

-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.
-i <inf> Used to specify the amount by which the brainhull.ply surface is inflated for the final headmodel. Defaults to 0.005, which inflates the surface by 0.5cm, preventing clipping. use -i0 for no inflation.
-t Do the Talairach transform as part of the preprocessing (recommended). This will be performed using the AFNI program @auto_tlrc. The Talairach transform will be stored in the header of the ortho+tlrc image.
-m Same as -t, but instead of TT_N27+tlrc, use MNI_caez_N27+tlrc as the template.
-o By default, the Talairach transform is performed on the ortho/MEG space image, which has been rotated such that all three fiducial points lie in a horizontal plane. Sometimes the Talairach transform will fail, because of the large initial mismatch between the ortho image and the template. This option requests that the Talairach transform be derived using the original space skull stripped image. In this case, the transform will be stored in the file ORTHO_to_TLRC.1D, and can be applied to MEG images using 3dWarp matvec_in2out.
-q Forces the output of the hull to be convex (only strictly necessary for problem surfaces)

Output Files

orthohull.py essentially runs a series of mostly AFNI commands. Output files are detailed below, grouped according to the routine that generated them. These are for the default implementation, with no prefix specified.

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

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

SpharmDeco: Produces smooth_ortho_brainhull.ply

meshnorm: Produces hull.shape

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