Differences between revisions 2 and 5 (spanning 3 versions)
⇤ ← Revision 2 as of 2006-05-31 18:13:26 →
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Editor: NickSchmansky
Comment: updated (still needs more)
← Revision 5 as of 2006-06-01 14:38:00 → ⇥
Size: 2655
Editor: NickSchmansky
Comment:
Deletions are marked like this. Additions are marked like this.
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= DISCLAIMER NOTE =

THIS PAGE '''NEEDS''' FIGURES and some further edits.
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For each cut, select the points (LEFT-CLICK) and then press the Cut icon (scissors with an open triangle for a line cut). Make the points fairly close together; if they are too far apart, the cut fails.
 For each cut, select the points (left-click) and then press the Cut icon (scissors with an open triangle for a line cut). Make the points fairly close together; if they are too far apart, the cut fails.
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 1. Encircle midline region (corpus callosum and mid-brain structures) to remove:
  * LEFT-CLICK sequence

 1. Make closed-line cut.
  * CUTAREA button

 1. Mark and fill region to save.
  * Single left-click in region to save.
  * Press Fill Uncut Area button (icon = filled triangle). This will fill the patch with white. The non-patch area will be unaccessible through the interface.

 1. Save patch.
  * Select File->Patch->SaveAs. Specify the patch name in the patch field.
  * The default names for the full cortical surfaces with the midline removed are:
   * rh.full.patch.3d
   * lh.full.patch.3d		  2. Encircle midline region (corpus callosum and mid-brain structures) to remove:
  * Left-click a circle of points, being sure to encompass the ends of the radial cuts
  * Once the circle of points are selected, click the Cut Closed Line icon
  * Single left-click in the newly cut circle
  * Press Fill Uncut Area button (icon = filled triangle)
 3. Save patch:
  * Select File->Patch->Save Patch As. Specify the patch name in the Selection field:
   * The default names for the full cortical surfaces with the midline removed are:
    * lh.full.patch.3d
    * rh.full.patch.3d
 4. Create flattened patch:
{{{
mris_flatten lh.full.patch.3d lh.full.flat.patch.3d
}}}
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1. Specify cutting plane.		  2. Specify cutting plane.
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1. Make the planar cut.		  3. Make the planar cut.
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1.. Save patch.		  4.. Save patch.

This process provides the user with flattened images of the whole brain or select parts (e.g. occipital lobe) of the brain.

Cutting the Full Surface

The full surface represents an entire hemisphere without the mid-brain (middle of the medial surface). First, load the subject surface into tksurfer: 

tksurfer subjid lh inflated

Load the curvature through the File->Curvature->Load menu (load lh.curv). This should show a green/red curvature pattern. Red = sulci.

Right click before making a cut; this will clear previous points. This is needed because it will string together all the previous places you have clicked to make the cut.

  1. Make 5 relaxation cuts. For each cut, select the points (left-click) and then press the Cut icon (scissors with an open triangle for a line cut). Make the points fairly close together; if they are too far apart, the cut fails.
    • 1 cut down the calcarine (same cut as for the occiput surface)
    • 3 equally spaced radial cuts on the medial surface
    • 1 sagitally oriented cut around the temporal pole
  2. Encircle midline region (corpus callosum and mid-brain structures) to remove:
    • Left-click a circle of points, being sure to encompass the ends of the radial cuts
    • Once the circle of points are selected, click the Cut Closed Line icon
    • Single left-click in the newly cut circle
    • Press Fill Uncut Area button (icon = filled triangle)
  3. Save patch:

    • Select File->Patch->Save Patch As. Specify the patch name in the Selection field:

      • The default names for the full cortical surfaces with the midline removed are:
        • lh.full.patch.3d
        • rh.full.patch.3d
  4. Create flattened patch: 

mris_flatten lh.full.patch.3d lh.full.flat.patch.3d

Cutting the Occiput Surface

The occiput patch represents the occipital pole with a cut down the calcarine fissure. This cortical patch is particularly useful for displaying the results of visual experiments.

In tksurfer:

  1. Make calcarine sulcus relaxation cut.
    • Select points (left-click) along the calcarine fissure beginning at the occipital pole and moving anteriorly.
    • Open-line cut with CUTLINE (surfer tools).
  2. Specify cutting plane.
    • Select three points (labeled 1, 2, and 3 below) to define the cutting plane, and a fourth point (labeled 4 below) to specify which portion of the surface to keep (left-click).
  3. Make the planar cut.
    • CUTPLANE button.
    4.. Save patch.
    • Specify the patch name in the patch field and press WRITE.
    • ...
    • The default names for the occiput cortical surfaces are:
      • rh.occip.patch.3d
      • lh.occip.patch.3d

FreeSurferOccipitalFlattenedPatch (last edited 2021-07-15 08:06:05 by DevaniCordero)