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Brain picture
Beauchamp Lab

Previous step is Getting raw data from the scanner

Averaging Anatomical Scans Using AFNI

To register all the anatomicals to the space of the anatomical closest in time to the functional data (generally anatr1), this is with just two anatomical's:

 3dAllineate -base ${subj}anatr1+orig -source ${subj}anatr2+orig -prefix ${subj}anatr2_2RegTo1 -verb -warp shift_rotate -cost mi -automask -1Dfile ${subj}anatr2toanatr1

Average anatomicals into one dataset:

 3dmerge -gnzmean -nscale -prefix ${subj}anatavg ${subj}anatr1+orig ${subj}anatr2_2RegTo1+orig

MRI: Cortical Surface Models

There is a simple three step process for creating surface models. The steps assume that you are in the afni subdirectory of the subject for which a surface is to be created.

 cd /Volumes/data/UT/IZ/afni

Step 1: Prepare the FreeSurfer directory tree

 /Volumes/data/scripts/@prep_dir IZanatavg+orig.BRIK  

Step 2: Reconstruct the surface. Note that the name of the anatomy is not needed, but if you are using the up arrow in the UNIX shell to recall the last command and edit it, there is no need to delete the filename. This step takes many hours!

 /Volumes/data/scripts/@recon IZanatavg+orig.BRIK

Step 3: Finish the surface

 /Volumes/data/scripts/@finish IZanatavg+orig.BRIK

step 4: Check the created surface

 cd ..

Or in a more economical way:

 set ec = IZ
 cd /Volumes/data/UT/{$ec}/afni
 /Volumes/data/scripts/@prep_dir {$ec}anatavg+orig.BRIK  
 /Volumes/data/scripts/@recon {$ec}anatavg+orig.BRIK
 /Volumes/data/scripts/@finish {$ec}anatavg+orig.BRIK
 cd ..

For more details, see the following web pages:

  1. Preparation for Creating Cortical Surface Models
  2. Creating Cortical Surface Models
  3. Final touches and using Cortical Surface Models
  4. What If a Cortical Surface Model Exists Already
  5. What If Cortical Surface Model Looks Bad
  6. Creating Standardized Surface Models
  7. FreeSurfer Standard Surface Models
  8. Finding Distances on the Surface
  9. Finding Closest node on the Surface
  10. SUMA
  11. Free Surfer
  12. Caret
  13. How to make 3D print outs of cortical surface models
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