Beauchamp:EditingCortSurf: Difference between revisions

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(New page: == What if I have scanned a subject for whom a surface model already exists? == == Automation == All of the steps below are contained in the scripts file /Volumes/data9/surface/scripts/@...)
 
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== What if I have scanned a subject for whom a surface model already exists? ==
== What if I have created a surface model and it looks bad? ==


== Automation ==
Sometimes the cortical surface model created by FreeSurfer contains large errors.
For instance, in this picture, part of the pia-arachnoid-dura has been classified as part of the cortex.


All of the steps below are contained in the scripts file
To fix this error, AFNI's "draw dataset" plug-in can be used to try and fix the problem.
/Volumes/data9/surface/scripts/@alreadymade
Change the {$ec}_anatavg+orig dataset directly. (If something goes wrong, a new one can be made from the original T1s).
Set the drawing value to 0 and pick a paintbrush style.
Identify the offending voxels and paint them in black.
Then, rerun the surface creation routine.


To run this command type,
  mv graham_tim graham_tim_v0
   /Volumes/data9/surfaces/scripts/@alreadymade current_ec subjname original_surface_ec
   /Volumes/data9/surfaces/scripts/@prep_dir {$ec} $subj
Where current_ec is the current two-letter experiment code
   /Volumes/data9/surfaces/scripts/@recon {$ec} $subj
subjname is the subject's name in the format lastname_firstname.
original_surface_ec is the two letter experiment code which the surface was originally constructed from
(this must be determined by looking in the surfaces directory).
Note that an anatavg must exist in the afni directory. If it doesn't create with
  3dcopy 3DSAG_T1.nii ${ec}anatavg
 
== Aligning to Experiment ==
The scripts assumes that all of the steps performed the script file @prep_dir have been performed (see Preparation for Creating Cortical Surface Models page)
e.g.
   /Volumes/data9/surfaces/scripts/@recon BD doe_jane

Revision as of 11:07, 29 April 2009

What if I have created a surface model and it looks bad?

Sometimes the cortical surface model created by FreeSurfer contains large errors. For instance, in this picture, part of the pia-arachnoid-dura has been classified as part of the cortex.

To fix this error, AFNI's "draw dataset" plug-in can be used to try and fix the problem. Change the {$ec}_anatavg+orig dataset directly. (If something goes wrong, a new one can be made from the original T1s). Set the drawing value to 0 and pick a paintbrush style. Identify the offending voxels and paint them in black. Then, rerun the surface creation routine. 

 mv graham_tim graham_tim_v0
 /Volumes/data9/surfaces/scripts/@prep_dir {$ec} $subj
 /Volumes/data9/surfaces/scripts/@recon {$ec} $subj
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