Beauchamp:CorticalSurfaceOverview: Difference between revisions
No edit summary |
No edit summary |
||
| Line 7: | Line 7: | ||
Previous step is | Previous step is | ||
[[Beauchamp:CreateAFNIBRIKfromMR|Getting raw data from the scanner]] | [[Beauchamp:CreateAFNIBRIKfromMR|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== | ==MRI: Cortical Surface Models== | ||
Revision as of 13:46, 1 May 2014
|
Beauchamp Lab
|
|
Previous step is Getting raw data from the scanner
Averaging Anatomical Scans Using AFNITo 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 ${subj}anatr2_2RegTo1+orig
MRI: Cortical Surface ModelsThere is a simple three step process for creating surface models. The steps assume that you are in the afni subdirectory of the subject for which a surface is to be created. cd /Volumes/data/UT/IZ/afni Step 1: Prepare the FreeSurfer directory tree /Volumes/data/scripts/@prep_dir IZanatavg+orig.BRIK Step 2: Reconstruct the surface. Note that the name of the anatomy is not needed, but if you are using the up arrow in the UNIX shell to recall the last command and edit it, there is no need to delete the filename. This step takes many hours! /Volumes/data/scripts/@recon IZanatavg+orig.BRIK Step 3: Finish the surface /Volumes/data/scripts/@finish IZanatavg+orig.BRIK step 4: Check the created surface cd .. ./@ec Or in a more economical way: set ec = IZ
cd /Volumes/data/UT/{$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 ..
./@ec
For more details, see the following web pages:
|
