Beauchamp:IfCortModExists: Difference between revisions
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There are two procedures for this situation. The old method, developed when storage space was expensive, was to have one copy of each subject's surface model (in a /surfaces directory) and to align each new scanning session (and all its constituent data) to that surface. The new method is to create a copy of each subject's surface model in each experiment directory, so there is one surface for each scanning session. This is simpler although it uses more space. | There are two procedures for this situation. The old method, developed when storage space was expensive, was to have one copy of each subject's surface model (in a /surfaces directory) and to align each new scanning session (and all its constituent data) to that surface. The new method is to create a copy of each subject's surface model in each experiment directory, so there is one surface for each scanning session. This is simpler although it uses more space. | ||
=== | |||
== OLD METHOD == | |||
= Automation = | |||
All of the steps below are contained in the scripts file | All of the steps below are contained in the scripts file | ||
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3dcopy 3DSAG_T1.nii ${ec}anatavg | 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) | 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. | e.g. | ||
Revision as of 07:29, 4 November 2013
What if I have scanned a subject for whom a surface model already exists?
There are two procedures for this situation. The old method, developed when storage space was expensive, was to have one copy of each subject's surface model (in a /surfaces directory) and to align each new scanning session (and all its constituent data) to that surface. The new method is to create a copy of each subject's surface model in each experiment directory, so there is one surface for each scanning session. This is simpler although it uses more space.
OLD METHOD
Automation
All of the steps below are contained in the scripts file /Volumes/data9/surface/scripts/@alreadymade
To run this command type,
/Volumes/data9/surfaces/scripts/@alreadymade current_ec subjname original_surface_ec
Where current_ec is the current two-letter experiment code 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 ${ec}anatavg
Aligning to Experiment
The scripts assumes that all of the steps performed the script file @prep_dir have been performed (see Preparation for Creating Cortical Surface Models page) e.g.
/Volumes/data9/surfaces/scripts/@recon BD doe_jane
First, check to make sure that the already created surface has the necessary components created by the @finish script
FSread_annot -input ../label/lh.aparc.a2005s.annot -roi_1D ./lh.aparc.a2005s.1D.roi
FSread_annot -input ../label/rh.aparc.annot -roi_1D ./rh.aparc.1D.roi
FSread_annot -input ../label/lh.aparc.annot -roi_1D ./lh.aparc.1D.roi
mris_convert -c ../surf/lh.sulc ../surf/lh.smoothwm ./lh.sulc.asc
mris_convert -c ../surf/rh.sulc ../surf/rh.smoothwm ./rh.sulc.asc
set ec = TA203
SurfSmooth -spec {$ec}_both.spec -surf_A lh.smoothwm.asc -met NN_geom -surf_out lh.smoothwm.SS500.ply -Niter 500 -match_area 0.01
SurfSmooth -spec {$ec}_both.spec -surf_A rh.smoothwm.asc -met NN_geom -surf_out rh.smoothwm.SS500.ply -Niter 500 -match_area 0.01
cp /Volumes/data9/surfaces/scripts/both.spec ./both.spec
Next, go to the surfaces directory, create a copy of the new anatomy, and align it the new data with the old surface model.
3dcopy /Volumes/data1/UT/CZ/afni/CZanatr1+orig ./CZanatr1 @SUMA_AlignToExperiment -exp_anat CZanatr1+orig -surf_anat TA203_SurfVol+orig -prefix CZ_SurfVol_Alnd_Exp mv CZ_SurfVol_Alnd_Exp+orig.* /Volumes/data1/UT/CZ/afni/
Next, create an @EC file that points to the appropriate directory:
cat >> @CZ /Volumes/data9/surfaces/scripts/@ec CZ /Volumes/data9/surfaces/TandonLang/TA203/SUMA
