CallingAFNISUMA
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It can be quite a chore to invoke AFNI and SUMA and set up the viewers in an aesthetically appealing way. To automate this process, in each subject directory we create a script in each subject’s home directory called “@ec” that is invoked like this:
./@ec
This does all of the work required to call AFNI and SUMA. The @ec script contains the following lines:
#! /bin/tcsh -f
echo "Calling full version of @ec that loads the std141 brains. Do it this way for easy updates of @ec script without updating multiple copies"
/Volumes/data/scripts/@ec_home_std141 $1
There are multiple copies of the @ec script (one in each subject directory). Each @ec script calls the same “home” script, @ec_home_std141 . As suggested by the comments, this script is structured this way because then only one script has to be updated (the home script) instead of updating every individual copy of the @ec script. The script @ec_home_std141 contains the following lines:
#! /bin/tcsh -f
echo "@ec: A script that automatically loads AFNI and SUMA for the current directory. See the Beauchamp Lab wiki ([Beauchamp](/LabWiki/pages/Beauchamp/)) for more details."
echo "This version of the script (@ec_home_std141) loads the std 141 brains because they are better for intersubject comparisons. This is designed for use with FreeSurfer 6.0. Michael S Beauchamp, August 2017."
echo "It should be run from an experiment directory. Example usage 1: cd /Volumes/data/BCM/XX \n ./@ec \n"
set scriptsdir = /Volumes/data/scripts
set subjdir = `pwd`
cd afni
set afnidir = `pwd`
cd ../fs/SUMA
set sumadir = `pwd`
# Check if T1 anatomy exists for surface volume. If not, create it (required because AFNI multiple sessions functionality does not work with SUMA.)
cd $afnidir
if ( -f T1.nii ) then
echo "T1.nii already in place, loading AFNI and SUMA right away."
else
cd $sumadir
if ( -f T1.nii ) then
echo "Copying T1.nii from SUMA directory to AFNI directory."
cp T1.nii {$afnidir}
else
echo "Please create a T1.nii file in the AFNI directory to serve as SUMA's surface volume reference. e.g. 3dcopy XXanatavg+orig T1.nii"
goto END
endif
endif
cd $afnidir
afni -R -niml . $sumadir &
suma -niml -spec {$sumadir}/std.141.fs_both.spec -sv {$afnidir}/T1.nii &
DriveSuma -com surf_cont -load_dset {$sumadir}/std.141.lh.sulc.niml.dset -surf_label lh.smoothwm.gii -view_surf_cont y -load_cmap {$scriptsdir}/nice.1D.cmap -Dim 0.6
DriveSuma -com surf_cont -switch_cmap nice.1D -Dim 0.6
DriveSuma -com viewer_cont -key b -1_only n
DriveSuma -com viewer_cont -key F3
DriveSuma -com viewer_cont -load_view {$scriptsdir}/nice.niml.vvs -com surf_cont -switch_surf lh.inf_200.gii
DriveSuma -com viewer_cont -key t
DriveSuma -com surf_cont -1_only n
END:
This script references the following files. nice.1D.cmap contains the following lines
0.30 0.30 0.30
0.33 0.33 0.33
0.35 0.35 0.35
0.38 0.38 0.38
0.41 0.41 0.41
0.43 0.43 0.43
0.46 0.46 0.46
0.48 0.48 0.48
0.51 0.51 0.51
0.54 0.54 0.54
0.56 0.56 0.56
0.59 0.59 0.59
0.62 0.62 0.62
0.64 0.64 0.64
0.67 0.67 0.67
0.69 0.69 0.69
0.72 0.72 0.72
0.75 0.75 0.75
0.77 0.77 0.77
0.80 0.80 0.80
nice.niml.vvs contains the following lines
# <Viewer_Visual_Setting
# self_idcode = "XYZ_DwOIIz5Qag0UTN_FQL9Ytw"
# domain_parent_idcode = "~"
# geometry_parent_idcode = "~"
# currentQuat = "0.500000 -0.500000 -0.500000 0.500000 "
# translateVec = "0.000000 0.000000 "
# clear_color = "1.000000 1.000000 1.000000 0.000000 "
# FOV = "55.518543"
# Aspect = "1.000000"
# WindWidth = "350"
# WindHeight = "350"
# BF_Cull = "0"
# Back_Modfact = "3.000000"
# PolyMode = "1"
# ShowEyeAxis = "0"
# ShowMeshAxis = "0"
# ShowWorldAxis = "0"
# ShowCrossHair = "0"
# ShowForeground = "1"
# ShowBackground = "0"
# />