Was playing around with resting state data using new to me tools of SS Warper combined with Afni_proc.py with anaticor (akin to example 9B but with B-O-B's SS Warper suggestions).
Questions:
(a) is this a reasonable combination of SS Warper results with AFNI_PROC?
(b) any suggestions for speeding this up?
Was playing on my quad core MacBook Pro to test it before rolling it out to our SLURM scheduling/REDHAT 7 computer cluster.
But--it's taking forever.
Tnx and Happy Spring to All!
SCRIPT USED/RUNNING AS WE SPEAK:
set subjects = (1234 5678)
set topdir = /Users/ddickstein/GROUP
set task = REST
set group = PEEPS
set subjdata = $topdir/RawImagingData/$group
set results = $topdir/IndvlLvlAnalyses_Cnsr1mm
# Go to the results tree and work from there
cd $results
# If it does not yet exist, create the group directory within the results directory
# ! = not; -d = directory
if ( ! -d $group ) mkdir $group
# Go to the newly created, or already exsting group directory
cd $group
# If it does not yet exist, create the task directory within the group directory
# ! = not; -d = directory
if ( ! -d $task ) mkdir $task
# Go to the newly created, or already exsting task directory
cd $task
# For each of the subjects, specified in the subjects list...
foreach subj ( $subjects )
# Delete the subject's existing results folder
if ( -d $subj ) then
# Print the following message to the screen
echo "-- deleting old results for $subj"
# Force recursive removal
rm -fr $subj
endif
# Make a new subject's results folder, and go into that folder to work
mkdir $subj
cd $subj
set subj_dir = $subjdata/$subj
set btemplate = MNI152_2009_template_SSW.nii.gz
set tpath = `@FindAfniDsetPath ${btemplate}`
if( "$tpath" == "" ) exit 1
afni_proc.py -subj_id ${subj} \
-dsets $subj_dir/afni/${subj}_REST.nii.gz \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $subj_dir/anat/anatSS.${subj}.nii \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-align_opts_aea -ginormous_move -deoblique on -cost lpc+ZZ \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp -tlrc_base $tpath/$btemplate \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
$subj_dir/anat/anatQQ.${subj}.nii \
$subj_dir/anat/anatQQ.${subj}.aff12.1D \
$subj_dir/anat/anatQQ.${subj}_WARP.nii \
-mask_epi_anat yes \
-regress_anaticor \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.05 \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_run_clustsim no \
-regress_est_blur_epits \
-regress_est_blur_errts \
cd ..
end
