Dear AFNI experts,

we collected resting state data from our participants before and after they performed a task (including between subject experimental manipulation). Each of these resting state runs lasts 10 minutes. We are interested in changes in resting state functional connectivity between MTL and midbrain and whether there are group differences in this and whether it relates to performance in the task. The task is to rate movie clips. Task data and resting state data have been acquired with the same scanning parameters and we have already processed the task data and would like to use the same processing for the resting state data. We implemented the code as shown below, but with this procedure, I only get one final errts* file. How can I then use that to look at the changes in functional connectivity between pre and post task? Or would I have to specify the afniproc.py differently to achieve this? Of not, we are also interested in using both, the pre and post task resting state data for other analyses, so it would be beneficial to have the errts* file for both runs separately.


Any suggestions are highly appreciated.
Many thanks,
Stef


#!/bin/tcsh
source ~/.cshrc

module load afni19.2.07

# --------------------------------------------------------------------
# Script: s.2016_ChenEtal_02_ap.tcsh
#
# From:
# Chen GC, Taylor PA, Shin Y-W, Reynolds RC, Cox RW (2016). Untangling
# the Relatedness among Correlations, Part II: Inter-Subject
# Correlation Group Analysis through Linear Mixed-Effects
# Modeling. Neuroimage (in press).
#
# Originally run using: AFNI_16.1.16
# --------------------------------------------------------------------


# FMRI processing script, ISC movie data.
# Assumes previously run FS and SUMA commands, respectively:
# $ recon-all -all -subject $subj -i $anat
# $ @SUMA_Make_Spec_FS -sid $subj -NIFTI

# Set top level directory structure
set topdir = /storage/shared/research/cinn/2018/MAGMOT #study folder
echo $topdir
set task = restingstate
set fsroot = $topdir/derivatives/FreeSurfer
set outroot = $topdir/derivatives/$task/afniproc

# define subject listecho $
set BIDSdir = $topdir/MAGMOT_BIDS

cd $BIDSdir
set subjects =(`ls -d sub*`) # this creates an array containing all subjects in the BIDS directory
echo $subjects
echo $#subjects


#set subjects = ( sub-control001 sub-control002 sub-control003 sub-experimental004 sub-experimental005 sub-experimental006)
#set subjects = ( sub-control001 sub-control002 sub-control003)
set subjects = ( sub-control001 )
echo $#subjects


# for each subject in the subjects array

foreach subj ($subjects)


#set subj = "sub-experimental005"
echo $subj

# define PWD in which the script should get saved
cd $topdir/derivatives/$task/afniproc

# Input directory: unprocessed FMRI data
set indir = $BIDSdir/$subj/func

set fsindir = $fsroot/$subj/SUMA


# Output directory: name for output
set outdir = $outroot/$subj

# Input data: list of partitioned EPIs (resting state)
set epi_dpattern = $indir"/"${subj}"_task-rest_run-*_bold.nii.gz"
echo $epi_dpattern

# Input data: FreeSurfer results (anatomy, ventricle and WM maps)
# all these files are in the ../derivatives/FreeSurfer/$SUBJ_ID/SUMA directory
set fsanat = ${subj}"_SurfVol.nii"
set fsvent = FSmask_vent.nii
set fswm = FSmask_WM.nii

# specify actual afni_proc.py
afni_proc.py -subj_id $subj.$task \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat $fsindir/$fsanat \
-anat_follower_ROI aaseg anat $fsindir/aparc.a2009s+aseg_rank.nii \
-anat_follower_ROI aeseg epi $fsindir/aparc.a2009s+aseg_rank.nii \
-anat_follower_ROI FSvent epi $fsindir/$fsvent \
-anat_follower_ROI FSWMe epi $fsindir/$fswm \
-anat_follower_erode FSvent FSWMe \
-dsets $epi_dpattern \
-tcat_remove_first_trs 0 \
-tlrc_base /usr/share/afni/atlases/MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-regress_ROI_PC FSvent 3 \
-regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast \
-regress_anaticor_label FSWMe \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-regress_polort 5 # default: 1 + floor(run_length / 150.0) run_length = 600 seconds


# execute script
tcsh -xef proc.$subj.$task |& tee output.proc.$subj.$task


end