Dear all,

I am currently stuck on the problem that my resting-state analysis with afni_proc.py results in a flawed outcome. This problem only occurs for my resting-state runs (for all subjects) and not for the task-based runs. The results of the latter are fine.

The problem is that when I open my errts file (e.g. "errts.Subject1_Rest.anaticor+tlrc") there is activation all around the brain (once I increase the threshold slightly) but not in the brain. Please notice the screenshot that I added, it makes the problem all clear.

Please let me know what you think. Where do you think could the problem be located? In what direction should I look?

By the way: A friend of mine reminded me that I have to use the errts for a resting-state analysis as underlay in the AFNI Gui. I did that. Even if I choose AnatQQ or AnatSS as underlay (and then errts as overlay) the problem remains the same for all kinds of combinations. So I think the problem is not that I simply don't use the Gui accordingly, but the problem has to be somewhere else.

This is my resting-state analysis script:

## Resting-State Preprocessing
for subject in Subject1 Subject2
do

# Set directories
directory_subjects=/users/philipp/desktop/fmri/dataset/subjects/$subject
directory_subjects_general=/users/philipp/desktop/fmri/dataset/subjects
directory_fMRIruns=$directory_subjects/raw
directory_anatomical=$directory_subjects/raw
directory_SSwarper=$directory_subjects/SSwarper

# Run SSwarper
mkdir $directory_subjects/SSwarper
@SSwarper \
-input $directory_anatomical/3dto3d+orig \
-base MNI152_2009_template_SSW.nii.gz \
-subid $subject \
-odir $directory_subjects/SSwarper

cd $directory_subjects

# AFNI_proc.py
afni_proc.py \
-subj_id ${subject}_Rest \
-out_dir $directory_subjects/Preprocessing_RestingState \
-dsets \
$directory_fMRIruns/restto3d+orig \
-blocks despike tshift align tlrc volreg mask blur scale regress \
-copy_anat $directory_SSwarper/anatSS.$subject.nii \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-align_opts_aea -cost nmi \
-volreg_align_e2a \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
$directory_subjects/SSwarper/anatQQ.$subject.nii \
$directory_subjects/SSwarper/anatQQ.$subject.aff12.1D \
$directory_subjects/SSwarper/anatQQ.${subject}_WARP.nii \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_anaticor \
-regress_ROI WMe \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.05 \
-regress_bandpass 0.02 0.2 \
-blur_size 6.0 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic \
-execute

done