Dear all,

I wrote the following script shown at the end of my post to utilize resting-state FC measurements via AFNI. I have some basic questions concerning FC calculation. Some facts about my dataset and preprocessing with AFNI_proc:
- TR=1s
- No bandpassing in AFNI_proc
- Physiological nuisance regression (of both respiration and cardiac signals) via RetroTS and the subsequent embedding of its result in AFNI_proc

First question: is it still necessary or suggested to use bandpassing in the first part of the script, that is in 3dRSFC (e.g. 0.01 to 0.1 Hz?), even though respiration and cardiac signals are regressed out? I read that bandpassing should not be applied in AFNI_proc when the preprocessed errts file is subsequently used for FC measurements in AFNI. At the same time, bandpassing is then used in 3dRSFC. Is the result then not the same, i.e., using bandpassing first in AFNI_proc or in a second step in 3dRSFC?

Second question: my script works. In the final (third part) of the script, that is, when using 3dGroupInCorr, I start AFNI via "AFNI -niml", then I paste my 3dGroupInCorr script into the terminal (I am on a Mac), and AFNI recognizes the script. I can then select the seed voxel and inspect the correlation map via the AFNI GUI. However, I don't understand where I can find the results such as the Z-scores etc. They are neither printed in the terminal, nor are there files created as output. I would really like to directly save the results as files, this is why I additionally used the "batch mode" of 3dGroupInCorr in the end. But again, it seems that no result files are created and saved even when using the batch mode. What am I missing?

Thanks,
Philipp

Here is my script (currently only 2 subjects for testing are included)

# 3dRSFC
for subject in Subject1 Subject2
do
for fMRIruns (errts.${subject}_Rest.anaticor+tlrc)
do

directory_subjects=/volumes/sandisk/fmri/dataset/processed/$subject/preprocessing_restingstate
mkdir /volumes/sandisk/fmri/dataset/processed/$subject/Functional_Connectivity
cd $directory_subjects

3dRSFC \
-band 0.01 0.1 \
-input errts.${subject}_Rest.anaticor+tlrc \
-prefix /volumes/sandisk/fmri/dataset/processed/$subject/Functional_Connectivity/$subject

done
done

# 3dSetupGroupInCorr
mkdir /volumes/sandisk/fmri/dataset/Average_Values_RestingState
directory_subjects=/volumes/sandisk/fmri/dataset/processed
directory_average=/volumes/sandisk/fmri/dataset/Average_Values_RestingState

cd $directory_average

# Combine functional masks into a group mask
3dMean \
-verbose \
-prefix 3dSetup_AverageMask \
$directory_subjects/subject1/Preprocessing_RestingState/full_mask.Subject1_Rest+tlrc \
$directory_subjects/subject2/Preprocessing_RestingState/full_mask.Subject2_Rest+tlrc \

3dSetupGroupInCorr \
-mask $directory_average/3dSetup_AverageMask+tlrc \
-prefix 3dSetupGroupInCorr \
$directory_subjects/subject1/Functional_Connectivity/Subject1_LFF+tlrc \
$directory_subjects/subject2/Functional_Connectivity/Subject2_LFF+tlrc

3dGroupInCorr \
-setA /volumes/sandisk/fmri/dataset/Average_Values_RestingState/3dSetupGroupInCorr.grpincorr.niml \
-verb \
-seedrad 15 \
-sendall \
-labelA LFF_FC

# Alternative: 3dGroupInCorr via its "Batch Mode"

cd /volumes/sandisk/fmri/dataset/Average_Values_RestingState

3dGroupInCorr \
-batch XYZ /volumes/sandisk/fmri/dataset/Average_Values_RestingState/LFF_FC_Coordinates.txt \
-seedrad 15 \
-sendall \
-setA /volumes/sandisk/fmri/dataset/Average_Values_RestingState/3dSetupGroupInCorr.grpincorr.niml