Summary of what happened:
I am trying to use output of fMRIprep 23.0.2 with AROMA in FSL’s MELODIC ICA to run a longitudinal resting state analysis (pre/post treatment). I am wondering if I should use this output:
sub-PP_ses-01_task-restingstate_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
And if adding regressors or using other input is needed?
Moreover, using FSL guide for a multisession concatenated ICA automatically enables co-registration step, so to avoid this I am trying out the bash script below with registration options set to 0.
Lastly, if anyone has experience with multisession ICA in melodic, please advise if you used both sessions or only the first for the group level ICA? My aim is run a group ICA followed by dual-regression on components covering resting-state netowrks using the Smith et al 2009 masks.
Command used (and if a helper script was used, a link to the helper script or the command generated):
OUTPUT_DIR="MELODIC_ICA/output"
# TR(s)
TR=1.56
# Total volumes
NPTS=230
# Number of first-level analyses
MULTIPLE=60
# Input type (cope images from FEAT directories)
INPUT_TYPE=2
# Pre-stats processing
FILTERING_YN=1
# Brain/background threshold, %
BRAIN_THRESH=0
# Motion correction (None)
MC=0
# Slice timing correction (None)
ST=0
# BET brain extraction (None)
BET_YN=0
# Spatial smoothing FWHM (mm)
SMOOTH=0
# Intensity normalization (None)
NORM_YN=0
# Highpass temporal filtering
TEMPHP_YN=1
# MELODIC ICA data exploration
MELODIC_YN=0
# Carry out main stats
STATS_YN=1
# Carry out prewhitening
PREWHITEN_YN=1
# Higher-level modelling (FLAME 1)
MIXED_YN=2
# Higher-level permutations
RANDOMISE_PERMUTATIONS=5000
# Number of EVs
EVS_ORIG=1
EVS_REAL=1
EVS_VOX=0
# Number of contrasts
NCON_ORIG=1
NCON_REAL=1
# Post-stats steps
POSTSTATS_YN=1
# Thresholding (Cluster-based)
THRESH=3
PROB_THRESH=0.05
Z_THRESH=3.1
# Registration settings (Turned Off)
REGINITIAL_HIGHRES_YN=0
REGHIGHRES_YN=0
REGSTANDARD_YN=0
# High pass filter cutoff
PARADIGM_HP=100
# Process each 4D AVW data
INPUT_FILES=(
"/data1/mudarrismaa/Edinburgh_Data/MELODIC_ICA/BOLD_Aroma/sub-PP1_ses-01_task-restingstate_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold"
"/data1/mudarrismaa/Edinburgh_Data/MELODIC_ICA/BOLD_Aroma/sub-PP1_ses-02_task-restingstate_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold"
"/data1/mudarrismaa/Edinburgh_Data/MELODIC_ICA/BOLD_Aroma/sub-PP2_ses-01_task-restingstate_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold"
"/data1/mudarrismaa/Edinburgh_Data/MELODIC_ICA/BOLD_Aroma/sub-PP2_ses-02_task-restingstate_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold"
...
)
# Run FEAT for each input file
for FILE in "${INPUT_FILES[@]}"; do
echo "Processing: $FILE"
feat "$FILE"
done
echo "FEAT processing complete."
Version:
fMRIprep 23.0.2; FSL 6.0.4
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS Validator