Summary of what happened:
Ran nibabies and then xcpd in hbcd mode (running on infants 3-6months) and put in 15-35 bandstop (due to babies high breathing rate). But this was changed by xcpd due to “Nyquist frequency constraints”. Is there a recommended way to process infant data with xcpd (eg HBCD), and is it fine to use this processing with 15-25 as was modified ?
Thanks
NB
Command used (and if a helper script was used, a link to the helper script or the command generated):
sub-nibabies-25.0.1 -i /MRI_DATA/mritesting/marscombo/rawdata/ -o /MRI_DATA/mritesting/marscombo/derivatives/nibabies/v25_0_1 -d /MRI_DATA/mritesting/marscombo/derivatives/nibabies/work -l /MRI_DATA/mritesting/marscombo/derivatives/nibabies/v25_0_1/v_25_sub-marscombo329567_multi.log -a "--participant-label marscombo329567 --norm-csf --cifti-output 91k"
sub-xcp_d-0.10.7 -i /MRI_DATA/mritesting/marscombo/derivatives/nibabies/v25_0_1 -o /MRI_DATA/mritesting/marscombo/derivatives/xcp_d_0_10_7 -l /MRI_DATA/mritesting/marscombo/derivatives/xcp_d_0_10_7/marscombo218838_xcpd.log -a " --mode hbcd --participant-label marscombo218838 --min-time 30 --motion-filter-type notch --band-stop-min 15 --band-stop-max 35"
Version:
0.10.7
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
[environment]
cpu_count = 40
exec_env = "posix"
free_mem = 123.3
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "24.2.2"
version = "0.10.7"
[execution]
fmri_dir = "/input"
aggr_ses_reports = 4
bids_database_dir = "/tmp/working_dir/20250610-183517_8a8ac1ca-6308-4101-a86d-c32220e1ed1a/bids_db"
bids_description_hash = "071fbb55a084eed12bd9f5c0dd248695a3e0f9eb63bf34465ce7aada5ca6d46a"
boilerplate_only = false
confounds_config = "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/nuisance/36P.yml"
debug = []
fs_license_file = "/opt/freesurfer/license.txt"
layout = "BIDS Layout: .../input | Subjects: 1 | Sessions: 1 | Runs: 3"
log_dir = "/output/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
reports_only = false
output_dir = "/output"
atlases = [ "4S1056Parcels", "4S156Parcels", "4S256Parcels", "4S356Parcels", "4S456Parcels", "4S556Parcels", "4S656Parcels", "4S756Parcels", "4S856Parcels", "4S956Parcels", "Glasser", "Gordon", "HCP", "MIDB", "MyersLabonte", "Tian",]
run_uuid = "20250610-183517_8a8ac1ca-6308-4101-a86d-c32220e1ed1a"
participant_label = [ "marscombo565325",]
templateflow_home = "/home/xcp_d/.cache/templateflow"
work_dir = "/tmp/working_dir"
write_graph = false
[workflow]
mode = "hbcd"
file_format = "cifti"
dummy_scans = 0
input_type = "nibabies"
despike = true
smoothing = 6
output_interpolated = true
combine_runs = true
motion_filter_type = "notch"
band_stop_min = 15.0
band_stop_max = 35.0
motion_filter_order = 4
head_radius = 50
fd_thresh = 0.3
min_time = 30.0
bandpass_filter = true
high_pass = 0.01
low_pass = 0.08
bpf_order = 2
min_coverage = 0.5
correlation_lengths = []
process_surfaces = true
abcc_qc = true
linc_qc = true
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 2
omp_nthreads = 1
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 57726
[execution.datasets]
xcpdatlases = "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases"
xcpd4s = "/AtlasPack"
[execution.dataset_links]
preprocessed = "/input"
templateflow = "/home/xcp_d/.cache/templateflow"
atlas = "/output/atlases"
xcpdatlases = "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases"
xcpd4s = "/AtlasPack"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
