Cant get func - cifti outputs

[nbustos]

What happened?

Am only getting MNI space func ouputs, not cifti. I would expect both to be output such as in fmriprep. (I do get anat cifti outputs).

When changing input for --cifti-output flag it will only change anat outputs but not func ?

Shouldn't default be to output both mni and cifti space func outputs ?

What command did you use?

sub-nibabies-23.1.0 -i /MRI_DATA/mritesting/marscombo/rawdata/ -o /MRI_DATA/mritesting/marscombo/derivatives/nibabies -d /MRI_DATA/mritesting/marscombo/derivatives/nibabies/work -l /MRI_DATA/mritesting/marscombo/derivatives/nibabies/sub-marscombo305402.log -a "--participant-label sub-marscombo305402 --cifti-output 91k --project-goodvoxels --age-months 4 --skip_bids_validation"

What version of NiBabies are you using?

23.1.0

Relevant log output

[environment]
cpu_count = 24
exec_env = "docker"
free_mem = 114.2
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "23.1.0"
version = "23.1.0"

[execution]
bids_dir = "/data"
bids_database_dir = "/work/20240116-172609_4e842562-eddb-41d4-b02d-ce3c92b04fff/bids_db"
bids_description_hash = "6ef18c859337aa2808b2b7a6da1c25dea0724d5fcbbf2a2b56a23b07ae39f803"
boilerplate_only = false
sloppy = false
debug = []
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/out/sourcedata/freesurfer"
layout = "BIDS Layout: .../data | Subjects: 3 | Sessions: 3 | Runs: 6"
log_dir = "/out/logs"
log_level = 10
low_mem = false
md_only_boilerplate = false
nibabies_dir = "/out"
notrack = false
output_dir = "/out"
me_output_echos = false
output_layout = "bids"
reports_only = false
run_uuid = "20240116-172609_4e842562-eddb-41d4-b02d-ce3c92b04fff"
participant_label = [ "marscombo305402",]
templateflow_home = "/home/nibabies/.cache/templateflow"
unique_labels = [ [ "marscombo305402", "20686",],]
work_dir = "/work"
write_graph = false

[workflow]
age_months = 4
analysis_level = "participant"
anat_only = false
aroma_err_on_warn = false
aroma_melodic_dim = -200
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = "91k"
fd_radius = 45
fmap_bspline = false
force_syn = false
hires = true
ignore = []
longitudinal = false
medial_surface_nan = false
project_goodvoxels = true
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "UNCInfant:cohort-1"
skull_strip_t1w = "force"
slice_time_ref = 0.5
surface_recon_method = "infantfs"
use_aroma = false
use_bbr = false
use_syn_sdc = false

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 24
omp_nthreads = 1
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 38198
ants = 3473
numpy = 48639

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

Add any additional information or context about the problem here.

No response

[mgxd]

Do you see any error messages in the log? And you may have better luck with the latest development release

[nbustos]

Just tried with Version 24.0.0a1 and same thing - no errors/crash in log

[tsalo]

@nbustos can you share the full stdout and stderr files?