Summary of what happened:
I want to use rapidtide to denoise my rs-fMRI data after preprocessing it with fMRIPrep. It might be due to the size of the data, but the process is being killed.
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run --cleanenv \
-B /home/jovyan/Desktop/dataset/derivatives/sub-01:/data_in \
-B /home/jovyan/Desktop/dataset/rapidtide:/data_out \
/home/jovyan/Desktop/rapidtide/rapidtide.sif \
rapidtide \
/data_in/func/sub-01_task-rest_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold_masked.nii.gz \
/data_out/ \
--denoising \
--brainmask /data_in/func/sub-01_task-rest_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz \
--graymattermask /data_in/anat/sub-01_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz \
--whitemattermask /data_in/anat/sub-01_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz \
--csfmask /data_in/anat/sub-01_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii.gz \
--premasktissueonly \
--motionfile /data_in/func/sub-01_task-rest_desc-confounds_timeseries.tsv \
--filterband lfo \
--outputlevel more
Version:
rapidtide v3.1.2.84
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer.
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):
setting initregressorinclude mask to gray matter mask
setting corrmaskinclude mask to gray matter mask
setting refineinclude mask to gray matter mask
setting offsetinclude mask to gray matter mask
setting initregressorinclude mask to gray matter mask
WARNING:rapidtide.workflows.rapidtide_parser:Using "denoising" analysis mode. Overriding any affected arguments.
overriding lagmin
overriding lagmax
pfftw does not exist
no aggressive optimization
will not use numba even if present
garbage collection is on
INFO:GENERAL:Removing existing file: /data_out/_log.txt
INFO:GENERAL:Removing existing file: /data_out/_runtimings.tsv
INFO:GENERAL:Removing existing file: /data_out/_memusage.tsv
starting rapidtide v3.1.2.84+g2dd9e4d5
loading data from /data_in/func/sub-01_task-rest_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold_masked.nii.gz
fmri data: 482 timepoints, tr = 0.6069999933242798, oversamptr = 0.3034999966621399
1082035 spatial locations, 482 timepoints
startpoint set to 0
endpoint set to maximum, ( 481 )
startpoint set to 0
endpoint set to maximum, ( 481 )
Killed