I am running into a fatal error in BIDS-Apps HCPPipelines.
The script gets to the “DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh” and then an error message is sent to the screen:
Traceback (most recent call last):
File “/run.py”, line 410, in
stage_func()
File “/run.py”, line 139, in run_generic_fMRI_volume_processsing
run(cmd, cwd=args[“path”], env={“OMP_NUM_THREADS”: str(args[“n_cpus”])})
File “/run.py”, line 29, in run
raise Exception(“Non zero return code: %d”%process.returncode)
Exception: Non zero return code: 1
Hi,
Thank you for your advice!
Yes! I used phase-difference map method instead of topup method.
I have put “IntendedFor” field as below.
“IntendedFor”: [“func/sub-001_task-rest_run-01_bold.nii.gz”,
“func/sub-001_task-rest_run-02_bold.nii.gz”,
“func/sub-001_task-rest_run-03_bold.nii.gz”]
Is something wrong?
When I ran “fmriprep”, this worked well.
But this did not work for “HCPPipelines”.