Hi,
I am new to fmriprep. I have run a fmriprep pipeline with a relatively large dataset on a HPC using slurm. The error script is the following. I guess I am puzzled with the warning messages, and not sure if these messages are fatal to the pipeline. Or I can just ignore these messages?
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: userwarning: no contour levels were found within the data range.
warnings.warn("no contour levels were found"
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: userwarning: no contour levels were found within the data range.
warnings.warn("no contour levels were found"
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: userwarning: no contour levels were found within the data range.
warnings.warn("no contour levels were found"
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: userwarning: no contour levels were found within the data range.
warnings.warn("no contour levels were found"
/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/viz/utils.py:423: futurewarning: using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. in the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
maximum_intensity_data = data[finds]
/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1182: futurewarning: `rcond` parameter will change to the default of machine precision times ``max(m, n)`` where m and n are the input matrix dimensions.
to use the future default and silence this warning we advise to pass `rcond=none`, to keep using the old, explicitly pass `rcond=-1`.
betas = np.linalg.lstsq(x, data.t)[0]
/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1182: futurewarning: `rcond` parameter will change to the default of machine precision times ``max(m, n)`` where m and n are the input matrix dimensions.
to use the future default and silence this warning we advise to pass `rcond=none`, to keep using the old, explicitly pass `rcond=-1`.
betas = np.linalg.lstsq(x, data.t)[0]
exception ignored in: <finalize object, dead>
traceback (most recent call last):
file "/usr/local/miniconda/lib/python3.7/multiprocessing/util.py", line 189, in __call__
res = self._callback(*self._args, **self._kwargs)
file "/usr/local/miniconda/lib/python3.7/multiprocessing/synchronize.py", line 87, in _cleanup
sem_unlink(name)
filenotfounderror: [errno 2] no such file or directory
exception ignored in: <finalize object, dead>
traceback (most recent call last):
file "/usr/local/miniconda/lib/python3.7/multiprocessing/util.py", line 189, in __call__
res = self._callback(*self._args, **self._kwargs)
file "/usr/local/miniconda/lib/python3.7/multiprocessing/synchronize.py", line 87, in _cleanup
sem_unlink(name)
filenotfounderror: [errno 2] no such file or directory
exception ignored in: <finalize object, dead>
traceback (most recent call last):
file "/usr/local/miniconda/lib/python3.7/multiprocessing/util.py", line 189, in __call__
res = self._callback(*self._args, **self._kwargs)
file "/usr/local/miniconda/lib/python3.7/multiprocessing/synchronize.py", line 87, in _cleanup
sem_unlink(name)
filenotfounderror: [errno 2] no such file or directory
exception ignored in: <finalize object, dead>
traceback (most recent call last):
file "/usr/local/miniconda/lib/python3.7/multiprocessing/util.py", line 189, in __call__
res = self._callback(*self._args, **self._kwargs)
file "/usr/local/miniconda/lib/python3.7/multiprocessing/synchronize.py", line 87, in _cleanup
sem_unlink(name)
filenotfounderror: [errno 2] no such file or directory
exception ignored in: <finalize object, dead>
traceback (most recent call last):
file "/usr/local/miniconda/lib/python3.7/multiprocessing/util.py", line 189, in __call__
res = self._callback(*self._args, **self._kwargs)
The command I was running:
singularity run --cleanenv -B /group/rwhuskeygrp/bids_nii:/data \
-B /home/xjgong/.cache/templateflow:/templateflow \
-B /group/rwhuskeygrp/fmriprepwork:/work \
/group/rwhuskeygrp/images/fmriprep-20.0.5.simg \
/data /data/derivatives/fmriprep-20.0.5 \
participant -w /work/ -vv --nthreads 16 --mem_mb 55000 \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym \
--use-aroma --fs-license-file /group/rwhuskeygrp/license.txt
I really appreciate your help! Many thanks!
Best,
Jason