Hello All,
I was hoping someone might be able to advise me on an error I keep getting while attempting to run fmriprep through 20.2.1.simg singularity image? The output from the crashlog is appended below the message.
Weirdly, I only get this error for one study’s data on my university HPC (I’ve tried for many different subs from this problematic study as well). The other study datasets I have run fmriprep on, using the same code, all complete successfully on my HPC (and beautifully I might add!).
The data used in the unsuccessful fmriprep attempts are a bit larger, so I’ve also tweaked the virtual memory avail and cores up to 264 GB mem and 20 cores…along with using the --use-plugin and --low-mem switches, as well as various other switches to control the dedicated resources and/or simplify the dataset.
Any assistance you can offer would be extremely appreciated, as I am at a bit of an impasse here.
PS- also just wanted to give a HUGE thanks to the developers/testers of this program, it really is superb!
Very Best,
Nick
Node inputs:
args =
bias_iters =
bias_lowpass =
environ = {‘FSLOUTPUTTYPE’: ‘NIFTI_GZ’}
hyper =
img_type =
in_files =
init_seg_smooth =
init_transform =
iters_afterbias =
manual_seg =
mixel_smooth =
no_bias = True
no_pve =
number_classes =
other_priors =
out_basename =
output_biascorrected =
output_biasfield =
output_type = NIFTI_GZ
probability_maps = True
segment_iters =
segments = True
use_priors =
verbose =
Traceback (most recent call last):
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/legacymultiproc.py”, line 67, in run_node**
** result[“result”] = node.run(updatehash=updatehash)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run**
** result = self._run_interface(execute=True)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface**
** return self._run_command(execute)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command**
** result = self._interface.run(cwd=outdir)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 419, in run**
** runtime = self._run_interface(runtime)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 814, in _run_interface**
** self.raise_exception(runtime)**
** File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 745, in raise_exception**
** ).format(runtime.dictcopy())
RuntimeError: Command:
fast -N -p -g -S 1 /workdir/fmriprep_wf/single_subject_BANDA001_wf/anat_preproc_wf/t1w_dseg/sub-BANDA001_T1w_corrected_xform_masked.nii.gz
Standard output:
Exception: Not enough classes detected to init KMeans
Standard error:
Return code: 255