Dtype('float64') error using fmriprep v1.5.1

Dear fmriprep users,

I upgraded fmriprep to v1.5.1 to process my fMRI data, and encountered the following errors. I previously processed the same dataset with fmriprep v1.2.5 and v1.3.1.post1, but did not have this error. I ran fmriprep using Singularity on an SGE cluster. The error presents for all individuals, not just for specific ones. Any advice is much appreciated!

Regards,
Jiyang


[jiyang@nil-rocks7 20191128-200643_1b9fb965-e9b7-42c7-9cf8-612de3a06f0a]$ cat crash-20191128-212731-jiyang-skull_strip_extern-2db610f3-131d-4ffd-893b-f9bd1798868d.txt
Node: fmriprep_wf.single_subject_100396_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern
Working directory: /work/fmriprep_wf/single_subject_100396_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern

Node inputs:

in_brain =
subject_id =
subjects_dir =

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nibabel/freesurfer/mghformat.py”, line 224, in set_data_dtype
code = self._data_type_codes[datatype]
File “/usr/local/miniconda/lib/python3.7/site-packages/nibabel/volumeutils.py”, line 163, in getitem
return self.field1[key]
KeyError: dtype(‘float64’)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 479, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 585, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 678, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 382, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/freesurfer.py”, line 135, in _run_interface
self.inputs.in_brain)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/freesurfer.py”, line 379, in inject_skullstripped
masked_image = new_img_like(img, img.get_fdata() * resampled_mask.dataobj)
File “/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/image.py”, line 656, in new_img_like
return klass(data, affine, header=header)
File “/usr/local/miniconda/lib/python3.7/site-packages/nibabel/freesurfer/mghformat.py”, line 528, in init
extra=extra, file_map=file_map)
File “/usr/local/miniconda/lib/python3.7/site-packages/nibabel/spatialimages.py”, line 466, in init
self._header.set_data_dtype(dataobj.dtype)
File “/usr/local/miniconda/lib/python3.7/site-packages/nibabel/freesurfer/mghformat.py”, line 226, in set_data_dtype
raise MGHError(‘datatype dtype “%s” not recognized’ % datatype)
nibabel.freesurfer.mghformat.MGHError: datatype dtype “float64” not recognized

1 Like

This will be fixed in the next release.

1 Like