Hi fmriprep experts,
I am running fmriprep on a bare-metal installation. I recently upgraded to fmriprep version 20.2.1 and am running into some errors. I was able to run fmriprep to completion on the older version (20.1.1). The error I am getting is below:
Node: fmriprep_wf.single_subject_006_wf.anat_preproc_wf.brain_extraction_wf.init_aff
Working directory: /gs/gsfs0/users/yifeman/work/fmriprep_wf/single_subject_006_wf/anat_preproc_wf/brain_extraction_wf/init_affNode inputs:
args =
convergence = (10, 1e-06, 10)
dimension = 3
environ = {‘NSLOTS’: ‘7’}
fixed_image = /gs/gsfs0/users/yifeman/work/fmriprep_wf/single_subject_006_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_regrid.nii.gz
fixed_image_mask = /gs/gsfs0/users/yifeman/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
metric = (‘Mattes’, 32, ‘Regular’, 0.25)
moving_image = /gs/gsfs0/users/yifeman/work/fmriprep_wf/single_subject_006_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-006_ses-1_acq-3D_T1w_ras_valid_maths_corrected_regrid.nii.gz
moving_image_mask =
num_threads = 7
output_transform = initialization.mat
principal_axes = False
search_factor = (15.0, 0.1)
search_grid = (40.0, (0.0, 40.0, 40.0))
transform = (‘Affine’, 0.1)
verbose = TrueTraceback (most recent call last):
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 390, in run
self._check_version_requirements(self.inputs)
File “/gs/gsfs0/users/yifeman/.local/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 311, in _check_version_requirements
% (name, self.class.name, version, min_ver)
Exception: Trait search_grid (AI) (version 2.2.0 < required 2.3.0)
At first I thought this is an issue with my version of ANTs but I am running ANTs 2.3.1 which should work with fmriprep (correct me if I’m wrong here). Also have freesurfer 6.0.0, and nipype 1.6.0 installed.
If anyone has any suggestions or can point me in a different direction to look for one that would be much appreciated.
Thanks!
Yisrael