Summary of what happened: I can’t analyze because fmriprep is not updated.
I tried to analyze fMRI images on my lab’s HPC. After installing the singularity container (code: singularity pull docker://poldracklab/fmriprep), I ran a test and got the following error.
I followed the web page to update fmriprep, but it keeps saying that files and directories are not found.
do I just need to delete singularity and reinstall ?
The same issue appears when using this code.(singularity build /my_images/fmriprep-24.0.0.simg docker://poldracklab/fmriprep:24.0.0)
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity build /my_images/fmriprep-24.0.0.simg docker://nipreps/fmriprep:24.0.0
Version:
singularity : 3.5.3
fmriprep : 20.2.0
Environment
Singularity
Relevant log outputs (up to 20 lines):
/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
warnings.warn("The ability to pass arguments to BIDSLayout that control "
You are using fMRIPrep-20.2.0, and a newer version of fMRIPrep is available: 24.0.0.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
WARNING: Version 20.2.0 of fMRIPrep (current) has been FLAGGED
That means some severe flaw was found in it and we strongly
discourage its usage.
240708-15:58:09,438 nipype.workflow IMPORTANT:
Running fMRIPREP version 20.2.0:
* BIDS dataset path: /combinelab/03_user/thkim/01_project/01_NCMH_MDD/00_test_prep.
* Participant list: ['B040'].
* Run identifier: 20240708-155736_48365fb3-a427-4787-9d31-9f2d46938bea.
* Output spaces: T1w MNI152NLin2009cAsym:res-native.
* Pre-run FreeSurfer's SUBJECTS_DIR: /combinelab/03_user/thkim/01_project/01_NCMH_MDD/00_test_prep/derivatives/freesurfer.
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
31.6kB [00:03, 9.08kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz
2.53kB [00:01, 1.78kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
259B [00:00, 321B/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_probseg.nii.gz
3.96kB [00:01, 2.87kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_probseg.nii.gz
437B [00:00, 543B/s]
240708-15:58:28,41 nipype.workflow INFO:
No single-band-reference found for B040_rest_bold.nii.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/workflow.py", line 84, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 64, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 304, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/bold/base.py", line 272, in init_func_preproc_wf
tr=metadata.get("RepetitionTime")),
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 633, in __init__
from_file=from_file, resource_monitor=resource_monitor, **inputs
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 183, in __init__
self.inputs = self.input_spec(**inputs)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/specs.py", line 66, in __init__
super(BaseTraitedSpec, self).__init__(**kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py", line 172, in error
value )
traits.trait_errors.TraitError: The 'tr' trait of a FunctionalSummaryInputSpec instance must be a float, but a value of None <class 'NoneType'> was specified.
singularity build /my_images/fmriprep-20.2.0.simg docker://nipreps/fmriprep:20.2.0
INFO: Starting build...
Getting image source signatures
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Copying config c2efe13b4b done
Writing manifest to image destination
Storing signatures
2024/07/08 17:11:59 info unpack layer: sha256:0a01a72a686c389637334de1e2d0012da298960366f6d8f358b8e10dc3b5e330
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INFO: Creating SIF file...
FATAL: While performing build: while creating SIF: while creating container: container file creation failed: open /my_images/fmriprep-20.2.0.simg: no such file or directory
