fmriprep: CRCError for NIfTI in working directory

@effigies and @mgxd Thanks. Now I was able to process one subject fMRI data without any errors and I still didn’t get a time to check those results. I also processed two other subjects and got the following two different errors from them.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/nibabel.py", line 191, in _run_interface
    img_4d = nb.concat_images(nii_list)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/funcs.py", line 141, in concat_images
    raise ValueError(f'Affine for image {i} does not match affine for first image')
ValueError: Affine for image 3 does not match affine for first image



Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/nilearn.py", line 176, in _run_interface
    new_nii = concat_imgs(self.inputs.in_files, dtype=self.inputs.dtype)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg_conversions.py", line 471, in concat_niimgs
    niimg = check_niimg(niimg, ensure_ndim=ndim)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg_conversions.py", line 283, in check_niimg
    niimg = load_niimg(niimg, dtype=dtype)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg.py", line 134, in load_niimg
    dtype = _get_target_dtype(_get_data(niimg).dtype, dtype)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg.py", line 24, in _get_data
    data = np.asanyarray(img._dataobj)
  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/core/_asarray.py", line 171, in asanyarray
    return array(a, dtype, copy=False, order=order, subok=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 391, in __array__
    arr = self._get_scaled(dtype=dtype, slicer=())
  File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 358, in _get_scaled
    scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 332, in _get_unscaled
    return array_from_file(self._shape,
  File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/volumeutils.py", line 519, in array_from_file
    infile.seek(offset)
  File "indexed_gzip/indexed_gzip.pyx", line 651, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.CrcError: CRC/size validation failed - the GZIP data might be corrupt (file: /gpfs/projects/fmriprep/scR21_outputs_Sep_2021_N/derivatives/scratch/fmriprep_wf/single_subject_50144_wf/func_preproc_ses_1_task_RSFC_run_4_wf/bold_t1_trans_wf/bold_to_t1w_transform/vol0412_xform-00412.nii.gz)

_Originally posted by @sameera2004 in https://github.com/nipreps/fmriprep/issues/2534#issuecomment-922476583_

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 25 (8 by maintainers)

Most upvoted comments

@pauldmccarthy @effigies I just want to report back after upgrading indexed-gzip 1.6.4. It fixed the error and the subject’s data is processed completely without errors. Thank you so much.

yenwchen on Oct 22, 2021

20.2.6 is now available on docker hub and should resolve this error - please reopen if it does not!

mgxd on Oct 28, 2021

Yes, I was able to preprocess the 6 subjects data without any issue this time. I didn’t see this error again. We will compare the outputs and let you know whether it solved the SDC issue. Thank you.

sameera2004 on Oct 12, 2021

@effigies and @pauldmccarthy,I am so sorry I have been busy with so many other projects. Therefore, I didn’t get a time to check this. Last Friday, I reran the analysis after deleting the directory. However, it was not successful. I will check those error reports and share you an image by tomorrow. Thank you so much.

sameera2004 on Sep 30, 2021