Fix nibabel import

[tsalo]

Closes #300.

Changes proposed in this pull request

• Replace nb.processing.smooth_image with a direct from nibabel.processing import smooth_image import.

[Luoyu-Wang]

Thank you for your patience, and I would like to ask you another question. Whenever I use ASLprep, I find myself having to download the tpl-MNI152NLin2009cAsym_from-MNI152NLin6Asym_mode-image_xfm.h5 file every time I run the process. Is there a way to avoid repeated downloads?

Additionally, I wanted to mention that tomorrow we will be installing ASL sequences based on multi-PLD on our lab GE machine. I was wondering if ASLprep could handle this type of data. I'm looking forward to your response.

[tsalo]

Thank you for your patience, and I would like to ask you another question. Whenever I use ASLprep, I find myself having to download the tpl-MNI152NLin2009cAsym_from-MNI152NLin6Asym_mode-image_xfm.h5 file every time I run the process. Is there a way to avoid repeated downloads?

You can pre-cache templates on your machine and then mount the templateflow folder to your container. Since ASLPrep is built off of fMRIPrep, the instructions on this page should work.

Additionally, I wanted to mention that tomorrow we will be installing ASL sequences based on multi-PLD on our lab GE machine. I was wondering if ASLprep could handle this type of data.

I haven't tried out ASLPrep on multi-PLD data from a GE scanner, but I believe it should be fine as long as the sequence is PCASL. We don't have multi-delay PASL supported at the moment (see #272).

[Luoyu-Wang]

Thanks for your reply and I will try it out.

[Luoyu-Wang]

We pulled the latest docker version（0.4.0） and replaced the ge.py file, but there were 3 errors reported, what is the reason for this?

error1:
Node: aslprep_wf.single_subject_101_wf.anat_preproc_wf.anat_derivatives_wf.gen_ref
Working directory: /work/aslprep_wf/single_subject_101_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_ref

Node inputs:

fixed_image =
fov_mask = None
keep_native = True
moving_image =
xform_code = None

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 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gen_ref.

Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/nibabel.py", line 430, in _run_interface
self._results["out_file"] = _gen_reference(
File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/nibabel.py", line 609, in _gen_reference
resampled = nli.resample_img(
File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/image/resampling.py", line 445, in resample_img
img = _utils.check_niimg(img)
File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg_conversions.py", line 286, in check_niimg
niimg = load_niimg(niimg, dtype=dtype)
File "/usr/local/miniconda/lib/python3.8/site-packages/nilearn/_utils/niimg.py", line 137, 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 26, in _get_data
data = np.asanyarray(img._dataobj)
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 426, in array
arr = self._get_scaled(dtype=dtype, slicer=())
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 393, 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 363, in _get_unscaled
return array_from_file(
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/volumeutils.py", line 461, in array_from_file
raise OSError(
OSError: Expected 17060042 bytes, got 17053871 bytes from object
- could the file be damaged?

error2:
Node: aslprep_wf.single_subject_101_wf.anat_preproc_wf.anat_norm_wf.registration
Working directory: /work/aslprep_wf/single_subject_101_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration

Node inputs:

explicit_masking = True
flavor = precise
float = True
initial_moving_transform =
lesion_mask =
moving = T1w
moving_image =
moving_mask =
num_threads = 5
orientation = RAS
reference = T1w
reference_image =
reference_mask =
settings =
template = MNI152NLin2009cAsym
template_resolution =
template_spec =

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 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node registration.

Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/norm.py", line 183, in _run_interface
ants_args = self._get_ants_args()
File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/norm.py", line 457, in _get_ants_args
args["fixed_image"] = mask(
File "/usr/local/miniconda/lib/python3.8/site-packages/niworkflows/interfaces/norm.py", line 506, in mask
data = in_nii.get_fdata()
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 368, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 426, in array
arr = self._get_scaled(dtype=dtype, slicer=())
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/arrayproxy.py", line 393, 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 363, in _get_unscaled
return array_from_file(
File "/usr/local/miniconda/lib/python3.8/site-packages/nibabel/volumeutils.py", line 461, in array_from_file
raise OSError(
OSError: Expected 17060042 bytes, got 17053871 bytes from object
- could the file be damaged?

• could the file be damaged?

error3:
Node: aslprep_wf.single_subject_101_wf.asl_preproc_asl.asl_t1_trans_wf.asl_to_t1w_transform
Working directory: /work/aslprep_wf/single_subject_101_wf/asl_preproc_asl/asl_t1_trans_wf/asl_to_t1w_transform

Node inputs:

args =
copy_dtype = True
default_value = 0.0
dimension =
environ = {}
float = True
input_image =
input_image_type =
interpolation = LanczosWindowedSinc
interpolation_parameters =
invert_transform_flags =
num_threads = 5
out_postfix = _trans
output_image =
print_out_composite_warp_file =
reference_image =
save_cmd = True
transforms =

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 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node asl_to_t1w_transform.

Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/aslprep/niworkflows/interfaces/itk.py", line 177, in _run_interface
tmp_folder.cleanup()
File "/usr/local/miniconda/lib/python3.8/tempfile.py", line 832, in cleanup
self._rmtree(self.name)
File "/usr/local/miniconda/lib/python3.8/tempfile.py", line 814, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/usr/local/miniconda/lib/python3.8/shutil.py", line 719, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/usr/local/miniconda/lib/python3.8/shutil.py", line 717, in rmtree
os.rmdir(path)
OSError: [Errno 26] Text file busy: '/work/aslprep_wf/single_subject_101_wf/asl_preproc_asl/asl_t1_trans_wf/asl_to_t1w_transform/tmp-qtx8k5tj'

[tsalo]

@Luoyu-Wang thank you for following up. I have opened a new issue with your traceback and I'll follow up there.