effigies on master
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effigies on 1.8.1
effigies on master
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effigies on master
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I found it before... but because of that signs I was not sure If it should work in general... and if I have to upgrade to a newer pipeline or something like manuelly
Ah, that's bad metadata (and my fault). The location is https://github.com/niflows/nipype1-workflows
Have anyone here used the spm interface FieldMap( ) function. I am new to nipype and trying to create a workflow but this function will not work for me.
I follow the example and documentation strictly:
from nipype.interfaces.spm import FieldMap
fm = FieldMap()
fm.inputs.phase_file = 'phase.nii' # Here I find my own phase_file
fm.inputs.magnitude_file = 'magnitude.nii' # Here my own mag file
fm.inputs.echo_times = (5.19, 7.65)
fm.inputs.blip_direction = -1
fm.inputs.total_readout_time = 15.6
fm.inputs.epi_file = 'epi.nii' # here my own epi file
fm.run()
But It wont run. It simply tells me that "No such file or directory '/indirect/users/kristianlarsen/python/phase_0/vdm5_scphase.nii' for output 'vdm' of a FieldMap interface' .
I don't understand the message, the function should create this file (with the prefix 'vdm5_sc') NOT look for it, so I have no idea how to move further. If I create an empty file (with the prefix name) in the working directory the program runs, but does not do anything to the file.
Any help please? and thank you!
Hi there, I got the following 4 fails after running python -c "import nipype; nipype.test()"
. I installed Nipype using pip install nipype[all]
================================================== short test summary info ==================================================FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/registration.py::nipype.interfaces.ants.registration.Registration
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.N4BiasFieldCorrection
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/utils.py::nipype.interfaces.ants.utils.AI
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/base/tests/test_core.py::test_BaseInterface_load_save_inputs
====================== 4 failed, 2704 passed, 211 skipped, 5 xfailed, 37 warnings in 439.88s (0:07:19) =================
-- Docs: https://docs.pytest.org/en/stable/warnings.html
================================================== short test summary info ==================================================
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/registration.py::nipype.interfaces.ants.registration.Registration
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.Atropos
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.BrainExtraction
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.CorticalThickness
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.JointFusion
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.KellyKapowski
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/segmentation.py::nipype.interfaces.ants.segmentation.N4BiasFieldCorrection
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/utils.py::nipype.interfaces.ants.utils.AI
FAILED anaconda3/lib/python3.8/site-packages/nipype/interfaces/ants/utils.py::nipype.interfaces.ants.utils.ComposeMultiTransform
========================================= 9 failed, 100 passed, 1 warning in 12.81s =========================================
Expected:
'Atropos --image-dimensionality 3 --icm [1,1]
--initialization Random[2] --intensity-image structural.nii
--likelihood-model Gaussian --mask-image mask.nii --mrf [0.2,1x1x1] --convergence [5,1e-06]
--output [structural_labeled.nii,POSTERIOR_%02d.nii.gz] --posterior-formulation Socrates[1]
--use-random-seed 1'
Got:
'Atropos --image-dimensionality 3 --icm [1,1] --initialization Random[2] --intensity-image structural.nii --likelihood-model Gaussian --mask-image mask.nii --mrf [0.2,1x1x1] --convergence [5,1e-06] --output [structural_labeled.nii,POSTERIOR_%02d.nii.gz] --posterior-formulation Socrates[1] --use-random-seed 1'
Working through miykael's nipype tutorial. Using the Docker image and /data and other folders are mapped to local folders. In the introduction_showcase notebook, I can ls
the file being passed to slicetimer.inputs.in_file
, yet receive an error when running the cell.
TraitError: The 'in_file' trait of a SliceTimerInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz' <class 'str'> was specified.