nipy/nipype

Workflows and interfaces for neuroimaging packages

xd3262nd

@xd3262nd

^ yea I did but I will try to test them out

xd3262nd

@xd3262nd

Hello! 👋 I am trying to build a custom interface with nipype and having some trouble building the outputspec, is there anyone familiar with this?

ayushiiijoshi

@ayushiiijoshi

I am trying to use python to read .nii files. But I want to store the output in a .csv file where all the details are stored. Can someone let me know how do I do that?

1 reply

Harsh Rangwala

@HarshRangwala

Hi there. I am new here. I am looking for documentation on N4BiasFieldCorrection. The one that has description of all the functions, methods in N4BiasFieldCorrection. Can anyone point me where to look for it?

Chris Markiewicz

@markiewicz:matrix.org

[m]

https://manpages.debian.org/testing/ants/N4BiasFieldCorrection.1.en.html?

TonnarCastellano

@TonnarCastellano

Hey so I am trying to do the VBM preprocessing with nipype and I keep getting different results than manually doing it in SPM I am assuming I am suppose to use the New Segment.

I am using SPM 12 is that why? I see the note about VBM preprocessing on ther

Boojum

@intein

Hi! There is no option to realign volumes to the first volume in the SPM interface. There's only "register_to_mean" option which is boolean. Is "register_to_mean = False" equivalent to realigning to the first volume?

Chris Markiewicz

@markiewicz:matrix.org

[m]

That would be my interpretation of the SPM docs: https://github.com/neurodebian/spm12/blob/master/spm_realign.m

Boojum

@intein

Thank you!

balandong

@balandongiv

Hi, new to nipype. May I know relevant resource about returning output from Matlab upon executing nipype? This may be duplicate post, but I have post OP here: https://neurostars.org/t/return-matlab-output-using-nipype/20068 regarding this question. But, I really appreciate if anyone can share any resource about this question

BartTh

@BartTh

Hi guys, fairly new to nipype and I'm trying to follow this tutorial with the sample data: https://nipype.readthedocs.io/en/latest/users/examples/dmri_mrtrix_dti.html . I've just finished installing fsl, which I'm able to run from the same terminal as I am trying to run the script. However, I still get an error which I think is related to fsl?

OSError: No command "tensor2FA" found on host bart-2.local. Please check that the corresponding package is installed.

OSError: No command "tensor2ADC" found on host bart-2.local. Please check that the corresponding package is installed.

And several more OSerrors, looking forward to some help :)

Running everything on OSX big sur

andife

@andife

Hi is the niflow project still active? I wonder how to update https://github.com/nmningmei/BOLD5000_autoencoder/blob/master/scripts/utils.py in special from "nipype.workflows.fmri.fsl import preprocess" which seems deprecated... installing the niflow_nipype1_workflows does not work here.. what would be the correct way?

Chris Markiewicz

@markiewicz:matrix.org

[m]

Niflows is active, though that particular package is only going to get minimal maintenance. Curious what you mean "installing the niflow_nipype1_workflows does not work here"?

2 replies

Chris Markiewicz

@markiewicz:matrix.org

[m]

Ah, that's bad metadata (and my fault). The location is https://github.com/niflows/nipype1-workflows

andife

@andife

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

Chris Markiewicz

@markiewicz:matrix.org

[m]

It should be exactly the workflows that were previously in nipype. The issue we were having is that most of these workflows are very old and unmaintained, but there's no way to see that when you install the latest nipype. We would like to move to a system where individual or related sets of workflows are separately maintained, and it's obvious which ones see a lot of activity and which don't.

Not that low activity means that they don't work...

andife

@andife

good to hear that

kristian1801

@kristian1801

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!

Thanh-HN

@Thanh-HN

hi everyone

i have some problem when i'm trying to import N4BiasFieldCorrection

i run this command on gg colab: from nipype.interfaces.ants import N4BiasFieldCorrection

and have the error: No module named 'nipype'

Any help pls? Thank you!

Rinat Mukhometzianov

@rmukh

@Thanh-HN Well, you need to install it first on google colab. Run a cell with !pip install nipype

@Thanh-HN And to be honest, I am not sure if colab supports ANTS software. It might be hard to install it on colab

Zhengchen Cai

@zhengchencai

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) =================

Chris Markiewicz

@markiewicz:matrix.org

[m]

Looks like some issues in the doctests not normalizing whitespace. I can reproduce with `python -m pytest -sv --pyargs --doctest-modules nipype.interfaces.ants

Zhengchen Cai

@zhengchencai

Thanks, does this mean I have no problem for installation?

Chris Markiewicz

@markiewicz:matrix.org

[m]

It seems fine. I would use my command to see if the failures are just docstring formatting or if there's something more significant. We should fix it in the next release in any case.

Zhengchen Cai

@zhengchencai

Thanks a lot. I tried python -m pytest -sv --pyargs --doctest-modules nipype.interfaces.ants

and got

-- 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 =========================================

Chris Markiewicz

@markiewicz:matrix.org

[m]

That's what I got. If you scroll up, you should see details of each failure, and all of them are things like

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'

I would say that's fine.

Zhengchen Cai

@zhengchencai

Thanks!

johnatl

@johnatl:matrix.org

[m]

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.

johnatl

@johnatl:matrix.org

[m]

Turns out I needed to use datalad's get to get the actual data.
Does anyone use this chat service? lol

Chris Markiewicz

@markiewicz:matrix.org

[m]

Not really. Neurostars is more common these days.

ConnorBehnen

@ConnorBehnen

Can someone help me with clarification on the different Segment options from SPM (via Nipype). The Nipype documentation links to the SPM manual seem off (sometimes its halfway through a chapter). My understanding was Segment is the newest version, and that NewSegment is from SPM8 but maybe I have that backwards?

Sandesh Patil

@SandeshPatilCreatis

Hello,
Does anyone knows what Data composition pattern Nipype's algorithm supports (ono-to-one, all-to-all?)

Chris Markiewicz

@markiewicz:matrix.org

[m]

@SandeshPatilCreatis: Could you link to a resource that explains the sense in which you'reusing data composition patterns?

Sandesh Patil

@SandeshPatilCreatis

@markiewicz:matrix.org Thank you for your reply.
You can refer to 3. Data composition strategies(page 5) of this article - https://hal.archives-ouvertes.fr/hal-00691832/document

loukasilias

@loukasilias

Hello,

Is SAMSEG of FreeSurfer provided by nipype?

Thanks!

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