Sayyed's blog (A python way Neuroimaging Analysis)

nipype-workflow

Abdul Sayyed — Tue, 21 Jul 2020 17:24:13 GMT

My setup of nipype

I have successfully created a conda environment for nipype. it is located here (/home/sayyed/anaconda3/envs/nipype).
The directory I have chosen to work is /home/sayyed/neuro-science/projects/nikola the listing is given as below.
Since this package works with all existing neuroimaging software, it is recomended that it is installed on a machine where all other software can be installed and configured properly to work with nipype.
Once it is installed using conda install --channel conda-forge nipype. Its .yml file can be created using conda list --explicit > nipype.txt
Though the list is long but it does not install ipython or say a kernel so theat we can workwith jupyterlab. If ipython is installed , one can start the interactive shell and start working from terminal or command prompt. In reality ipython is not necessary as nipype install python packeage to srat with.
ipython is only necessary if you decide to work with Jupyter. It is same as python that is an interpreter but works interactively with Jupyter environment and hence knows as Python execusiton background in Jupyter environment.
Having said that ipykernel can still be installed in nipype environment using conda istall ipykernel. This will also install jupyter_cliend, core and other necessary packages. Once installed, ipython can be started from terminal and the availablity ofnipypepackage can be checked usingimport nipype as nyandny.get_info()`.
To check the proper installtion when the command was run it produced an error that pytest is not instlled use pip to install. So I did then ran a test.
When installation was tested using given instructions, it complained about the Sphinix extension documenter not found.
Furthermore, when example was started I encountered an error saying nilearn is not installed so I installed it as well.
today on 24 July 2020, I again encountered some problems so I read the instructions again and found that I need to install scikit-learning as well. So I installed it using conda -install scikit-learning. Aslo checked nilearn again and install it using conda install nilearn and one package was installed. It happened with nilearn as well all other dependencies were installed only this one was left.
To download data nipype uses a pyton module called datalad, use pip install datalad.
When working in notebook, I frequently encountered a problem with traversing the file path.
So I open the evironment in spyder but it says you need to install sypder kernel in your evnironment. so I did using pip install spyder-kernel. Then use `python -c "import sys; print(sys.executable)"
Once done you can open spyder from base environment and then using Preferences -> Python Interpreter -> select the python
While starting to work with given examples again encounter a problem so I ran a test nipype.test() and it said VTK was no found and nipype.interface WARNING: tvtk wasn't found, upgradeDIPY` verson.
Tried to upgrade and found that it is not installed so I installed using conda install DIPY. Then got thewarning Nipype 1 wrokflows have been moved to the niflow-nipype1-wrokflows padkage. pip install niflow-nipype1-wrokflows.
Got error about sphinix installed conda intall sphinx
Still getting an error about sphinxcontrib napoleon, using pip install sphinxcontrib-anpoleon though it said requirment already installed and instlled `pockets, shpinxcontrib-anpoleaon.
And finally import nipype; nipype.test() scucceded to run, it took 10 minutes or more to run and utilize all 8 processors, all memory and Gpu 3d up to 54%.
In the end one error I recieved and it was about workflow.
Today I ran another test using the following as mentioned in dcoument:

# Import the nipype module

import nipype

# Optional: Use the following lines to increase verbosity of output

nipype.config.set('logging', 'workflow_level', 'CRITICAL')
nipype.config.set('logging', 'interface_level', 'CRITICAL')
nipype.logging.update_logging(nipype.config)

# Run the test: Increase verbosity parameter for more info
nipype.test(doctests=False)

No this tiem I get this erro: ERROR: usage: ipykernel_launcher.py [options] [file_or_dir] [file_or_dir] [...] ipykernel_launcher.py: error: unrecognized arguments: --doctest-modules inifile: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/pytest.ini rootdir: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype
This time again using conda install doctest installed a new packgage called doctest-2.4.0.... but the test did not suceeded.

⋊> ~/n/p/nikola ll                                                                                                         (base) 17:32:36
total 52K
drwxrwxr-x 12 sayyed sayyed 4.0K Jul 10 21:35 demosite/
drwxrwxr-x  6 sayyed sayyed 4.0K Jul 18 00:27 Ex_01/
-rw-rw-r--  1 sayyed sayyed  28K Jul 16 18:15 installed-moudle.txt
drwxrwxr-x 13 sayyed sayyed 4.0K Jul 21 18:23 mysite/
lrwxrwxrwx  1 sayyed sayyed   31 Jul 21 16:11 nik-nip-vscode -> ./.vscode/Nikola.code-workspace
-rw-rw-r--  1 sayyed sayyed 8.1K Jul 16 18:13 requirement.txt
⋊> ~/n/p/nikola

The demosite I do not need and it will be deleted.
Mysite directory is the main directory of nikola blog.
The vsocde workspace is saved in .vscode folder and pointed by nik-nip-vscode link ( it is uselss at this moment)

How `notebook` differs when created in `nikola` or in `jupyterlab`?

Notebook can be created in many ways. But when nikola does its scanning it throws an error if it does not find the meta data it requires for a notebook to be a part of the nikola.
It does not matter where it can be created from, the meta data can be easily added. Inorder for nikola to open and work with notebook, it has to have some meta data inside it. It is not a rocket science as I had gread difficulty dealing with notebook when trying to open them with pelican or embed them in markdown file. Though I have not been successful to embed notebooks in markdown files using short code as described by nikola docuemtation.
Follwing is a meta data entries when the file is created by jupter lab selecting particular ipython kernel. Ipython kernil is just a python interpreter name that you have created in your conda or pip environment and given it a uniqure name. For exampe when I created nipype environment I installed different version of differnt software that can work together. This version is knows as your particular python kernel or interpreter.

"metadata": {
  "kernelspec": {
   "display_name": "Python (nipype)", # This is added when you choose you particular python kernel
   "language": "python",
   "name": "nipype"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.2"
  }

The above detail is enough for jupyter to open the file but not for nikola needs to know more to deal with correct theme and template to open notebook data. Follwing information is needed and can simply be added into the above meta data.

"nikola": {
   "author": "Abdul Sayyed",
   "category": "nipype",
   "date": "2020-07-10 15:43:54 UTC+01:00",
   "description": "",
   "link": "",
   "slug": "001_intro",
   "tags": "python, jupyter, nipype",
   "title": "001_intro",
   "type": "text"
  }

How to create a notebook with vscode.

Using command pattlet we can use > create notebook command. There are other worth exploring as of importing as well.
Running notebook in vscode and setting it properly can be handy. The scroll bar shows, wchic environmen is selected. If the wrong one is selected, by clicking on the status bar on the infromation it will open different environment where the right one can be opened. Once the right one is opened. The notebook already have installed module such as numpy, matplot or nipype exposed api avilable to use.
On the right hand top corner, vscode also shows the local server and the right kernel selected.
It is very handy that in my one notebook folder created in nikola top level directories, I can have different notebooks set and ready to be used with different environments.
They can all be opened from one place and knows which environment they are to be used as in their meta contents this information is saved.
If not the right kernel can be opened from the right corner.

Running code from different kernels

It is possible to run code from different kernel or executional environment in one note book.
Use %%bash or %%HTML or %% and run the particular command to execute it.

How this repo is committed

Since I am using nikola, whatever I do I keep the work under mysite folder so that it is also published as well.
I always work in dev branch. To publish my site , I switched to src by using git checkout src from here I use nikola github_deploy. This takes care of eveything and only deploy the output folder and whatever is necessary to produce a websit.
I also wanted to be able to use my repo with windows so I cloned it to my windwos environment but realised that it does not have any contents, it is only a publish html file repo. No markdown contents.
To resolve this issue I had to create a new repo which I named https://github.com/AbdulSayyed/nikola-website and added a remote in my local dev branch where I usually work from.
To add a new remote to a same repo I used this command git remote add niksrc https://github.com/AbdulSayyed/nikola-website.git as shown below. Now I have my dev branch set to a remote repo name nikola-website.git. This branch is added or referenced in my config file as niksrc. To pus or pull I would use git push niksrc dev or git pull niksrc dev

 ~/n/p/n/mysite on dev  git remote add niksrc https://github.com/AbdulSayyed/nikola-website.git                      (nikola) 12:59:21
⋊> ~/n/p/n/mysite on dev  git remote -v                                                                                (nikola) 12:59:43
niksrc  https://github.com/AbdulSayyed/nikola-website.git (fetch)
niksrc  https://github.com/AbdulSayyed/nikola-website.git (push)
origin  https://github.com/AbdulSayyed/AbdulSayyed.github.io.git (fetch)
origin  https://github.com/AbdulSayyed/AbdulSayyed.github.io.git (push)
⋊> ~/n/p/n/mysite on dev  git status                                                                                   (nikola) 12:59:49
On branch dev
nothing to commit, working tree clean
⋊> ~/n/p/n/mysite on dev  git push -u niksrc dev                                                                       (nikola) 13:00:10
Username for 'https://github.com': Abdulsayyed
Password for 'https://Abdulsayyed@github.com': 
Enumerating objects: 111, done.
Counting objects: 100% (111/111), done.
Delta compression using up to 8 threads
Compressing objects: 100% (97/97), done.
Writing objects: 100% (111/111), 259.39 KiB | 7.63 MiB/s, done.
Total 111 (delta 41), reused 6 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (41/41), done.
To https://github.com/AbdulSayyed/nikola-website.git
 * [new branch]      dev -> dev
Branch 'dev' set up to track remote branch 'dev' from 'niksrc'.
⋊> ~/n/p/n/mysite on dev ◦ git remote -v                                                                               (nikola) 13:01:08
niksrc  https://github.com/AbdulSayyed/nikola-website.git (fetch)
niksrc  https://github.com/AbdulSayyed/nikola-website.git (push)
origin  https://github.com/AbdulSayyed/AbdulSayyed.github.io.git (fetch)
origin  https://github.com/AbdulSayyed/AbdulSayyed.github.io.git (push)
⋊> ~/n/p/n/mysite on dev ◦

The reason it was done because I was having difficulty with shared folder with VBox and Ubuntu 20.04. As there are some material, especially some images that I wanted to use with nikola site.

Though I have started working from both machine, I need to understand that I can only work or update the contents from one machine, push it to the remote. And then when starting to work again in another machine I need to pull a repo and started woking with it. I can not start to wrok in both machine with the same repo as it would created confilicts and I will loose my work.

Problems faced with working nipype.

It has been a week I have not been able to solve the issue with an error I recieved, it comes when this package tries to read the bids file. It does not give any error when reading but it doe when I use BET and tries to output.
I can not run nipype on windows.

When looking at the examples of nipype I found a new term `BET`

As I have not worked with FSL software but here is an overview of FSL software
Tools used in FSL:[Taken from FSL oxford]
fMRI:FEAT, MELODIC,FABBER, BASIL,VERBENA
sMRI: BET,FAST,FIRST,FLIRT, FNIRT, FSLVBM,SIENA, DIENAX,fsl_anat
dMRI: FDT,TBSS, eddy,topup
GLM/ Stats:.
other tools: FSLView, Fslutils,Atlases, Atlasquery, etc
BET or Brain Extaction Tool is uses to delete non-brain tissu from an image of the whle head. It is used to estimate the inner and outer cell surfaces and outer scapl surface out of T1 and T2 images.

Nipype introduction

Abdul Sayyed — Sat, 18 Jul 2020 17:06:24 GMT

Starting with nipype¶

Nipype probably pronouncec as nipee..yipee is an abbreviation for Neuroimaging in Python pipleline and interfaces
It is a Toolbox for anylysing data coming from neuroimaging modalaties. It is written in Python.

Installation
Check your installation

Beginners Guide¶

It is year 2017 guide, it can be tested and re written for others
The main purpose of this toolbox is to provide an easy way to build a workflow termed as a pipleline, to facilitate the existing technologies used in neuroimaging analyis. All popular technololgies such as SPM, FreeSurfer, FSL etccan be used.
It allows to combine these techonolgies in an specifed workflow, it is what you decided to use which technology for which prupose.
For example
The whole idea is to provide an environment where reasearch can be reproduced with the same data by sharing with others.

Nipype architechture:¶

It consist of many components, important ones are interfaces,Workflow Engines and Execution Plugins.

Interfaces are the python programs (scripts) that are used to interface with existing technologies like MATLAB,AFNI,ANTs etc.
Workflow Engine is a part that deals with the complexities involve in executing diferent task by gluing eachother. It uses following terms interchanably.
- Node:An interface needs the information about the technologies it is dealing with and it is given in the form of node. A node describes these information.
- MapNode:It is similar to node and takes multiple inputs of same type. For example 10 patient of same data analysis is performed on them.
- Wordflow:It is graph a kind of directed acyclic graph or forest of grapsh that describes the dataflow interms of its Nodes, MapNodes or Workflows it self.
- Execution Plugins: They descirbe how to execute your workfow in a physical machine by leaverging the power of differnet cores.

A conventional way of neuro imaging¶

Acqusation of MRI data: you need to know how it is taken what varibales and terms are used. Which series of MRI is uses commonly known as modalaties. There are many like ( DTI, fMRI etc).
The format of resulted images: Different scanners uses different formats e.g. DICOM , PAR or REC. To analyse these images they are to be converted into different format so that un necessary details can be removed. Initially data is kept in K-space and converted into different space. Mostly the format used is either nifti and now recetnly is gifti.
Design of the experiment: Which kind of experimental design is used what parameters to take into accunt etc.
Preprocessing of data:
- Slice Timing Correction (fMRI images needes to be correcyted )

The below is taken verbatim from nipype Micheal tutorial.¶

Because functional MRI measurement sequences don’t acquire every slice in a volume at the same time we have to account for the time differences among the slices. For example, if you acquire a volume with 37 slices in ascending order, and each slice is acquired every 50ms, there is a difference of 1.8s between the first and the last slice acquired. You must know the order in which the slices were acquired to be able to apply the proper correction. Slices are typically acquired in one of three methods: descending order (top-down); ascending order (bottom-up); or interleaved (acquire every other slice in each direction), where the interleaving may start at the top or the bottom. (Left: ascending, Right: interleaved)

Slice Timing Correction is used to compensate for the time differences between the slice acquisitions by temporally interpolating the slices so that the resulting volume is close to equivalent to acquiring the whole brain image at a single time point. This temporal factor of acquisition especially has to be accounted for in fMRI models where timing is an important factor (e.g. for event related designs, where the type of stimulus changes from volume to volume).

Chec If nipype is working use import nipype or import nipype. Run the cell if gets error it means it is not working otherwise it is present.

Thouth the module has been imported successfully but it does not have any attribute or any function help() it thorws an error. The above command succeeded, it means it is working. we have nipype on our path. To see where it is loaded from use shift + tab

Getting ready for dataset¶

Make a directory data in current folder that is underneate your notebook folder. Then using datalad install dataset. Note the cell is used to execute bash programe, here it is refered as bash kernel. Other kernels can be used as well.

In [18]:

%%bash
mkdir -p data
cd data
datalad install -r ///workshops/nih-2017/ds000114

install(ok): /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114 (dataset)
install(ok): /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/fmriprep (dataset)
install(ok): /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/freesurfer (dataset)
action summary:
  install (ok: 3)
[INFO] Cloning dataset to <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114> 
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114 to /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114 
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/.git to /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114 
[INFO] Completed clone attempts for <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114> 
[INFO] access to 1 dataset sibling datalad not auto-enabled, enable with:
| 		datalad siblings -d "/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114" enable -s datalad 
[INFO] Installing <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114> underneath /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114 recursively 
[INFO] Cloning dataset to <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/fmriprep> 
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/derivatives/fmriprep/.git to /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/fmriprep 
[INFO] Completed clone attempts for <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/fmriprep> 
[INFO] Cloning dataset to <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/freesurfer> 
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/derivatives/freesurfer/.git to /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/freesurfer 
[INFO] Completed clone attempts for <Dataset path=/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/derivatives/freesurfer>

Looking into the dataset.

In [19]:

ls data/ds000114/

CHANGES                   sub-08/
dataset_description.json  sub-09/
derivatives/              sub-10/
dwi.bval@                 task-covertverbgeneration_bold.json
dwi.bvec@                 task-covertverbgeneration_events.tsv
sub-01/                   task-fingerfootlips_bold.json
sub-02/                   task-fingerfootlips_events.tsv
sub-03/                   task-linebisection_bold.json
sub-04/                   task-overtverbgeneration_bold.json
sub-05/                   task-overtverbgeneration_events.tsv
sub-06/                   task-overtwordrepetition_bold.json
sub-07/                   task-overtwordrepetition_events.tsv

In [34]:

# We have one anatomical image in every folder. Lets make sure it is there.
!ls data/ds000114/sub-01/ses-test/anat/

sub-01_ses-test_T1w.nii.gz

Using BET from fsl that we imorted in first step.¶

In [9]:

import os
from os.path import abspath

from nipype import Workflow, Node, MapNode, Function
from nipype.interfaces.fsl import BET, IsotropicSmooth, ApplyMask

from nilearn.plotting import plot_anat
%matplotlib inline
import matplotlib.pyplot as plt
from nipype.testing import  example_data

In [14]:

# reading file in a variable
working_dir = os.getcwd()
data_dir = working_dir + "/data"
print(data_dir)
input_file =  abspath(data_dir + "/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w")
print(input_file)
fn = "./sub-01_ses-test_T1w.nii.gz"

/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data
/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w

In [ ]:

In [19]:

bet = BET()
bet.inputs.in_file = input_file
bet.inputs.out_file = "T1.nii.gz"
res = bet.run()

---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-19-8f66ff4bee62> in <module>
      1 bet = BET()
----> 2 bet.inputs.in_file = input_file
      3 bet.inputs.out_file = "T1.nii.gz"
      4 res = bet.run()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py in validate(self, objekt, name, value, return_pathlike)
    328     def validate(self, objekt, name, value, return_pathlike=False):
    329         """Validate a value change."""
--> 330         value = super(File, self).validate(objekt, name, value, return_pathlike=True)
    331         if self._exts:
    332             fname = value.name

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py in validate(self, objekt, name, value, return_pathlike)
    133         if self.exists:
    134             if not value.exists():
--> 135                 self.error(objekt, name, str(value))
    136 
    137             if self._is_file and not value.is_file():

~/anaconda3/envs/nipype/lib/python3.8/site-packages/traits/base_trait_handler.py in error(self, object, name, value)
     72             The proposed new value for the attribute.
     73         """
---> 74         raise TraitError(
     75             object, name, self.full_info(object, name, value), value
     76         )

TraitError: The 'in_file' trait of a BETInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/sayyed/neuro-science/projects/nikola/mysite/notebooks/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w' <class 'str'> was specified.

Start working with nipype¶

Importing few things

In [3]:

import os
from os.path import abspath
from os.path import relpath

from nipype import Workflow, Node, MapNode, Function
from nipype.interfaces.fsl import BET, IsotropicSmooth, ApplyMask

from nilearn.plotting import plot_anat
%matplotlib inline
import matplotlib.pyplot as plt

In [3]:

# will use a T1w from ds000114 dataset
input_file =  abspath("/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz")

In [5]:

bet = BET()
bet.inputs.in_file = abspath("data/sample-nifiti-file.nii")
bet.imputs.int_file= input_file
help(bet.inputs)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-5-125541a3dc72> in <module>
      1 bet = BET()
      2 bet.inputs.in_file = abspath("data/sample-nifiti-file.nii")
----> 3 bet.imputs.int_file= input_file
      4 help(bet.inputs)

NameError: name 'input_file' is not defined

In [17]:

bet.inputs.out_file = "sample_bet.nii.gz"
res = bet.run()
res.outputs

Out[17]:

inskull_mask_file = <undefined>
inskull_mesh_file = <undefined>
mask_file = <undefined>
meshfile = <undefined>
out_file = /home/sayyed/neuro-science/projects/nikola/mysite/notebooks/sample_bet.nii.gz
outline_file = <undefined>
outskin_mask_file = <undefined>
outskin_mesh_file = <undefined>
outskull_mask_file = <undefined>
outskull_mesh_file = <undefined>
skull_file = <undefined>
skull_mask_file = <undefined>

In [18]:

plot_anat("sample_bet.nii.gz", 
          display_mode='ortho', dim=-1, draw_cross=False, annotate=False);

In [ ]:

002_basics

Abdul Sayyed — Fri, 10 Jul 2020 15:45:20 GMT

Python basics needed to do neuro imaginag¶

In [ ]:

001_intro

Abdul Sayyed — Fri, 10 Jul 2020 14:43:54 GMT

Jupyter note book basics¶

In [1]:

import os
print(os.name)
print(os.getcwd())
print(os.listdir( '.'))

posix
/home/sayyed/neuro-science/projects/nikola/mysite/notebooks
['002_intro.ipynb', '001_intro.ipynb', '002_basics.ipynb', '.ipynb_checkpoints', '005_intro.ipynb', '003_intro.ipynb', '004_intro.ipynb']

In [1]:

npm.install()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-c09f0e0ad088> in <module>
----> 1 npm.install()

NameError: name 'npm' is not defined

Running code from different kernel¶

In [5]:

%%bash
which bash

/usr/bin/bash

In [6]:

%%HTML
<h4>This is html 4 heading </h4>

This is html 4 heading

In [ ]:

Checking-nipype-Installation

Abdul Sayyed — Fri, 10 Jul 2020 14:43:54 GMT

Checking `nipype` installation¶

There are number of ways to check its installation as shown below.

In [2]:

import nipype; print(nipype.__version__)

1.5.0

In [1]:

import nipype; nipype.test()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     36         try:
---> 37             import pytest
     38         except ImportError:

ModuleNotFoundError: No module named 'pytest'

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-1-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     37             import pytest
     38         except ImportError:
---> 39             raise RuntimeError("py.test not installed, run: pip install pytest")
     40         args = []
     41         if not doctests:

RuntimeError: py.test not installed, run: pip install pytest

The above simply says that pytest is not installed and using the pip install it.
Installed pytest using pip install pytest and run the text again. When test is run it gives the following error.
Docs: https://docs.pytest.org/en/latest/warnings.html ======================================================== short test summary info ========================================================= ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/documenter.py - ModuleNotFoundError: No module nam... ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/init.py - ModuleNotFoundError: No modul... ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/docstring.py - ModuleNotFoundError: No modu... !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ===================================================== 9 warnings, 3 errors in 57.98s =====================================================
The error above is related to the Sphinix package which comes with nipype. We wil see it later.

In [3]:

import nipype as ny
ny.get_info()

Out[3]:

{'pkg_path': '/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype',
 'commit_source': 'archive substitution',
 'commit_hash': '%h',
 'nipype_version': '1.5.0',
 'sys_version': '3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52) \n[GCC 7.3.0]',
 'sys_executable': '/home/sayyed/anaconda3/envs/nipype/bin/python',
 'sys_platform': 'linux',
 'numpy_version': '1.18.5',
 'scipy_version': '1.5.0',
 'networkx_version': '2.4',
 'nibabel_version': '3.1.1',
 'traits_version': '6.1.0'}

Testing the installation¶

In [3]:

import nipype; nipype.test()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     36         try:
---> 37             import pytest
     38         except ImportError:

ModuleNotFoundError: No module named 'pytest'

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-3-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     37             import pytest
     38         except ImportError:
---> 39             raise RuntimeError("py.test not installed, run: pip install pytest")
     40         args = []
     41         if not doctests:

RuntimeError: py.test not installed, run: pip install pytest

In [ ]:

1. I installed `pytest` using `pip install pytest` it rand the test and filed on `Sphinix extension`.
2. When tried to import `nilearn` it also threw an error of not finding this package.

In [4]:

import nipype; nipype.test()

============================= test session starts ==============================
platform linux -- Python 3.8.2, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
rootdir: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype, inifile: pytest.ini
collected 2885 items / 2 errors / 2883 selected

==================================== ERRORS ====================================
________________ ERROR collecting sphinxext/apidoc/__init__.py _________________
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py:5: in <module>
    from sphinxcontrib.napoleon import (
E   ModuleNotFoundError: No module named 'sphinxcontrib.napoleon'
________________ ERROR collecting sphinxext/apidoc/docstring.py ________________
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/py/_path/local.py:704: in pyimport
    __import__(modname)
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py:5: in <module>
    from sphinxcontrib.napoleon import (
E   ModuleNotFoundError: No module named 'sphinxcontrib.napoleon'
=========================== short test summary info ============================
ERROR ../../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py
ERROR ../../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/docstring.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 17.92s ==============================

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-4-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     48             args.append("-n auto")
     49         args.append(os.path.dirname(__file__))
---> 50         pytest.main(args=args)
     51 
     52 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/config/__init__.py in main(args, plugins)
    122         else:
    123             try:
--> 124                 ret = config.hook.pytest_cmdline_main(
    125                     config=config
    126                 )  # type: Union[ExitCode, int]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/hooks.py in __call__(self, *args, **kwargs)
    284                     stacklevel=2,
    285                 )
--> 286         return self._hookexec(self, self.get_hookimpls(), kwargs)
    287 
    288     def call_historic(self, result_callback=None, kwargs=None, proc=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in _hookexec(self, hook, methods, kwargs)
     91         # called from all hookcaller instances.
     92         # enable_tracing will set its own wrapping function at self._inner_hookexec
---> 93         return self._inner_hookexec(hook, methods, kwargs)
     94 
     95     def register(self, plugin, name=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in <lambda>(hook, methods, kwargs)
     82             )
     83         self._implprefix = implprefix
---> 84         self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
     85             methods,
     86             kwargs,

    [... skipping hidden 3 frame]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/main.py in pytest_cmdline_main(config)
    238 
    239 def pytest_cmdline_main(config):
--> 240     return wrap_session(config, _main)
    241 
    242 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/main.py in wrap_session(config, doit)
    233                     session.exitstatus = exc.returncode
    234                 sys.stderr.write("{}: {}\n".format(type(exc).__name__, exc))
--> 235         config._ensure_unconfigure()
    236     return session.exitstatus
    237 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/config/__init__.py in _ensure_unconfigure(self)
    823         if self._configured:
    824             self._configured = False
--> 825             self.hook.pytest_unconfigure(config=self)
    826             self.hook.pytest_configure._call_history = []
    827         while self._cleanup:

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/hooks.py in __call__(self, *args, **kwargs)
    284                     stacklevel=2,
    285                 )
--> 286         return self._hookexec(self, self.get_hookimpls(), kwargs)
    287 
    288     def call_historic(self, result_callback=None, kwargs=None, proc=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in _hookexec(self, hook, methods, kwargs)
     91         # called from all hookcaller instances.
     92         # enable_tracing will set its own wrapping function at self._inner_hookexec
---> 93         return self._inner_hookexec(hook, methods, kwargs)
     94 
     95     def register(self, plugin, name=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in <lambda>(hook, methods, kwargs)
     82             )
     83         self._implprefix = implprefix
---> 84         self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
     85             methods,
     86             kwargs,

    [... skipping hidden 3 frame]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/conftest.py in pytest_unconfigure(config)
     42 def pytest_unconfigure(config):
     43     # Delete temp folder after session is finished
---> 44     shutil.rmtree(temp_folder)

~/anaconda3/envs/nipype/lib/python3.8/shutil.py in rmtree(path, ignore_errors, onerror)
    704             orig_st = os.lstat(path)
    705         except Exception:
--> 706             onerror(os.lstat, path, sys.exc_info())
    707             return
    708         try:

~/anaconda3/envs/nipype/lib/python3.8/shutil.py in rmtree(path, ignore_errors, onerror)
    702         # lstat()/open()/fstat() trick.
    703         try:
--> 704             orig_st = os.lstat(path)
    705         except Exception:
    706             onerror(os.lstat, path, sys.exc_info())

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpqoloi4y8'

In [2]:

# Import the nipype module
import nipype
# Optional: Use the following lines to increase verbosity of output
nipype.config.set('logging', 'workflow_level', 'CRITICAL')
nipype.config.set('logging', 'interface_level', 'CRITICAL')
nipype.logging.update_logging(nipype.config)
# Run the test: Increase verbosity parameter for more info
nipype.test()

ERROR: usage: ipykernel_launcher.py [options] [file_or_dir] [file_or_dir] [...]
ipykernel_launcher.py: error: unrecognized arguments: --doctest-modules
  inifile: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/pytest.ini
  rootdir: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype

In [ ]:

Sayyed's blog (A python way Neuroimaging Analysis)

nipype-workflow

My setup of nipype

How notebook differs when created in nikola or in jupyterlab?

How to create a notebook with vscode.

Running code from different kernels

How this repo is committed

Problems faced with working nipype.

When looking at the examples of nipype I found a new term BET

Nipype introduction

Starting with nipype¶

Beginners Guide¶

Nipype architechture:¶

A conventional way of neuro imaging¶

The below is taken verbatim from nipype Micheal tutorial.¶

Getting ready for dataset¶

Using BET from fsl that we imorted in first step.¶

Start working with nipype¶

002_basics

Python basics needed to do neuro imaginag¶

001_intro

Jupyter note book basics¶

Running code from different kernel¶

This is html 4 heading

Checking-nipype-Installation

Checking nipype installation¶

Testing the installation¶

How `notebook` differs when created in `nikola` or in `jupyterlab`?

When looking at the examples of nipype I found a new term `BET`

Checking `nipype` installation¶