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dipy/dipy

Diffusion MR Imaging in Python

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Ariel Rokem

@arokem

I think so. Maybe @mvgolub or @RafaelNH can say more?

Yaroslav Halchenko

@yarikoptic

AHA -- here is where all the DiPy folks hanging out! Will there be DiPy booth at SfN?

Ariel Rokem

@arokem

@yarikoptic : hello!

Nope. No SfN booth

smasjoodi

@smasjoodi

Hi every body. I analysed a DWI data set using DKI model (just as example code), but outputs are very noisy. DWI data parameters: b-values:0, 500, 1000, 2000 in the same 15 directions. Why AK and RK are so much noisy?

Ariel Rokem

@arokem

@smasjoodi : noisy data? What is your SNR? (https://dipy.org/documentation/1.0.0./examples_built/snr_in_cc/#example-snr-in-cc)

QuantumBrain®

@Quantum_Neuron_twitter

Hey, just a general question out of curiosity: What's causing the actual b-values to differ slightly from what I selected in the scanner console? e.g. b0 is actually not zero but around 26. or b=1000 is sometimes 999.34 or 1001.18 etc. Is this measured or calculated somehow from the gradient system? and does it improve the results significantly to use those actual values instead of the theoretical ones?

Ariel Rokem

@arokem

@Quantum_Neuron_twitter : I don't know the answer to this, but if no one here can provide an answer, I think that it would be a great question to ask on https://neurostars.org/

I do know that in some cases b-values also vary spatially

(empirical b-values, that is)

willi3by

@willi3by

@arokem @RafaelNH @mvgolub I was investigating and it seems the post that was linked in a previous response to nipy/dipy#1744 has not been updated since May 7. Is there a dipy work in progress repository where newer files might be stored? Thanks again for the help

Rafael Neto Henriques

@RafaelNH

Hi @willi3by! @mvgolub did sime very nice progress on this code. We didn't push any update because we are testing it offline in deep. At the moment, we already have the same performance when comparing to the state of art of single shell algorithms in the recent literature, however we are still not happy with what single shell algorithms can give us. We are still detecting massive issues with this technique in general, and we are trying the best to overcome its major limitations. By the end of the year, we are planing: 1) to have our advances pushed in dipy; 2) share a manuscript reporting the details of our implementations and tests. Keep posted!

Rafael Neto Henriques

@RafaelNH

Hi @smasjoodi! Actually, considering that you have only 15 directions per shell, your maps looks good. DKI provides you a nice quantification of non-Gaussian diffusion (information that you cannot capture using techniques such as DTI), however its limitation is that is noisy, particularly in perpendicular directions where diffusivities are low (e.g. see chapter 3 of https://core.ac.uk/download/pdf/12428129.pdf). Radial and axial kurtosis can also have a noisier aspect because these estimates are not well define in crossing white matter regions and grey matter, such and axial and radial diffusivity (https://www.sciencedirect.com/science/article/pii/S1053811915000968?via%3Dihub). To improve DKI performance try to Denoise your data, and also Gibbs unring (e.g. see chapter 3 of https://www.repository.cam.ac.uk/handle/1810/281993) - code available in dipy (https://dipy.org/documentation/1.0.0./examples_built/denoise_mppca/#example-denoise-mppca) (https://dipy.org/documentation/1.0.0./examples_built/denoise_gibbs/#example-denoise-gibbs). Also the mean signal DKI might provide you an alternative and more precise non-gaussian diffusion characterisation (https://dipy.org/documentation/1.0.0./examples_built/reconst_msdki/#example-reconst-msdki).

willi3by

@willi3by

@RafaelNH Thank you for the in depth update! I very much look forward to seeing this in Dipy.

Rafael Neto Henriques

@RafaelNH

Hi @Quantum_Neuron_twitter! Actual values consider other sequence parameters that induces extra diffusion weighting (e.g effects of crushers). Using that actual values provides you more accurate diffusion estimates.

nis02002

@nis02002

Hi everyone, when I try to visualize data with window import form viz module, it has error message "import error, can not import name ' window', how to solve this issue?

nis02002

@nis02002

I installed pury, the window import error is gone, but there are error to display with VTK, can not find a decent config

Nabila Abraham

@nabsabraham

hi everyone! I'm using 3D data for the first time ever and patient's slice dimensions don't always match up - is a simple affine registration sufficient to reproject all patients to a common shape? for example, I want all patients to have a shape of 15x128x128

any help appreciated!

AlexBadea

@portokalh

Depends what you want to do. An affine transform may change the scale of your patient's brain. If you want to simply match the image matrices consider ResampleImage in ants; or convert3d and you may also want to check https://github.com › rordenlab › spmScripts › blob › nii_reslice_target. It is so good to have options! Best of luck!

@RafaelNH can you point me to examples of massive issues in single shell methods, or maybe not at this time? Just curious. Thanks and the best of luck!

AlexBadea

@portokalh

@nabsabraham ; nice thing is you can do this in dipy !!! https://dipy.org/documentation/1.0.0./examples_built/affine_registration_3d/#example-affine-registration-3d excerpt: We can see that the images are far from aligned by drawing one on top of the other. The images don’t even have the same number of voxels, so in order to draw one on top of the other we need to resample the moving image on a grid of the same dimensions as the static image, we can do this by “transforming” the moving image using an identity transform

identity = np.eye(4)
affine_map = AffineMap(identity,
static.shape, static_grid2world,
moving.shape, moving_grid2world)
resampled = affine_map.transform(moving)

smasjoodi

@smasjoodi

Hi @RafaelNH . Thank you very much for your perfect explanation.

smasjoodi

@smasjoodi

How could I update my dipy version? Currently I cannot run mppca program to denoise my DKI dataset.

Every time I want to install dipy on my Anaconda it dipy0.16 is installed.

dipy conda-forge/linux-64::dipy-0.16.0-py27h4df700f_0

Nabila Abraham

@nabsabraham

Hi @portokalh , thanks for the great answer!
I am planning to use a rigid body transformation as I don't want to deform anything just yet - however, I am working with dicoms and was wondering if there is any simple method to retrieve the affine voxel-to-patient matrix to do the registration

Nabila Abraham

@nabsabraham

if anyone needs the answer to how to create the affine from a dicom header, nibabel has a great tutorial and what's more, this package has implemented the tutorial in their create_affine function!
https://dicom2nifti.readthedocs.io/en/latest/_modules/dicom2nifti/common.html#create_affine

au84

@au84

hi - are the b-vec and b-val files generated in every Diffusion weigted MRI sequence ?

AlexBadea

@portokalh

I am using dipy 1.0.0 in python 3.7 on mac os x mojave 10.14.5. I would be grateful for a suggestion on how to get over this error importing in jupyter notebook even when import statements run in terminal.

importError Traceback (most recent call last)

<ipython-input-4-4e678cb08f4a> in <module>
6 from dipy.data import get_fnames
7 import vtk
----> 8 from dipy.viz import window, actor
9 from dipy.tracking.streamline import Streamlines
10 from dipy.io.streamline import load_trk, save_trk

ImportError: cannot import name 'window' from 'dipy.viz' (/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/dipy/viz/init.py)

Romulus

@romainviard

Hello @portokalh Have you installed fury? pip install fury

AlexBadea

@portokalh

yes. i can import in the command line, but the jupyter notebook cannot

looks like things that have to do with dipy.viz have problems

cannot import name 'utils' from 'dipy.viz' (/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/dipy/viz/init.py)

do i need qt for this to be installed separately of dipy?

Romulus

@romainviard

@portokalh I don't think qt is required

It it the same version of python between terminal and jupyter ?

python -V on terminal

import sys
print (sys.version)

on jupyter

or "which python " on terminal

AlexBadea

@portokalh

good catch on terminal i am in
Python 3.5.6 :: Anaconda, Inc.

jupyter is at 3.7; how do i reconcile?

on jupyther :3.7.4 (v3.7.4:e09359112e, Jul 8 2019, 14:54:52)
[Clang 6.0 (clang-600.0.57)]

Romulus

@romainviard

Find the directory where anaconda is installed ....then used the pip from this directory ...it should be something like ...../anaconda3../bin

to fond tje directory use "which jupyter"

AlexBadea

@portokalh

pip install again dipy from here? /Library/Frameworks/Python.framework/Versions/3.7/bin/jupyter

Romulus

@romainviard

"Library/Frameworks/Python.framework/Versions/3.7/bin/pip install fury "

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