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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 "
maybe this is a nasty way to solve the problem ...(I m still beginner)
AlexBadea
@portokalh
Requirement already satisfied: fury in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (0.3.0)
Requirement already satisfied: scipy>=0.9 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from fury) (1.3.1)
Requirement already satisfied: vtk>=8.1.0 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from fury) (8.1.2)
Requirement already satisfied: numpy>=1.7.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from fury) (1.17.2)
Romulus
@romainviard
@portokalh did it solve the issue ?
from dipy.viz import window, actor
Serge Koudoro
@skoudoro
@smasjoodi , you are still using python2.7 . However dipy 1.0 is compatible only with python 3.5+. so you need to update you anaconda version to have python3. For your information, python 2.7 end of life is January 1rst 2020 so in 3month so I advise you to update your environnment
@portokalh, if you are using anaconda, do not forget to activate your environment, otherwise, it will always be the default python installation on your mac
use: source activate base
and then you can use pip install
AlexBadea
@portokalh
serge i am in py3.7.3 on terminal and 3.7.4 in jupyter and trying to synchronize those. why so many pythons?
AlexBadea
@portokalh
tried to clean things up now it looks like i may need to reinstall anaconda: conda install python=3.7; gives //anaconda3/bin/conda: //anaconda3/bin/python: bad interpreter: No such file or directory
AlexBadea
@portokalh
thanks @romainviard and @skoudoro all is well after reinstalling anaconda and dipy and reconciling the versions between jupyter and terminal! very grateful!
QuantumBrain®
@Quantum_Neuron_twitter
Is there a simple way to filter/select a subset of b-values within my dataset and gtable ? e.g. up to b<=2000
Ariel Rokem
@arokem
@Quantum_Neuron_twitter : yes, something like : idx = gtab.bvals<=2000; subset = data[..., idx]should give you a 4D array with data only from the bvals <=2000
QuantumBrain®
@Quantum_Neuron_twitter
ah great, thx Ariel
Eleftherios Garyfallidis
@Garyfallidis
Hey!! Registration for DIPY Workshop 2020 is now open. Visit https://workshop.dipy.org for information about dates, program and accommodation.
Hope to see you all in Bloomington this March for the workshop. Last year the workshop was a blast and people evaluated with 5 to 5 stars overall.
Shreyas Fadnavis
@ShreyasFadnavis
:rocket: :star2: :heart_eyes:
Eleftherios Garyfallidis
@Garyfallidis
:rocket: :heart: :rocket:
Bramsh Q Chandio
@BramshQamar
:rocket: :fire:
Kerolss
@Kerolss
Hello,
Can anyone help me?
I have got the following issue while running the below command
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
Issue: curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.
N. B) The installation has not done due to the PC shut down, and while I run the command again I have got the mentioned issue
curl: (35) schannel: next InitializeSecurityContext failed: Unknown error (0x80092012) - The revocation function was unable to check revocation for the certificate.