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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.
kimberlylray
@kimberlylray
@Garyfallidis Im interested in the 2020 DIPY course, could you explain the difference between the 3 and 5 day course registration options? Is it as simple as 3 day includes days 1-3 and 5 day is days 1-5?
Eleftherios Garyfallidis
@Garyfallidis
Yes, that is correct @kimberlylray
Rajikha Raja
@rajikha
Hi DIPY team, I am interested in trying out the various reconstruction models for estimating diffusion using DIPY. May I know , what are the models which can be used for reconstruction in case of single shell DWI and is there any constraints to have higher b-values such as b=2000 for using any specific model? Thank you
Ariel Rokem
@arokem
Hey @rajikha : that is the topic of this long-languishing PR: nipy/dipy#1919
So there's some information there