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Romulus
@romainviard
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
Rajikha Raja
@rajikha
@arokem Thank you
kimberlylray
@kimberlylray
@Garyfallidis great, thank you!
Thomas
@ThomasTT_gitlab
Hi :) I want to use another metric - MAM. Can anyone help me how to substitute this measure into QuickBundles in Python?
Serge Koudoro
@skoudoro
Hi @ThomasTT_gitlab, you can look at this blog post https://medium.com/isiway-tech/gps-trajectories-clustering-in-python-2f5874204a53 or this tutorial: https://dipy.org/documentation/1.0.0./examples_built/segment_extending_clustering_framework/#example-segment-extending-clustering-framework. Do not hesitate to send us a link of your code. We can see your mistake and it will be easier to help you.
Thomas
@ThomasTT_gitlab
@skoudoro THX a lot :)
Luke Bloy
@bloyl
Hi all, quick question.
I have a registration deformation field (from ITK or something similar) that I would like to apply to an image. it seems like differomorphic map like in this test (https://github.com/nipy/dipy/blob/05c2a75581525ccf2f32d418ebf57fb0c70d9f86/dipy/align/tests/test_imwarp.py#L569-L575) would do it,but i have two questions.
1) I only have a vector field mapping the fixed space to the moving. Where should i attach it as mapping.forward ormapping.backward.
2) Do i need to attach something to the other one
nis02002
@nis02002
Does any one where are the MRI database? both MRI image and b-vectors?
Thomas
@ThomasTT_gitlab
Hi :) As I wrote, I want to use another metric - MAM in QB.I already the distance function but something is not working :( What is wrong? I paste the code below:

class mam(Metric):
""" Computes the mam distance between two streamlines. """
def init(self):

    # For simplicity, features will be the vector between endpoints of a streamline.
    super(mam, self).__init__(feature=VectorOfEndpointsFeature())

def are_compatible(self, shape1, shape2):
    """ Checks if two features are vectors of same dimension.

    Basically this method exists so we don't have to do this check
    inside the `dist` method (speedup).
    """
    return shape1 == shape2 and shape1[0] == 1

def dist(self, v1, v2):

    track1 = np.ascontiguousarray(v1, dtype=np.float32)
    t1_len = track1.shape[0]
    track2 = np.ascontiguousarray(v2, dtype=np.float32)
    t2_len = track2.shape[0]
    # preallocate buffer array for track distance calculations

    #distances_buffer = np.zeros((t1_len ,), dtype=np.float32)
    min_t2t1 = np.zeros((t2_len ,), dtype=np.float32)
    min_t1t2 = np.zeros((t1_len ,), dtype=np.float32) 

    for t2_pi in range(0,t2_len):
        min_t2t1[t2_pi] = np.inf
    for t1_pi in range(0,t1_len):
        min_t1t2[t1_pi] = np.inf
    # pointer to current point in track 1
    t1_pt = track1
    t2_pt = track2
    # calculate min squared distance between each point in the two
    # lines.  Squared distance to delay doing the sqrt until after this
    # speed-critical loop
    for t1_pi in range(0,t1_len):
        # pointer to current point in track 2
        for t2_pi in range(0,t2_len):
            d0 = t1_pt[t1_pi][0] - t2_pt[t2_pi][0]
            d1 = t1_pt[t1_pi][1] - t2_pt[t2_pi][1]
            delta2 = d0*d0 + d1*d1 #+ d2*d2
            if delta2 < min_t1t2[t1_pi]:
                min_t1t2[t1_pi]=delta2

    for t2_pi in range(0,t2_len):
        # pointer to current point in track 2
        for t1_pi in range(0,t1_len):
            d0 = t1_pt[t1_pi][0] - t2_pt[t2_pi][0]
            d1 = t1_pt[t1_pi][1] - t2_pt[t2_pi][1]
            delta2 = d0*d0 + d1*d1 #+ d2*d2
            if delta2 < min_t2t1[t2_pi]:
                min_t2t1[t2_pi]=delta2

    # sqrt to get Euclidean distance from squared distance
    for t1_pi in range(0,t1_len):
        min_t1t2[t1_pi]=math.sqrt(min_t1t2[t1_pi])
    for t2_pi in range(0,t2_len):
        min_t2t1[t2_pi]=math.sqrt(min_t2t1[t2_pi])

    mean_t2t1 = 0
    mean_t1t2 = 0

    for t1_pi in range(0, t1_len):
        mean_t1t2+=min_t1t2[t1_pi]
    mean_t1t2=mean_t1t2 / t1_len
    for t2_pi in range(0, t2_len):
        mean_t2t1+=min_t2t1[t2_pi]
    mean_t2t1=mean_t2t1 / t2_len
    return np.min((mean_t2t1,mean_t1t2))

metric = mam()
qb2 = QuickBundles(threshold=0.15, metric=metric)
clus = qb2.cluster(streamlines)

I will be grateful for help :)
nis02002
@nis02002
how can I check the stanford database?
nis02002
@nis02002
where can I find the database before/after the operation?
Eleftherios Garyfallidis
@Garyfallidis
@nis02002 not sure iif I understand your question. But in your home folder there should be a folder called .dipy inside that folder are all the datasets that are fetched with dipy.