dipy/dipy

Diffusion MR Imaging in Python

Paolo Avesani

@Paolopost

A suggestion to improve the dipy_track_local workflow. Currently there is no opportunity to set the step-size parameter of tracking. It is fixed to 0.5mm. May be it would be worthwhile at least to set this value proportionally to the voxel size, e.g. half of it.

Serge Koudoro

@skoudoro

Thank you @Paolopost for the suggestion. This has been already added on master so it will be there for next release !

Yijun Liu

@snapfinger

Hi guys, does anyone have unprocessed diffusion weighted images of kids and acquired with 64 diffusion directions per shell (uniform distribution)? Didn't find suitable data in HCP/NITRC/OpenNeuro, if you have we can probably collaborate. And would appreciate if anyone can point to the link if you know there's such public dataset.

Michael Paquette

@mpaquette

@wayalan Might not be relevant anymore, as your question dates from April 11th, but using the G/DELTA/delta value you provided, I am estimating a b-value of 6703.35 s/mm^2, close enough to the 6650 reported by your scanner. You might be using wrong unit conversion or the wrong value of gyromagnetic ratio (should be ~(42.515e6 x 2pi) rad T^-1 s^-1)

Eleftherios Garyfallidis

@Garyfallidis

An alert here to say that we are making a lot of refactoring to accommodate the upcoming DIPY 1.0 release. If you are using dev version, please use caution.

Serge Koudoro

@skoudoro

FYI, We plan to cut the release this Wednesday. (31rst)

Daniel Haehn

@haehn

Hello Dipy Devs! I am getting involved in a diffusion project and I have the following question: How do you store streamlines and attached scalars and properties? We are running into limitations of the TrackVis file format and the scientists here so far used VTP - everything less than ideal. How do you do it? I saw dipy also exports TRK files.

Francois Rheault

@frheault

@haehn I am working on example for the new stateful_tractogram class made to facilitate loading/saving various file format (including trk)
The easiest way in the meantime to get an example is the test in https://github.com/nipy/dipy/blob/master/dipy/io/tests/test_stateful_tractogram.py and look for ''random_streamline_color'' or ''random_point_gray'' or ''random_point_color''.

That would cover data_per_point. For data_per_streamline it is easier, the new class accept a dictionnary. The key is the name is name of your metadata and the value is an array or a list and then len() must be the same as the number of streamlines.

Also this new class require a reference so make sure you have the nifti file they were generated with and know in which space they are when creating the object.
(If you have no idea what I meant, tell me)

Daniel Haehn

@haehn

Thanks. But which file format do you ultimately choose? TrackVis is too limited at this point in regards to scalars and properties.

VTP files are too large.

is DPY preferred?

Eleftherios Garyfallidis

@Garyfallidis

Hi @haehn, great to hear from you. Eventually DPY should be the preferred option. However, we are not promoting it much for now as we want to add some crucial new options. Can you give us an example of your user case?

Daniel Haehn

@haehn

Thank you, @Garyfallidis ! The use case is standard fiber bundles with flexible numbers of scalars (per fiber point) and flexible number of properties (per fiber). TRK files limit it to 10 each.

Is that supported yet with DPY?

Eleftherios Garyfallidis

@Garyfallidis

@haehn we can easily have support for any number of properties in DPY. However, not there yet. I will try to prioritize it so that others like you can be facilitated. Alternatively, you can create a very fast format with NPZ using the Streamlines API that we developed in Nibabel and use DIPY. Basically a Streamlines object can give you the arrays of the points and the metrics (of any number - look at the data_per_point attributes/parameters) as numpy arrays.

See here https://nipy.org/nibabel/reference/nibabel.streamlines.html#nibabel.streamlines.tractogram.Tractogram

Eleftherios Garyfallidis

@Garyfallidis

Look at the parameters that a Tractogram object can have data_per_point and per_streamline. You can then save these data as independent arrays and reconstruct the Tractogram on load.

Erin Teich

@erteich

Hi all! I'm a fairly new user of dipy, and I've been doing some playing around with the HARDI labeled dataset accessible via dipy.data.read_stanford_labels(). I saw that this is relabeled, such that white matter voxels have the label 1 or 2, regardless of what labels freesurfer originally gave them. I was wondering if it is possible to gain access to the original freesurfer labels for these voxels, however they were reduced from the original aparc+aseg file? Then I could delineate different white matter regions according to that parcellation. Thanks in advance for the help!

Eleftherios Garyfallidis

@Garyfallidis

And don't forget to save the streamlines too. From them Tractogram.streamlines you will need the data, offsets and lengths arrays to be saved in the NPZ (numpy compressed) format. It's an idea. Let me know if you try it. Right now we are busy with the upcoming release but building a tutorial with these issues and updating the DPY format should be an easy and fun project.

Eleftherios Garyfallidis

@Garyfallidis

@haehn issue added here nipy/dipy#1936 and targeted for release 1.1 aimed in October.

Daniel Haehn

@haehn

Thank you so much @Garyfallidis ! I will follow the DPY issue and also try the NPZ.. then I will compare file size against the TRK and VTP formats.

Casa Mofoekeng 'Moso

@CasaMofoekengMo_twitter

Hello, I am trying to implement Python code when given the names and GPS positions of 750 people (latitude, longitude and elevation) to find the names of the 10 closest neighbors of a randomly selected individual.

please help.

Eleftherios Garyfallidis

@Garyfallidis

This is not the right channel for this question @CasaMofoekengMo_twitter but hey you can google KNN and python I am sure they will be many solutions available. Best of luck.

Eleftherios Garyfallidis

@Garyfallidis

A historic moment. DIPY 1.0 is out!

See details here https://docs.google.com/document/d/1VBhd8kLR6f6SQiRJwMcO5m61wHzr7iCg-BH-udoDkBI/edit?usp=sharing

Serge Koudoro

@skoudoro

:thumbsup: :punch: :fire: :rocket:

Bramsh Q Chandio

@BramshQamar

A historic moment. DIPY 1.0 is out!

:thumbsup: :finnadie:

Eleftherios Garyfallidis

@Garyfallidis

:fire: :fire: :fire: :fire: :fire: :fire: :fire:

:roller_coaster: :roller_coaster: :roller_coaster:

Bramsh Q Chandio

@BramshQamar

:fireworks:

Eleftherios Garyfallidis

@Garyfallidis

:rocket: :rocket: :rocket: :rocket: :rocket: :rocket:

Shreyas Fadnavis

@ShreyasFadnavis

👌🏻👌🏻👌🏻👌🏻👌🏻🔥

Gabriel Girard

@gabknight

:thumbsup: :thumbsup:

Rafael Neto Henriques

@RafaelNH

Congrats to all ! Well done! Amazing !

Romulus

@romainviard

Thx u !! in hurry to try it

Paolo Avesani

@Paolopost

http://bit.ly/congratulation2you

Really great achievement!

Eleftherios Garyfallidis

@Garyfallidis

:wine_glass:

Kirstie Whitaker

@KirstieJane

:scream_cat: :scream_cat: :scream_cat: Congratulations!

Eleftherios Garyfallidis

@Garyfallidis

Thank you!!! :smile:

Jean-Christophe Houde

@jchoude

Hey Elef, congrats on the release!

When I try to access dipy.org in Firefox, I get a certificate invalidity message. You might want to look into that @Garyfallidis @skoudoro

Eleftherios Garyfallidis

@Garyfallidis

Yes, should be resolved in a few days. We have applied for the SSL certificate.

Jean-Christophe Houde

@jchoude

:thumbsup:

Fang-Cheng Yeh

@FangChengYeh_twitter

Congratulations to the new DIPY and Website. It looks awesome!

Eleftherios Garyfallidis

@Garyfallidis

Thank you @FangChengYeh_twitter and all for your help all these years.

Fang-Cheng Yeh

@FangChengYeh_twitter

You are welcome. Wish I could help more if I knew how to code in python.

Eleftherios Garyfallidis

@Garyfallidis

Never late! :D

nis02002

@nis02002

Anyone please let me know how to load dataset from HCP with DIPY?

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