dipy/dipy

Diffusion MR Imaging in Python

Serge Koudoro

@skoudoro

Futhermore, it seems there is an inversion between affine_labels and labels in your function arguments. To make sure that is correct, be explicit on your function:

utils.connectivitymatrix(streamlines, label_volume=labels.astype(int), affine=affine_labels,
return_mapping=False,
mapping_as_streamlines=False)

AlexBadea

@portokalh

Thanks @skoudoro : labels.dtype.kind='i'; labels.ndim=3; running what you suggested takes me to ile "/Users/alex/py3/lib/python3.7/site-packages/dipy/tracking/utils.py", line 164, in <listcomp>
endpoints = [sl[0::len(sl)-1] for sl in streamlines]
ValueError: slice step cannot be zero

2 replies

nis02002

@nis02002

hi everyone , in order to use water free DTI, do we have to get at least three different b-vales/b-vectors?

Ariel Rokem

@arokem

@nis02002 : at least two non-zero b-values, if you intend to use the method implemented here: https://github.com/nipy/dipy/blob/master/dipy/reconst/fwdti.py

There are new developments in the pipeline to remove this constraint, but these methods are not quite ready for general use yet

Hopefully in an upcoming release

zlf123-marker

@zlf123-marker

Excuse me, I want to know how to display t1 data and TRK files with dipy library?

Ariel Rokem

@arokem

@zlf123-marker : you should take a look at the examples on the website: https://dipy.org/tutorials/

zlf123-marker

@zlf123-marker

I have a look, but I want to display my TRK file and t1 data, I don't know what to change?Can you help me @arokem

robertl1996

@robertl1996

Does anybody know where the source code for this denoise library can be found: https://dipy.org/documentation/1.0.0./reference/dipy.denoise/. Particularly the nl means filters

Brian

@bhsilverstein

Hey folks - newbie question here: is there a simple way to concatenate data from two or more stateful tractograms into a single tractogram? I could just pull the streamlines and concatenate them, but I'd like all the metadata to come along with the streamlines.

Jon Haitz Legarreta Gorroño

@jhlegarreta

@robertl1996

Does anybody know where the source code for this denoise library can be found: https://dipy.org/documentation/1.0.0./reference/dipy.denoise/. Particularly the nl means filters

The source code is found here: https://github.com/nipy/dipy/blob/master/dipy/denoise/

Jon Haitz Legarreta Gorroño

@jhlegarreta

@zlf123-marker

I have a look, but I want to display my TRK file and t1 data, I don't know what to change?Can you help me @arokem

DIPY examples/tutorials use data that is fetched directly from a few sites that host the data of interest. If you want to adapt the examples to use your own data, then, instead of using the fetch_* and read_ * commands, you will need to read your local files.

In order to read your t1, you will need to use NiBabel as in
https://nipy.org/nibabel/nibabel_images.html

something like

import nibabel as nib

t1_img =  nib.load(your_t1_filename)
t1 = t1_img.get_data()
fig = plt.figure()
plt.imshow(t1, cmap="gray")

Similarly, to show your TRK file, you can do something similar to this

from dipy.io.streamline import load_tractogram
from fury import window, actor

tractogram = load_tractogram(your_trk_filename, your_t1_filename)
streamlines = tractogram.streamlines
renderer = window.Renderer()
stream_actor = actor.line(streamlines)
renderer.add(stream_actor)
window.record(renderer)

If you want to display your streamlines and your T1 at the same time, you will need to add both actors to the same scene, adding to the above something like

t1_actor = actor.slicer(t1)
renderer.add(t1_actor)

Jakob Wasserthal

@wasserth

Hi, is there a function in dipy to resample streamlines to make all points have a specific distance (in mm) from each other? So longer streamlines would have more points than shorter streamlines.

Wade Weber

@wadeatUT

Hi all. When I convert my Freesurfer apar+aseg back to native space to use as my WM label file in DIPY, it won't let me reslice it. I used Freesurfer's recomendations to go from Tal back to native space and to convert to NIFTI. When I load that file into DIPY and use DIPY's reslice command (from 0.8mm to 2mm), it looks like it's processing, but the shape and zooms haven't changed. Is there something special that I have to do with data converted from Freesurfer? Thanks!

zlf123-marker

@zlf123-marker

@jhlegarreta Thank you very much

Shreyas Fadnavis

@ShreyasFadnavis

Hi @wadeatUT, Can you share the piece of code where you are reslicing the data.. I don't think anything special is needed.. it would be helpful to see what the exact issue is!

Wade Weber

@wadeatUT

@ShreyasFadnavis Thanks for the help. Here's a screenshot of my Jupyter Notebook:

@ShreyasFadnavis Also, if I change "new_zooms" to (3., 3., 3.), the new vox size comes out as (1.2, 1.2, 1.2) instead of 3mm iso? Weird.

Shreyas Fadnavis

@ShreyasFadnavis

@wadeatUT I guess this line is missing: zooms = orig_t1FS_img.header.get_zooms()[:3] and should solve the issue!

Shreyas Fadnavis

@ShreyasFadnavis

Hi everyone! The DIPY Workshop 2020 Early Bird registration ends in 3 days! To all those interested, visit: https://workshop.dipy.org/ | for any questions mail us: dipy@python.org and for updates, follow us on Twitter: @dipymri !! Looking forward to see you in March at Indiana University Bloomington!

Eleftherios Garyfallidis

@Garyfallidis

:star2: :star: :rocket: :rocket: :rocket: :rocket: :rocket: :rocket: :star: :star2:

Eleftherios Garyfallidis

@Garyfallidis

Thank you for sharing @ShreyasFadnavis

Serge Koudoro

@skoudoro

:+1: :+1: :+1:

zlf123-marker

@zlf123-marker

@jhlegarreta Traceback (most recent call last):
File "C:/Users/20190401-1/Desktop/image-registration/viz_t1_dti.py", line 55, in <module>
tractogram = load_tractogram('AF_left.trk',example_filename)
File "D:\Anaconda3\lib\site-packages\dipy\io\streamline.py", line 129, in load_tractogram
if not is_header_compatible(filename, reference):
File "D:\Anaconda3\lib\site-packages\dipy\io\utils.py", line 233, in is_header_compatible
reference_2)
File "D:\Anaconda3\lib\site-packages\dipy\io\utils.py", line 195, in get_reference_info
voxel_order = ''.join(nib.aff2axcodes(affine))
TypeError: sequence item 0: expected str instance, NoneType found

@jhlegarreta It's running like an error

Francois Rheault

@frheault

@zlf123-marker is your affine all zeros?

Scott Trinkle

@scott-trinkle

quick visualization question. is there a way to get different segments of individual streamlines to have different colors? right now the default "directional" colormap seems to give the whole streamline the same color based on the overall direction, but I would like to see how the direction changes across long streamlines

zlf123-marker

@zlf123-marker

@frheault

not all zeroes

zlf123-marker

@zlf123-marker

Hello everyone, I want to know how to display TRK file and t1 file at the same time?

Everybody, I want to know how to display my TRK file and t1 file at the same time?

Eleftherios Garyfallidis

@Garyfallidis

@scott-trinkle yes you can. You can set the colors for every point of the streamline.

@zlf123-marker are your t1 and TRK in the same coordinate system? If yes then see https://dipy.org/documentation/1.0.0./examples_built/viz_advanced/#example-viz-advanced and dipy_horizon. If not then you have to do registration first.

zlf123-marker

@zlf123-marker

Ok, thank you very much

paras sethi

@dreadysharp_twitter

Hey guys.. I wanted to read about how blockwise 3d denoising has been implemented ..

But I see 2 methods nlmeans and non_local_means different

Can you help which one is the actual implementation

Serge Koudoro

@skoudoro

Hi @dreadysharp_twitter, the actual one is nlmeans. We plan to remove the non_local_means and improve memory management for nlmeans.

paras sethi

@dreadysharp_twitter

I need to know the one which uses block averaging

I am thinking about working on it for a college project . I feel like the nlmeans doesn't have block averaging abilities as mentioned in the documentation. Can you mention the implementation which uses block averaging for 3d denoising

Boojum

@intein

Hello. No eddy current correction at the moment?

Eleftherios Garyfallidis

@Garyfallidis

@Boojum you can do eddy current correction by affinely registering all non b0 volumes to the b0. We are planning to have a tutorial and interface about that but in the meantime I can send you an example script.

Boojum

@intein

@Garyfallidis Sounds great. If it's not a problem for you, please send me the script

maruti07

@maruti07

Hi, i donot have a reverse phase encoded b0. I do have a spin echo feild maps but its echospacing and EPI factor do not match the diffusion parameters. I wanted to know if i can use them for distortion correction?

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