zlf123-marker
@zlf123-marker
@Garyfallidis That is to say I want to display t1 data as a whole rather than as a slice of x,y, and z, what should I do?
zlf123-marker
@zlf123-marker
May I ask how the dipy library displays NRRD data?
paras sethi
@dreadysharp_twitter
I would also need to know how can we display the data in volume instead of just some slices
My email Id is psethi432@gmail.com
anm-ranjan
@anm-ranjan
@Garyfallidis Could you provide me with the eddy current correction script as well? My email ID is anm.ranjan@gmail.com. It will be of great help!
Eleftherios Garyfallidis
@Garyfallidis
Apologies for any delays in sending you the script. Will do this by the end of the day.
The DIPY team is currently attending NeurIPS. If you are at NeurIPS meet us to discuss collaboration, workshop, GSoC and PhD opportunities!
Daniel Lurie
@danlurie
Hi there! Is there any sort of system in place for connecting people who are interested in sharing accommodations during the March workshop?
Eleftherios Garyfallidis
@Garyfallidis
I am not aware of any system in place. But please suggest a way forward. It could be useful for many people.
Jon Haitz Legarreta Gorroño
@jhlegarreta

Hi there! Is there any sort of system in place for connecting people who are interested in sharing accommodations during the March workshop?

@danlurie Thinking out loud: may be creating a specific dipy_workshop_accommodation channel in the brainhack Mattermost workspace could help?

Shreyas Fadnavis
@ShreyasFadnavis
@jhlegarreta I think this is a very good idea! I will go ahead and create a private channel on Mattermost!
Keeping it private just for safety purposes...
Some people might not be comfortable sharing information publicly
Eleftherios Garyfallidis
@Garyfallidis
Sounds good.
Bojing Jia
@b2jia
Hello! Is there a specific forum where I can ask questions about image registration, namely DIPY's nifty symmetric diffeomorphic registration in 3D?
Serge Koudoro
@skoudoro
Hi @b2jia , you can ask them here or create an issue on dipy repository(GitHub).
EndritPJ
@EndritPJ

Hello, I'm not sure if this is the right place to ask. When using nipype, I found the c3d wrapper to be lacking in lots of different functions such as thresholding: https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.interfaces.c3.html

Is there any way I can access all c3d functions from the nipype module? If not are there any plans to add this? Thank you!

Jon Haitz Legarreta Gorroño
@jhlegarreta
@EndritPJ while people in this gitter room will surely use nipype, you are far more likely to get an answer for your question in the nipype gitter room: https://gitter.im/nipy/nipype
EndritPJ
@EndritPJ
Thank you, I will ask there.
Eleftherios Garyfallidis
@Garyfallidis
Many apologies for the delay. Here is the link for the motion_correction (eddy current correction script) https://gist.github.com/Garyfallidis/42dd1ab04371272050221275c6ab9bd6 If you have one b0 this should work fine. If you have multiple you will have to register each of the b0 volumes to one b0 before registering all the non-b0 volumes to the b0 volume.
A follow up PR in dipy will be up soon.
ɐuoʌɐu
@navonacalarco
Hello! I am trying to use dipy to convert from .vtk to .trk. from dipy.io.vtk import load_vtk_streamlines doesn't seem to be working. I don't see a utils vtk file under https://github.com/nipy/dipy/blob/master/dipy/viz/__init__.py. Is it possible to convert .vtk to .trk? Thanks! :)
Serge Koudoro
@skoudoro
Hi, you look at the wrong place @navonacalarco, I can see the function here https://github.com/nipy/dipy/blob/master/dipy/io/vtk.py#L161
So what is your error?
ɐuoʌɐu
@navonacalarco
Oh thank you!
NameError: name 'vtk' is not defined
Serge Koudoro
@skoudoro

just make sure that vtk and fury packages are installed:

pip install vtk fury

ɐuoʌɐu
@navonacalarco
Thanks! I do have both (fury-0.4.0), and vtk (8.1.2).
Oh man, sorry -- my fault. It didn't work from a notebook, but did in the terminal
Sorry! And thank you! :D
Serge Koudoro
@skoudoro
no problem! :+1:
safwan20
@safwan20
hello guys i am new over here may I know how can I contribute ?
Serge Koudoro
@skoudoro
Hi @safwan20, you can look at the contributing page on DIPY website: https://github.com/nipy/dipy/blob/master/CONTRIBUTING.md and then you can try to fix a beginner friendly issue. There is a list in the following page:
Thank you for looking at this project !
safwan20
@safwan20
@skoudoro your website github login is not working can I fix it ?
Bojing Jia
@b2jia

Hi @skoudoro . I'm picking up after another researcher's project. Specifically, they used DIPY's symmetric diffeomorphic coregistration tool to extract a deformation map between two co-registered images. From what I understand, deformation maps tell how to "warp" features of one image to another registered image.

Extracting these deformation maps are very clear and easy (ie. get_forward_map). I currently have a set of deformation map and no longer have the latent data. It is not clear given the deformation map how I can warp an image to produce the registered image. Would you or someone else be able to comment/advise? Thank you!

Serge Koudoro
@skoudoro

Hi @b2jia, You need to create a DiffeormorphicMap object and then apply the transformation to the desired image. it should be something like:

# Read your deformation map. I do not know how you save it. Then, create a object
diff_map = imwarp.DiffeomorphicMap(3, domain_shape, domain_grid2world,
                                       domain_shape, domain_grid2world,
                                       codomain_shape, codomain_grid2world,
                                       None)
# warp using linear interpolation
warped = diff_map.transform(moving_image, 'linear')

But that is a good catch, we should update our Tutorial. Feel Free to create a PR and send us your small example for updating our Tutorial

BTW, Happy New Year for all DIPY Developers and Users !!! I wish you the best for 2020 !!! :rocket: :rocket: :rocket: :tada: :tada: :tada:

Ariel Rokem
@arokem
Happy new year Serge! :tada: :fireworks:
And everyone!
Bojing Jia
@b2jia

@skoudoro Thank you so much! I'm happy to contribute to the community!

The diffeomorphic maps were saved as three separate images, corresponding (presumably) to translation along x, y, and z directions. I've written more extensively about my problem on GitHub, I will move my discussion there (hopefully it helps others as well!). Thanks for your response!

metasebiya
@Matt-arch
hello
marutimishra
@marutimishra
Hi, I was wondering if anyone has used MNI co-ordinates to create individual specific ROI's to select FA,MD,AD and RD values in native space for diffusion imaging analysis and also to be used as seeds for tractography.
Eleftherios Garyfallidis
@Garyfallidis
Definitely, @marutimishra this is a standard procedure.
marutimishra
@marutimishra
Is it possible to share some link to implementing this? I have difficulty in a) accurately using xyz from a resampled mni template to the dwi final output maps as my dwi output is in different dimension b) what coregistration steps are to be done properly to achieve this... Any help would be great! Thank you
Navnit Kumar
@theNaavik
Hi DIPY team! I would like to know if DIPY is participating in the upcoming GSoC '20, I really missed it in the previous edition of GSoC . Thanks
Eleftherios Garyfallidis
@Garyfallidis
The answer is Yes. We plan to get involved in GSoC this year both for DIPY and FURY.
Navnit Kumar
@theNaavik
@Garyfallidis This is great !
Serge Koudoro
@skoudoro
Given the large growth of DIPY and the large need for sub-projects, DIPY moved to its own organization in Github. Long live to https://github.com/dipy/dipy !!! The previous link (https://github.com/nipy/dipy) will remain active for the next 6 months.