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Francois Rheault
@frheault

@KulikovaSofya The load_trk API drastically change recently. This function does not return a tuple (streamlines, header) anymore but an object called StatefulTractogram
Use it as follow:
sft = load_trk('../data/tracts.trk', 'same')
streamlines = sft.streamlines
affine, dimensions, voxel_sizes, voxel_order = sft.space_attributes
OR
affine = sft.affine
dimensions = sft.dimensions
voxel_sizes = sft.voxel_sizes
voxel_order = sft.voxel_order

(Some example available here:https://dipy.org/documentation/1.0.0./examples_built/streamline_formats/)

This object contains numerous function related to spatial manipulation (to_vox(), to_rasmm(), to_voxmm(), etc.)
But you can manipulate streamlines 'by hand' like before if you choose to.
Shreyas Fadnavis
@ShreyasFadnavis
Hi @ShrishtiHore ! Looks like your PR was merged :)
Shrishti Hore
@ShrishtiHore
Thank you @ShreyasFadnavis
Actually there is another pull request patch 2 dipy/dipy#2094 @Garyfallidis @ShreyasFadnavis @skoudoro . It would be really nice if you check that out. It's a proposal to add tutorials in a beginner friendly manner in Github DIPY repo.
salomaaa
@salomaaa
Microsoft Visual C++ 14.0 standalone: Visual C++ Build Tools 2015 (x86, x64, ARM) i can not find them in the website
Serge Koudoro
@skoudoro
Hi @ShrishtiHore, please don't use gitter tchat for asking to review a pull request. We receive email for any activity. Just be patient please, someone will always get back to you
I suppose there is a most recent version @salomaaa. It should work too! It is ok as soon as you have a compiler in your machine
Shrishti Hore
@ShrishtiHore
Okay @skoudoro Thank you for your response.
Shreya Kapoor
@ShreyaKapoor18
Hi, I wanted to ask if there is some way to do whole brain tractography with Dipy
Serge Koudoro
@skoudoro
yes @ShreyaKapoor18, I recommend you to have a look on the tutorial, tractography / Fiber tracking section : https://dipy.org/tutorials .
Shreya Kapoor
@ShreyaKapoor18
@skoudoro thanks for your reply. I looked at that section but is the whole brain tractography accomplished using the local tracking method only? I don't really understand.
arnaudbore
@arnaudbore
pip doesnt find dipy==1.1.1 :(
Serge Koudoro
@skoudoro
Strange @arnaudbore, if you look this link https://pypi.org/project/dipy/#files dipy 1.1.1 is present for many OS
What is your environment ?
Yijun Liu
@snapfinger
Hi there, I have questions about the usage of the word “reconstruction” in dipy’s documentation. e.g. for tensor model, the tutorial’s title is “Reconstruction of the diffusion signal with the Tensor model“. Is it really “reconstruction”? Or it’s some “modeling”. Because I saw in MRI field, reconstruction usually refers to reconstruct the MR image from k-space data, but here we actually already have the images, which makes me confused.
archerdb
@archerdb
@Garyfallidis @RafaelNH Hello! Our group is very interested in moving our single-shell free-water elimination analysis from MATLAB (Pasternak code) to DIPY. Is there any estimation for when this would be available in DIPY?
Pietro Astolfi
@pietroastolfi
@arokem Hi. I'm trying to apply pyAFQ in these days. I do not apply it using the cli, but I use directly some of the defined functions. In my case I have available the tractogram coregistered to MNI space, but not the DWI data, and I m trying to apply only AFQ segmentation to the tractogram. Now, because of the lack of the dwi I m calling the function Segmentation.segment by providing reg_tamplate, img_affine, and mapping where reg_template is MNI152_T1_1mm, img_affine is the affine of this mni_t1, and mapping is the indentity mapping (since tractogram and template are already in the same space). After this premise I explain the problem: The segmentation seems to work in the first step, waypoints rois filtering, but it produces a strange behaviour in the second step, endpoints filtering, where some tracts like ATR have a huge drop in terms of number of streamlines. I looked into detail on the reason of this drop, by saving the endpoints AAL rois corresponding to the ATR_L, and I overlap it with the segmentation produced by AFQ without endpoints filtering.
Schermata 2020-04-24 alle 14.08.07.png
here what I obtain: the endpoint roi is in the wrong hemisphere.
Ariel Rokem
@arokem
@pietroastolfi : thanks for reporting. Could you please post an issue on the pyAFQ repo: https://github.com/yeatmanlab/pyAFQ/issues ?
That's a great find and might be related to things that others have seen: yeatmanlab/pyAFQ#235
My main conclusion is that this part of the processing is not yet robust enough. Works sometimes, but not bullet proof yet
So, we need to investigate
tecork
@tecork
I've been searching for a few days, but does dipy support 2D rigid registration?
should work in 2d as well
If not, in a pinch I might try adding a singleton dimension to your data just to get it in there
salomaaa
@salomaaa
hello guys i have problem with this lib
from dipy.tracking.local import LocalTracking, ThresholdTissueClassifier
the error : No module named 'dipy.tracking.local'
Shreya Kapoor
@ShreyaKapoor18
@salomaaa it's probably that these commands work with a different version than you are currently using. According to version 1.1.0 you can use the command
from dipy.tracking.local_tracking import LocalTracking
According to the api documentation https://dipy.org/documentation/1.1.0./api_changes/ , ThresholdTissueClassifier -> ThresholdStoppingCriterion
Shreya Kapoor
@ShreyaKapoor18
@salomaaa so you can do this with from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
Ariel Rokem
@arokem
@salomaaa : how did you install DIPY?
araikes
@araikes
Posted a question on GitHub (dipy/dipy#2164) but I'll throw it here for visibility too. Ran DKI reconstruction and got some weird outputs. The DTI scalars look ok but the DKI scalars don't resemble white matter paths. Any help would be great.
Eleftherios Garyfallidis
@Garyfallidis
@RafaelNH do get back to @araikes
araikes
@araikes
Thanks @Garyfallidis
Reshu Singh
@sreshu
Hi everyone ! I got to know about DIPY via GSoD'20 :) Looking forward to working alongside developers to document cool stuffs !!
Serge Koudoro
@skoudoro
Welcome @sreshu! looking forward to your contribution!
John Samuelsson
@johnsam7
Hi everyone, I am moving over from ANTsPy to Dipy and was wondering how I can apply a diffeomorphic transform to points after the registration is done. That is, I am looking for a function that takes a set of points and a registration transformation as input and outputs the transformed points moved along the velocity field of the transform, like ants.apply_transforms_to_points in the AntsPy package. Many thanks for any help!
Alessandro Daducci
@ADaducci_twitter
Hi @Garyfallidis , how are you doing? A question to the guru: once I perform clustering with QuickBundles, how do I get access to the streamline that is the closest to the centroid in its cluster? In my application, I cannot simply take the resulting centroid, as it has a lower number of points. Any help would be appreciated! ;-)
Eleftherios Garyfallidis
@Garyfallidis
Hi @ADaducci_twitter do you mean you want to get the medoid?
Alessandro Daducci
@ADaducci_twitter
In general, once I obtain a cluster, I'd like to extract the streamline (from the input set, i.e., exactly the same geometry, nb of points etc) that best represents the cluster. We implemented a way, by recomputing the distance of each streamline from the centroid, but I was wondering whether there was a more direct way from the output of QuickBundles. For instance, without the need to recompute the distances
Eleftherios Garyfallidis
@Garyfallidis
That is the correct way to do this Alessandro. You can use an existing function called bundles_distances_mdf or bundles_distances_mam to calculate all the distances from the centroid and find the closest (most similar) streamline.
geophysics91
@geophysics91
Good morning.hope everyone is fine.I have a small problem.. I would like to minimize the test_function. basically, test_function() takes 3 variables - m, n and p. The goal is to find such values of these 3 variables that the function returns the minimal possible value.I am using nelder-mead minimization problem. while running my script for x0 = [25.0, 45.0, 10.0] i am getting error like Maximum number of function evaluations has been exceeded. Anyway I followed the stackoverflow link to write my code. https://stackoverflow.com/questions/55751317/minimize-multivariable-function please help me on this.Thanks.My data and script is attached here https://i.fluffy.cc/HLR1jCJLLV8lX4NfjSqbjRKG6DsB4bwS.html stackoverflow link is blocked in my area.
CherylMcC
@CherylMcC
Hi. I'm new to dipy and would like to set up an analysis pipeline using the free water elimination model. As I'm working through the preprocessing examples, I did not find information for motion and geometric correction. This will be an important step for me. Can you point me in the right direction? Should I use another tool to generate motion/eddy current - corrected data first? Thanks.
Matt Cieslak
@mattcieslak
Hi @CherylMcC I'd suggest trying QSIPrep: https://qsiprep.readthedocs.io/en/latest/. It will do both of these corrections with a single interpolation
CherylMcC
@CherylMcC
Thanks @mattcieslak