[Neuroimaging] [DIPY] Question about whole tracks *.trk registration using SLR

Perea Camargo, Rodrigo Dennis RPEREACAMARGO at mgh.harvard.edu
Mon Sep 25 09:47:57 EDT 2017

Hi Eleftherios,
I am included both *.trk files in here: http://www.nmr.mgh.harvard.edu/~rdp20/drop/trk_slf/
IIT2mean.trk was a template TRK downloaded from the tract_querier example (http://tract-querier.readthedocs.io/en/latest/ ) and ADRC_TMP_wholeBrain.trk.gz was generated using dsi_studio (http://dsi-studio.labsolver.org/)

Thanks again,


On Sep 21, 2017, at 3:46 PM, Eleftherios Garyfallidis <elef at indiana.edu<mailto:elef at indiana.edu>> wrote:

Hi Rodrigo,

Whole brain SLR is a great idea! Thank you for your question.  :)

Have in mind that nibabel.trackvis is the old API. Use nibabel.streamlines.load instead.

Can you please share with me (off the list) your trk files so that I can correct your

A wild guess is that you are not loading the streamlines correctly.

Did you use DIPY to create those trks or another software?

Also, another suggestion is to run QuickBundles first to reduce the size of your
datasets. I mean before starting the SLR.

Here is a sample script (in one of my branches).

We are working on making something similar available asap in master.


On Thu, Sep 21, 2017 at 1:36 AM Perea Camargo, Rodrigo Dennis <RPEREACAMARGO at mgh.harvard.edu<mailto:RPEREACAMARGO at mgh.harvard.edu>> wrote:
Hi Eleftherios & DIPY community,
I am trying to register two whole brain tracts as shown in your recent publication using the streamline-based linear registration. I am diving into Dipy now and I might have some problems loading the files or registering them.
Following your example ( http://nipy.org/dipy/examples_built/bundle_registration.html#example-bundle-registration), there are 2 issues that may arise when I try it.

1) How to load *.trk files is not shown in your example (it looks like you added to cingulum bundles from your dataset using the dipy.data value…) So I follow this tutorial (http://nipy.org/dipy/examples_built/streamline_formats.html ) to load the streamline and hdr but I am not sure if this is the format SLF() wants it in.

2) So then I try using the srr.optimize( ) function but I get the following problems (check below).

I hope you can help me.

Here is my Jupyter notebook with the errors I found (any help will be greatly appreciate it):

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