Hi,
I am trying to use the atlas of 80 bundles you distribute here
https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737…
<https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737…>,
but I am encountering some issues.
It is written that the files are in MNI space ICBM 2009a, which has affine
equal to
array([[ 1., 0., 0., -98.],
[ 0., 1., 0., -134.],
[ 0., 0., 1., -72.],
[ 0., 0., 0., 1.]])
…
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However, all the trk files have affine equal to the identity matrix. Is
there a reason why you stored in the header of the trk files the identity
matrix? This for example prevents their correct visualization in TrackVis.
[image: ifof_r_dipy_trackvis.png]
Another question: the file whole_brain_MNI.trk, besides having the same
issue with the affine, has 144678 streamlines. Is it the same whole brain
tractogram Yeh is referring to in their paper? In that paper they obtained
a tractogram of 550000 streamlines. Or is it maybe the union of the 80
bundles?
Thank you a lot for your help,
best regards,
Giulia
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Yes, you can correct the affine by using the StatefulTractogram and the
affine of the data that generated the tracks or the original tractogram
https://dipy.org/documentation/1.0.0./examples_built/streamline_formats/#ex…
On Thu, Nov 21, 2019 at 12:28 PM Giulia Berto' <gberto(a)fbk.eu> wrote:
> Hi,
>
> I am trying to use the atlas of 80 bundles you distribute here
> https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737…
> <https://figshare.com/…
[View More]articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/737…>,
> but I am encountering some issues.
>
> It is written that the files are in MNI space ICBM 2009a, which has affine
> equal to
> array([[ 1., 0., 0., -98.],
> [ 0., 1., 0., -134.],
> [ 0., 0., 1., -72.],
> [ 0., 0., 0., 1.]])
>
> However, all the trk files have affine equal to the identity matrix. Is
> there a reason why you stored in the header of the trk files the identity
> matrix? This for example prevents their correct visualization in TrackVis.
>
> [image: ifof_r_dipy_trackvis.png]
>
> Another question: the file whole_brain_MNI.trk, besides having the same
> issue with the affine, has 144678 streamlines. Is it the same whole brain
> tractogram Yeh is referring to in their paper? In that paper they obtained
> a tractogram of 550000 streamlines. Or is it maybe the union of the 80
> bundles?
>
> Thank you a lot for your help,
> best regards,
> Giulia
>
>
> --
> Le informazioni contenute nella presente comunicazione sono di natura privata
> e come tali sono da considerarsi riservate ed indirizzate esclusivamente
> ai destinatari indicati e per le finalità strettamente legate al relativo
> contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di
> eliminarlo e di inviare una comunicazione all’indirizzo e-mail del
> mittente.
> --
> The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. If you received this in error, please contact the sender and
> delete the material.
>
[View Less]