DIPY

Download

dipy@python.org

November 2019

3 participants
2 discussions

Affine issue with atlas of 80 Bundles in MNI space
by Giulia Berto' March 19, 2020

March 19, 2020

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.]]) 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.

8 8

Re: Affine issue with atlas of 80 Bundles in MNI space
by Eleftherios Garyfallidis Nov. 21, 2019

Nov. 21, 2019

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/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. >

3 4