Most likely. Please add an issue in Github! Thank you Giulia! On Thu, Nov 21, 2019 at 1:37 PM Giulia Berto' <gberto@fbk.eu> wrote:

Great, thank you!

Does then the example "Automatic Fiber Bundle Extraction with RecoBundles" here https://dipy.org/documentation/1.0.0./examples_built/bundle_extraction/ need to be updated? I guess that sft_atlas = load_trk(atlas_file, "same", bbox_valid_check=False) needs a reference rather that "same".

Thank you. best, Giulia

On Thu, Nov 21, 2019 at 6:30 PM Eleftherios Garyfallidis <elef@indiana.edu> wrote:

...

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/#exa...

On Thu, Nov 21, 2019 at 12:28 PM Giulia Berto' <gberto@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/7375... <https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/7375...>, 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.

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/

Beat you to it :-) https://github.com/nipy/dipy/issues/2007 On Thu, Nov 21, 2019 at 10:45 AM Giulia Berto' <gberto@fbk.eu> wrote:

I will, thank you!

Best, Giulia

On Thu, Nov 21, 2019 at 7:40 PM Eleftherios Garyfallidis <elef@indiana.edu> wrote:

...

Most likely. Please add an issue in Github! Thank you Giulia!

On Thu, Nov 21, 2019 at 1:37 PM Giulia Berto' <gberto@fbk.eu> wrote:

...

Great, thank you!

Does then the example "Automatic Fiber Bundle Extraction with RecoBundles" here https://dipy.org/documentation/1.0.0./examples_built/bundle_extraction/ need to be updated? I guess that sft_atlas = load_trk(atlas_file, "same", bbox_valid_check=False) needs a reference rather that "same".

Thank you. best, Giulia

On Thu, Nov 21, 2019 at 6:30 PM Eleftherios Garyfallidis < elef@indiana.edu> wrote:

...

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/#exa...

On Thu, Nov 21, 2019 at 12:28 PM Giulia Berto' <gberto@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/7375... <https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/7375...>, 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.

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/

Most likely. Please add an issue in Github! Thank you Giulia! On Thu, Nov 21, 2019 at 1:37 PM Giulia Berto' <gberto@fbk.eu> wrote:

Great, thank you!

Does then the example "Automatic Fiber Bundle Extraction with RecoBundles" here https://dipy.org/documentation/1.0.0./examples_built/bundle_extraction/ need to be updated? I guess that sft_atlas = load_trk(atlas_file, "same", bbox_valid_check=False) needs a reference rather that "same".

Thank you. best, Giulia

On Thu, Nov 21, 2019 at 6:30 PM Eleftherios Garyfallidis <elef@indiana.edu> wrote:

...

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/#exa...

On Thu, Nov 21, 2019 at 12:28 PM Giulia Berto' <gberto@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/7375... <https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/7375...>, 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.

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/

Beat you to it :-) https://github.com/nipy/dipy/issues/2007 On Thu, Nov 21, 2019 at 10:45 AM Giulia Berto' <gberto@fbk.eu> wrote:

I will, thank you!

Best, Giulia

On Thu, Nov 21, 2019 at 7:40 PM Eleftherios Garyfallidis <elef@indiana.edu> wrote:

...

Most likely. Please add an issue in Github! Thank you Giulia!

On Thu, Nov 21, 2019 at 1:37 PM Giulia Berto' <gberto@fbk.eu> wrote:

...

Great, thank you!

Does then the example "Automatic Fiber Bundle Extraction with RecoBundles" here https://dipy.org/documentation/1.0.0./examples_built/bundle_extraction/ need to be updated? I guess that sft_atlas = load_trk(atlas_file, "same", bbox_valid_check=False) needs a reference rather that "same".

Thank you. best, Giulia

On Thu, Nov 21, 2019 at 6:30 PM Eleftherios Garyfallidis < elef@indiana.edu> wrote:

...

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/#exa...

On Thu, Nov 21, 2019 at 12:28 PM Giulia Berto' <gberto@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/7375... <https://figshare.com/articles/Advanced_Atlas_of_80_Bundles_in_MNI_space/7375...>, 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.

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/

-- 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. _______________________________________________ Dipy mailing list -- dipy@python.org To unsubscribe send an email to dipy-leave@python.org https://mail.python.org/mailman3/lists/dipy.python.org/