[Freeview] [AnatomiCuts] Usage of embedded colors in tract visualizer + AC runtime error
External Email - Use Caution
Hi,
In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online.
I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6
If anyone could help me it would be very appreciated,
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
Hi Pietro,
I’m not familiar with AnatomiCuts so I can’t answer that part of your question. For visualizing tracts, freeview can load .trk files generated by TrackVis/DTK. They do not support embedded colors. It can also load tract volumes in 4D mgz format, which do support embedded colors.
Best, Ruopeng
On Jan 5, 2021, at 6:32 PM, Pietro Astolfi <pastolfi@fbk.eumailto:pastolfi@fbk.eu> wrote:
External Email - Use Caution
Hi,
In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online.
I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6
If anyone could help me it would be very appreciated,
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Ruopeng,
thanks for the reply. Actually, I’m not really interested in using AnatomiCuts, but since I tried it I wanted to signal the error. Concerning the embedded colors in FreeView, I was thinking they were value inserted as `data_per_streamlines` inside the .trk file, which is something possible. Also, by looking at the gif image of this tutoria https://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeviewthis https://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeview tutorial of AnatomiCuts it seems the embedded colors are intrinsic of the tracts loaded as .trk.
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
Il giorno 06 gen 2021, alle ore 18:24, Wang, Ruopeng RWANG4@MGH.HARVARD.EDU ha scritto:
Hi Pietro,
I’m not familiar with AnatomiCuts so I can’t answer that part of your question. For visualizing tracts, freeview can load .trk files generated by TrackVis/DTK. They do not support embedded colors. It can also load tract volumes in 4D mgz format, which do support embedded colors.
Best, Ruopeng
On Jan 5, 2021, at 6:32 PM, Pietro Astolfi <pastolfi@fbk.eu mailto:pastolfi@fbk.eu> wrote:
External Email - Use CautionHi,
In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online.
I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6
If anyone could help me it would be very appreciated,
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gxPogOZRa_LBKlD9lBThdJTtJM9NCUbwYlTox5XIfzUOXv...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gxPogOZRa_LBKlD9lBThdJTtJM9NCUbwYlTox5XIfzUOXv...
That’s right. The .trk files generated by AnatomiCuts have a color tag saved in a private location in the header, as I remember now. I think it is only effective when loaded as tract cluster. Are you going to write .trk files by yourself? If so I can point you to where to write the color bytes in the header.
On Jan 6, 2021, at 2:17 PM, Pietro Astolfi <pastolfi@fbk.eumailto:pastolfi@fbk.eu> wrote:
External Email - Use Caution
Hi Ruopeng,
thanks for the reply. Actually, I’m not really interested in using AnatomiCuts, but since I tried it I wanted to signal the error. Concerning the embedded colors in FreeView, I was thinking they were value inserted as `data_per_streamlines` inside the .trk file, which is something possible. Also, by looking at the gif image of https://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeview thishttps://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeview tutorial of AnatomiCuts it seems the embedded colors are intrinsic of the tracts loaded as .trk.
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
Il giorno 06 gen 2021, alle ore 18:24, Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> ha scritto:
Hi Pietro,
I’m not familiar with AnatomiCuts so I can’t answer that part of your question. For visualizing tracts, freeview can load .trk files generated by TrackVis/DTK. They do not support embedded colors. It can also load tract volumes in 4D mgz format, which do support embedded colors.
Best, Ruopeng
On Jan 5, 2021, at 6:32 PM, Pietro Astolfi <pastolfi@fbk.eumailto:pastolfi@fbk.eu> wrote:
External Email - Use Caution
Hi,
In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online.
I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6
If anyone could help me it would be very appreciated,
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1gxPogOZRa_LBKlD9lBThdJTtJM9NCUbwYlTox5XIfzUOXvBsuCenyHlQgn_31dciYLnR0Y80k1Oc5G0aWxcWcuz9gmLX5xYYXrrFLHiQ-kXla8tdGdhxuzu4crLGNiae0O6Kr991mdcTInQJwyo6o02KFKIf5ZgAZ_YMAnw1oxgS7q7BHkRSfMruZ6oclvOIXOcT7h6za4SV9SIBSVMby1LzjMHDI9IdaayF_PozPFuon7Jk3LhSqTmAd7_lyE8I-SEv0ihiTVwZo1-kiVk1qg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Yes it would be helpful. I usually Dipy interface to write .trk, and thus adding a field to the header should be a simple operation. However, I was aiming at coloring each streamline diffferently with some random picked color. I guess it is not possible by adding if the embedded color is just one value in the header.
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
Il giorno 06 gen 2021, alle ore 21:39, Wang, Ruopeng RWANG4@MGH.HARVARD.EDU ha scritto:
That’s right. The .trk files generated by AnatomiCuts have a color tag saved in a private location in the header, as I remember now. I think it is only effective when loaded as tract cluster. Are you going to write .trk files by yourself? If so I can point you to where to write the color bytes in the header.
On Jan 6, 2021, at 2:17 PM, Pietro Astolfi <pastolfi@fbk.eu mailto:pastolfi@fbk.eu> wrote:
External Email - Use CautionHi Ruopeng,
thanks for the reply. Actually, I’m not really interested in using AnatomiCuts, but since I tried it I wanted to signal the error. Concerning the embedded colors in FreeView, I was thinking they were value inserted as `data_per_streamlines` inside the .trk file, which is something possible. Also, by looking at the gif image of https://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeviewthis https://secure-web.cisco.com/1bCTmdHOhpmCAVqsfY7cH5W2KiZubfIX_xThDXmmjn90Re5GNRsFK91P0ow-PzO6Oi_cHEL8EZs-5m-Rrxaxayro1MfLELnf4eCWGVwQoc8GivhGn5doq5n93oCZ9Q9kRPcwFB0mVz3Riv8wBv8M8JBEsNd7Vtod42yO56ToDf-0K3VKRWeiy4ND5ObI5eCOx7ZdqVGm0W2Pj43FHe9HhSIQ_lxyHm71UDE4oF4O38kYB6AzxQO37GIXVZuop94zQKBrGlEnXocuG8g7Aq---LA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAnatomiCuts%23VisualizingAnatomiCutsinFreeview tutorial of AnatomiCuts it seems the embedded colors are intrinsic of the tracts loaded as .trk.
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
Il giorno 06 gen 2021, alle ore 18:24, Wang, Ruopeng <RWANG4@MGH.HARVARD.EDU mailto:RWANG4@MGH.HARVARD.EDU> ha scritto:
Hi Pietro,
I’m not familiar with AnatomiCuts so I can’t answer that part of your question. For visualizing tracts, freeview can load .trk files generated by TrackVis/DTK. They do not support embedded colors. It can also load tract volumes in 4D mgz format, which do support embedded colors.
Best, Ruopeng
On Jan 5, 2021, at 6:32 PM, Pietro Astolfi <pastolfi@fbk.eu mailto:pastolfi@fbk.eu> wrote:
External Email - Use CautionHi,
In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online.
I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6
If anyone could help me it would be very appreciated,
Best,
Pietro
Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-... https://secure-web.cisco.com/1gxPogOZRa_LBKlD9lBThdJTtJM9NCUbwYlTox5XIfzUOXvBsuCenyHlQgn_31dciYLnR0Y80k1Oc5G0aWxcWcuz9gmLX5xYYXrrFLHiQ-kXla8tdGdhxuzu4crLGNiae0O6Kr991mdcTInQJwyo6o02KFKIf5ZgAZ_YMAnw1oxgS7q7BHkRSfMruZ6oclvOIXOcT7h6za4SV9SIBSVMby1LzjMHDI9IdaayF_PozPFuon7Jk3LhSqTmAd7_lyE8I-SEv0ihiTVwZo1-kiVk1qg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-... https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-e7Wpw3MucfNkDpNjn2eA2xThhHUSKK4zAI2VVPY4e71JxmmGQhsTlWJaKOoR9D3hA_7w5epIu8Gk0yQ5gh61K4aAPgSWiC-NWSVdUv6KyrMNTUojLGauUrz6UNGbcis5Q8npGyrTJwokFGrepVA_N3BpIwQ1M_RBOJgaa2Ou0f6Isi6LzCfo38XP591PKn0OddRcmZdIS5dem7YTj5uUj6O5GZ_1wZAU3M8d2A8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-... https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-e7Wpw3MucfNkDpNjn2eA2xThhHUSKK4zAI2VVPY4e71JxmmGQhsTlWJaKOoR9D3hA_7w5epIu8Gk0yQ5gh61K4aAPgSWiC-NWSVdUv6KyrMNTUojLGauUrz6UNGbcis5Q8npGyrTJwokFGrepVA_N3BpIwQ1M_RBOJgaa2Ou0f6Isi6LzCfo38XP591PKn0OddRcmZdIS5dem7YTj5uUj6O5GZ_1wZAU3M8d2A8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-... https://secure-web.cisco.com/1dbxQY-renvaQ1MjA7pUO_pYo08qofJeQ8FZdMIyBZ9iAQ-e7Wpw3MucfNkDpNjn2eA2xThhHUSKK4zAI2VVPY4e71JxmmGQhsTlWJaKOoR9D3hA_7w5epIu8Gk0yQ5gh61K4aAPgSWiC-NWSVdUv6KyrMNTUojLGauUrz6UNGbcis5Q8npGyrTJwokFGrepVA_N3BpIwQ1M_RBOJgaa2Ou0f6Isi6LzCfo38XP591PKn0OddRcmZdIS5dem7YTj5uUj6O5GZ_1wZAU3M8d2A8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
freesurfer@nmr.mgh.harvard.edu
-
Pietro Astolfi -
Wang, Ruopeng