Dear DiPy fellas, I am trying to improve my DiPy pipeliene. Would you always recommend to use Linear fascicle evaluation (LiFE) and Anatomically-constrained tractography (ACT) jointly? I post the original links I am looking right now here as wellDIPY : Docs 1.4.1. - Linear fascicle evaluation (LiFE) DIPY : Docs 1.1.0. - Using Various Stopping Criterion for Tractography Best,Alex
Hi Alex, On Sun, Sep 26, 2021 at 6:51 PM Alex Crimi via DIPY <dipy@python.org> wrote:
The devil seems to be in the details, and I would say that it really depends on what you intend to do with the results of your tractography. For example, in a recent paper by Gab Girard and colleagues ( https://www.sciencedirect.com/science/article/pii/S105381192030687X) they demonstrate that if you are using the MRTRIX ACT, then using an approach like LiFE (SIFT, in this case, a similar approach) seems to contribute to the accuracy of the results (see . On the other hand, if you use DIPY's PFT, something like LiFE (in this case, COMMIT, also a similar approach) does not seem to contribute much in terms of accuracy. I would guess that it may or may not matter depending on both the nature of the question that you are asking, as well as the nature of your data. Sorry - that's not a clear-cut answer. I'd be curious if others have a different take. Cheers, Ariel
Hi, thanks actually your answers have branched/forked my questions. Can we try to put some order?It SHOULD be a good idea to use an anatomical constraints and then a filtering like: 1. ACT or PFT2. then LIFE or COMMIT. Now, which one SHOULD be better ACT or PFT? and LIFE or COMMIT? Life is already included in Dipy while COMMIT is from Daducci? I am scared of start having an hybrid script. yes, I recently also discovered Scilpy, but would like to avoid getting lost into a further thing. I understood it probably depends on the resolution, sequence.... but I am trying to find a general pipeline which should be most correct. Best,Alex On Monday, September 27, 2021, 04:11:16 AM GMT+2, Ariel Rokem <arokem@uw.edu> wrote: Hi Alex, On Sun, Sep 26, 2021 at 6:51 PM Alex Crimi via DIPY <dipy@python.org> wrote: Dear DiPy fellas, I am trying to improve my DiPy pipeliene. Would you always recommend to use Linear fascicle evaluation (LiFE) and Anatomically-constrained tractography (ACT) jointly? The devil seems to be in the details, and I would say that it really depends on what you intend to do with the results of your tractography. For example, in a recent paper by Gab Girard and colleagues (https://www.sciencedirect.com/science/article/pii/S105381192030687X) they demonstrate that if you are using the MRTRIX ACT, then using an approach like LiFE (SIFT, in this case, a similar approach) seems to contribute to the accuracy of the results (see . On the other hand, if you use DIPY's PFT, something like LiFE (in this case, COMMIT, also a similar approach) does not seem to contribute much in terms of accuracy. I would guess that it may or may not matter depending on both the nature of the question that you are asking, as well as the nature of your data. Sorry - that's not a clear-cut answer. I'd be curious if others have a different take. Cheers, Ariel I post the original links I am looking right now here as wellDIPY : Docs 1.4.1. - Linear fascicle evaluation (LiFE) DIPY : Docs 1.1.0. - Using Various Stopping Criterion for Tractography Best,Alex _______________________________________________ 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/ Member address: arokem@gmail.com
Hi Alex, I have no counter indication on using Life with ACT. I the end, you'll end up with a more anatomically valid tractogram than you would get from ACT alone, probably less dense though. However, there is better alternatives available right now, from using for example ACT tracking conjointly with COMMIT filtering. https://github.com/daducci/COMMIT You can also find a good script interface for COMMIT through Scilpy : https://github.com/scilus/scilpy Alex On Sun., Sep. 26, 2021, 21:52 Alex Crimi via DIPY, <dipy@python.org> wrote:
Hi Alex, On Sun, Sep 26, 2021 at 6:51 PM Alex Crimi via DIPY <dipy@python.org> wrote:
The devil seems to be in the details, and I would say that it really depends on what you intend to do with the results of your tractography. For example, in a recent paper by Gab Girard and colleagues ( https://www.sciencedirect.com/science/article/pii/S105381192030687X) they demonstrate that if you are using the MRTRIX ACT, then using an approach like LiFE (SIFT, in this case, a similar approach) seems to contribute to the accuracy of the results (see . On the other hand, if you use DIPY's PFT, something like LiFE (in this case, COMMIT, also a similar approach) does not seem to contribute much in terms of accuracy. I would guess that it may or may not matter depending on both the nature of the question that you are asking, as well as the nature of your data. Sorry - that's not a clear-cut answer. I'd be curious if others have a different take. Cheers, Ariel
Hi, thanks actually your answers have branched/forked my questions. Can we try to put some order?It SHOULD be a good idea to use an anatomical constraints and then a filtering like: 1. ACT or PFT2. then LIFE or COMMIT. Now, which one SHOULD be better ACT or PFT? and LIFE or COMMIT? Life is already included in Dipy while COMMIT is from Daducci? I am scared of start having an hybrid script. yes, I recently also discovered Scilpy, but would like to avoid getting lost into a further thing. I understood it probably depends on the resolution, sequence.... but I am trying to find a general pipeline which should be most correct. Best,Alex On Monday, September 27, 2021, 04:11:16 AM GMT+2, Ariel Rokem <arokem@uw.edu> wrote: Hi Alex, On Sun, Sep 26, 2021 at 6:51 PM Alex Crimi via DIPY <dipy@python.org> wrote: Dear DiPy fellas, I am trying to improve my DiPy pipeliene. Would you always recommend to use Linear fascicle evaluation (LiFE) and Anatomically-constrained tractography (ACT) jointly? The devil seems to be in the details, and I would say that it really depends on what you intend to do with the results of your tractography. For example, in a recent paper by Gab Girard and colleagues (https://www.sciencedirect.com/science/article/pii/S105381192030687X) they demonstrate that if you are using the MRTRIX ACT, then using an approach like LiFE (SIFT, in this case, a similar approach) seems to contribute to the accuracy of the results (see . On the other hand, if you use DIPY's PFT, something like LiFE (in this case, COMMIT, also a similar approach) does not seem to contribute much in terms of accuracy. I would guess that it may or may not matter depending on both the nature of the question that you are asking, as well as the nature of your data. Sorry - that's not a clear-cut answer. I'd be curious if others have a different take. Cheers, Ariel I post the original links I am looking right now here as wellDIPY : Docs 1.4.1. - Linear fascicle evaluation (LiFE) DIPY : Docs 1.1.0. - Using Various Stopping Criterion for Tractography Best,Alex _______________________________________________ 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/ Member address: arokem@gmail.com
Hi Alex, I have no counter indication on using Life with ACT. I the end, you'll end up with a more anatomically valid tractogram than you would get from ACT alone, probably less dense though. However, there is better alternatives available right now, from using for example ACT tracking conjointly with COMMIT filtering. https://github.com/daducci/COMMIT You can also find a good script interface for COMMIT through Scilpy : https://github.com/scilus/scilpy Alex On Sun., Sep. 26, 2021, 21:52 Alex Crimi via DIPY, <dipy@python.org> wrote:
participants (3)
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Alex Crimi -
Alex Valcourt Caron -
Ariel Rokem