Streamline calculation from whole brain tractogram

[gaonkimusc]

Hello team!

I am wondering if I can get the total number of streamlines in my whole_brain_tractogram.trk file. Is there a command that outputs the total number of streamlines in my trk file? Thank you in advance :)

[arokem]

from dipy.io.streamline import load_tractogram
tgm = load_tractogram("whole_brain_tractogram.trk")
len(tgm)

[gaonkimusc]

Hello! I tried the load_tractogram command but noticed that it leads to a TypeError: TypeError: load_tractogram() missing 1 required positional argument: 'reference'

…

On Wed, Apr 17, 2024 at 3:06 PM Ariel Rokem ***@***.***> wrote: from dipy.io.streamline import load_tractogram tgm = load_tractogram("whole_brain_tractogram.trk") len(tgm) — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/dipy/dipy/discussions/3195*discussioncomment-9148143__;Iw!!LIr3w8kk_Xxm!tAeF_hZTKnqZLSz4comsB9eWs2IaSqbZ2k8jqIomGmvqpyqVh4Jkfyev3O4AUZoHt9TdvLBHg8CmeGMVfjSzEHA$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHQNYDMUHCMD4T5MZVOUUSDY53W63AVCNFSM6AAAAABGMDXTBKVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TCNBYGE2DG__;!!LIr3w8kk_Xxm!tAeF_hZTKnqZLSz4comsB9eWs2IaSqbZ2k8jqIomGmvqpyqVh4Jkfyev3O4AUZoHt9TdvLBHg8CmeGMVQgx9zRA$> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[arokem]

Sorry! I got it wrong, try:

from dipy.io.streamline import load_tractogram
tgm = load_tractogram("whole_brain_tractogram.trk", reference="same")
len(tgm)

[gaonkimusc]

This worked! Thank you so much!!

[skoudoro]

The cli give you this info also and more !

dipy_info whole_brain_tractogram.trk

[gaonkimusc]

Thank you!

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On Wed, Apr 17, 2024 at 5:01 PM Serge Koudoro ***@***.***> wrote: The cli give you this info also and more ! Dipy_info whole_brain_tractogram.trk — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/dipy/dipy/discussions/3195*discussioncomment-9148670__;Iw!!LIr3w8kk_Xxm!s_65u-5ikwW12nSLIfKfZVfowkpedLo3UuitAgHdjYcvkyHG_OZ_CikXD06EA1y0gwraPMh_CnyJQPY0eCMyJxg$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHQNYDMY6PGWQHY2AT2JNC3Y54ENJAVCNFSM6AAAAABGMDXTBKVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TCNBYGY3TA__;!!LIr3w8kk_Xxm!s_65u-5ikwW12nSLIfKfZVfowkpedLo3UuitAgHdjYcvkyHG_OZ_CikXD06EA1y0gwraPMh_CnyJQPY0H2bjRs0$> . You are receiving this because you authored the thread.Message ID: ***@***.***>