Hi dipy developers, I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README: “For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy@python.org<mailto:dipy@python.org> to learn how.” Could you give me guidance on this? I’m analyzing diffusion MRI data collected from epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much. Best, Marc Jaskir Neuroscience PhD candidate University of Pennsylvania
Hi dipy developers, Actually, no worries about this – I’ll directly use the HCP-1065 atlas which has the fornices in separate .trk files. Sorry to bother. Best, Marc From: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu> Date: Saturday, September 21, 2024 at 4:21 PM To: dipy@python.org <dipy@python.org> Subject: Separating the fornix .trk file Hi dipy developers, I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README: “For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy@python.org<mailto:dipy@python.org> to learn how.” Could you give me guidance on this? I’m analyzing diffusion MRI data collected from epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much. Best, Marc Jaskir Neuroscience PhD candidate University of Pennsylvania
Hi Marc, If you go back to the original data you may still have issues with coordinate systems. If you use dipy_horizon --cluster fornix.trk you will be able to select the parts of the fornix that you need and save them as new files. Best, Elef On Sun, Sep 22, 2024 at 9:18 AM Jaskir, Marc via DIPY <dipy@python.org> wrote:
Perfect, thank you so much! Best, Marc From: Eleftherios Garyfallidis <garyfallidis@gmail.com> Date: Sunday, September 22, 2024 at 9:51 AM To: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu> Cc: dipy@python.org <dipy@python.org> Subject: [External] Re: [DIPY] Re: Separating the fornix .trk file You don't often get email from garyfallidis@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Marc, If you go back to the original data you may still have issues with coordinate systems. If you use dipy_horizon --cluster fornix.trk you will be able to select the parts of the fornix that you need and save them as new files. Best, Elef On Sun, Sep 22, 2024 at 9:18 AM Jaskir, Marc via DIPY <dipy@python.org<mailto:dipy@python.org>> wrote: Hi dipy developers, Actually, no worries about this – I’ll directly use the HCP-1065 atlas which has the fornices in separate .trk files. Sorry to bother. Best, Marc From: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu<mailto:Marc.Jaskir@Pennmedicine.upenn.edu>> Date: Saturday, September 21, 2024 at 4:21 PM To: dipy@python.org<mailto:dipy@python.org> <dipy@python.org<mailto:dipy@python.org>> Subject: Separating the fornix .trk file Hi dipy developers, I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README: “For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy@python.org<mailto:dipy@python.org> to learn how.” Could you give me guidance on this? I’m analyzing diffusion MRI data collected from epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much. Best, Marc Jaskir Neuroscience PhD candidate University of Pennsylvania _______________________________________________ DIPY mailing list -- dipy@python.org<mailto:dipy@python.org> To unsubscribe send an email to dipy-leave@python.org<mailto:dipy-leave@python.org> https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: garyfallidis@gmail.com<mailto:garyfallidis@gmail.com>
Hi dipy developers, Actually, no worries about this – I’ll directly use the HCP-1065 atlas which has the fornices in separate .trk files. Sorry to bother. Best, Marc From: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu> Date: Saturday, September 21, 2024 at 4:21 PM To: dipy@python.org <dipy@python.org> Subject: Separating the fornix .trk file Hi dipy developers, I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README: “For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy@python.org<mailto:dipy@python.org> to learn how.” Could you give me guidance on this? I’m analyzing diffusion MRI data collected from epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much. Best, Marc Jaskir Neuroscience PhD candidate University of Pennsylvania
Hi Marc, If you go back to the original data you may still have issues with coordinate systems. If you use dipy_horizon --cluster fornix.trk you will be able to select the parts of the fornix that you need and save them as new files. Best, Elef On Sun, Sep 22, 2024 at 9:18 AM Jaskir, Marc via DIPY <dipy@python.org> wrote:
Perfect, thank you so much! Best, Marc From: Eleftherios Garyfallidis <garyfallidis@gmail.com> Date: Sunday, September 22, 2024 at 9:51 AM To: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu> Cc: dipy@python.org <dipy@python.org> Subject: [External] Re: [DIPY] Re: Separating the fornix .trk file You don't often get email from garyfallidis@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Marc, If you go back to the original data you may still have issues with coordinate systems. If you use dipy_horizon --cluster fornix.trk you will be able to select the parts of the fornix that you need and save them as new files. Best, Elef On Sun, Sep 22, 2024 at 9:18 AM Jaskir, Marc via DIPY <dipy@python.org<mailto:dipy@python.org>> wrote: Hi dipy developers, Actually, no worries about this – I’ll directly use the HCP-1065 atlas which has the fornices in separate .trk files. Sorry to bother. Best, Marc From: Jaskir, Marc <Marc.Jaskir@Pennmedicine.upenn.edu<mailto:Marc.Jaskir@Pennmedicine.upenn.edu>> Date: Saturday, September 21, 2024 at 4:21 PM To: dipy@python.org<mailto:dipy@python.org> <dipy@python.org<mailto:dipy@python.org>> Subject: Separating the fornix .trk file Hi dipy developers, I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README: “For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy@python.org<mailto:dipy@python.org> to learn how.” Could you give me guidance on this? I’m analyzing diffusion MRI data collected from epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much. Best, Marc Jaskir Neuroscience PhD candidate University of Pennsylvania _______________________________________________ DIPY mailing list -- dipy@python.org<mailto:dipy@python.org> To unsubscribe send an email to dipy-leave@python.org<mailto:dipy-leave@python.org> https://mail.python.org/mailman3/lists/dipy.python.org/ Member address: garyfallidis@gmail.com<mailto:garyfallidis@gmail.com>
participants (2)
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Eleftherios Garyfallidis -
Jaskir, Marc