Re: [HCP-Users] Transformation matrices for tractography
This earlier thread might be of use to you: <https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04257.html> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03768.html Best, Jenn <https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03768.html> Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Athanasia Metoki <athanasia.met...@temple.edu> Sent: Thursday, September 21, 2017 11:06:04 AM To: Glasser, Matthew Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Transformation matrices for tractography Hello Matt, I get the coordinates based on the peak activation for several brain areas for each subject. I get the peak activation by thresholding. I want to use these coordinates and make spherical ROIs in FSL. After I create these spherical ROIs, I want to use them as seeds for tractography. The ROIs will be in MNI space for each subject. Tractography only runs in diffusion space, so I would like to know whether the transformation matrices (MNI space to native space, and native space to MNI space) are available somewhere. Thanks. Best, Nasia Athanasia Metoki Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.met...@temple.edu<mailto:athanasia.met...@temple.edu> ___ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. On Thu, Sep 21, 2017 at 11:41 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Brain areas are not spheres. I don’t think this is a good approach. What is it that you are trying to do? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Athanasia Metoki <athanasia.met...@temple.edu<mailto:athanasia.met...@temple.edu>> Date: Thursday, September 21, 2017 at 10:25 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Transformation matrices for tractography Dear HCP experts, I am working with the HCP 900 release dataset. I am extracting coordinates for several brain areas using each subject's midthickness surface eg. "100206].L.midthickness_MSMall.32k_fs_LR.surf.gii". So the coordinates I get are in the MNI space. I want to use these coordinates to create spheres which I will then use as start and end seeds for tractography using FSL's probtrackx2. probtrackx2 always happens in native space. Given that my seeds will be in MNI space, I would have to give probtrackx2 transformation matrices so that seed transformation from MNI to diffusion space happens (and then tractography can run). Is there somewhere where I can find these matrices? Thank you. Best, Athanasia Metoki Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St.<https://maps.google.com/?q=1701+N+13th+St.+%0D+%0D+Philadelphia,+PA+19122=gmail=g> Philadelphia, PA 19122<https://maps.google.com/?q=1701+N+13th+St.+%0D+%0D+Philadelphia,+PA+19122=gmail=g> Email: athanasia.met...@temple.edu<mailto:athanasia.met...@temple.edu> ___ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient
Re: [HCP-Users] Transformation matrices for tractography
Hello Matt, I get the coordinates based on the peak activation for several brain areas for each subject. I get the peak activation by thresholding. I want to use these coordinates and make spherical ROIs in FSL. After I create these spherical ROIs, I want to use them as seeds for tractography. The ROIs will be in MNI space for each subject. Tractography only runs in diffusion space, so I would like to know whether the transformation matrices (MNI space to native space, and native space to MNI space) are available somewhere. Thanks. Best, Nasia *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.met...@temple.edu ___ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. On Thu, Sep 21, 2017 at 11:41 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > Brain areas are not spheres. I don’t think this is a good approach. What > is it that you are trying to do? > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Athanasia > Metoki <athanasia.met...@temple.edu> > Date: Thursday, September 21, 2017 at 10:25 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Transformation matrices for tractography > > Dear HCP experts, > > I am working with the HCP 900 release dataset. > > I am extracting coordinates for several brain areas using each subject's > midthickness surface eg. "100206].L.midthickness_ > MSMall.32k_fs_LR.surf.gii". > > So the coordinates I get are in the MNI space. > > I want to use these coordinates to create spheres which I will then use as > start and end seeds for tractography using FSL's probtrackx2. > > probtrackx2 always happens in native space. Given that my seeds will be in > MNI space, I would have to give probtrackx2 transformation matrices so that > seed transformation from MNI to diffusion space happens (and then > tractography can run). Is there somewhere where I can find these matrices? > > Thank you. > > Best, > *Athanasia Metoki* > Psychology Doctoral Student - Brain and Cognitive Sciences Program > Cognitive Neuroscience Laboratory > Temple University > Department of Psychology > 1701 N 13th St. > <https://maps.google.com/?q=1701+N+13th+St.+%0D+%0D+Philadelphia,+PA+19122=gmail=g> > Philadelphia, PA 19122 > <https://maps.google.com/?q=1701+N+13th+St.+%0D+%0D+Philadelphia,+PA+19122=gmail=g> > Email: athanasia.met...@temple.edu > > > ___ > The contents of this email message and any attachments are intended solely > for the addressee(s) and may contain confidential and/or privileged > information and may be legally protected from disclosure. If you are not > the intended recipient of this message or their agent, or if this message > has been addressed to you in error, please immediately alert the sender by > reply email and then delete this message and any attachments. If you are > not the intended recipient, you are hereby notified that any use, > dissemination, copying, or storage of this message or its attachments is > strictly prohibited. > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Transformation matrices for tractography
Brain areas are not spheres. I don’t think this is a good approach. What is it that you are trying to do? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Athanasia Metoki <athanasia.met...@temple.edu<mailto:athanasia.met...@temple.edu>> Date: Thursday, September 21, 2017 at 10:25 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Transformation matrices for tractography Dear HCP experts, I am working with the HCP 900 release dataset. I am extracting coordinates for several brain areas using each subject's midthickness surface eg. "100206].L.midthickness_MSMall.32k_fs_LR.surf.gii". So the coordinates I get are in the MNI space. I want to use these coordinates to create spheres which I will then use as start and end seeds for tractography using FSL's probtrackx2. probtrackx2 always happens in native space. Given that my seeds will be in MNI space, I would have to give probtrackx2 transformation matrices so that seed transformation from MNI to diffusion space happens (and then tractography can run). Is there somewhere where I can find these matrices? Thank you. Best, Athanasia Metoki Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.met...@temple.edu<mailto:athanasia.met...@temple.edu> ___ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Transformation matrices for tractography
Dear HCP experts, I am working with the HCP 900 release dataset. I am extracting coordinates for several brain areas using each subject's midthickness surface eg. "100206].L.midthickness_MSMall.32k_fs_LR.surf.gii". So the coordinates I get are in the MNI space. I want to use these coordinates to create spheres which I will then use as start and end seeds for tractography using FSL's probtrackx2. probtrackx2 always happens in native space. Given that my seeds will be in MNI space, I would have to give probtrackx2 transformation matrices so that seed transformation from MNI to diffusion space happens (and then tractography can run). Is there somewhere where I can find these matrices? Thank you. Best, *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St. Philadelphia, PA 19122 Email: athanasia.met...@temple.edu ___ The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
