External Email - Use Caution
Dear experts,
I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?
Thanks - Don
Department of Neurological Surgery University of Pittsburgh
Hi Don
By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Krieger, Donald N. Sent: Wednesday, July 21, 2021 10:53 AM To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] shortest distance between two points along the gray/white boundary
External Email - Use Caution Dear experts,
I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?
Thanks - Don
Department of Neurological Surgery University of Pittsburgh
External Email - Use Caution
Thanks, Bruce, and thanks for getting back so quickly.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Wednesday, July 21, 2021 11:08 AM To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] shortest distance between two points along the gray/white boundary
Hi Don
By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Krieger, Donald N. Sent: Wednesday, July 21, 2021 10:53 AM To: 'freesurfer@nmr.mgh.harvard.edu' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] shortest distance between two points along the gray/white boundary
External Email - Use Caution Dear experts,
I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with "white" parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?
Thanks - Don
Department of Neurological Surgery University of Pittsburgh
External Email - Use Caution
Don,
I have found the following library to be useful for this purpose
https://secure-web.cisco.com/1U3Y67JfA4BlNJYX4ut9RehuCYpVbRmTunPkJWXOMufx-L2...
See here specifically:
https://secure-web.cisco.com/1F0B-uHPcON288SnpntFlNmHKtJKwLNJDJW38TSBDx59rT-...
HTH,
john
On Wed, 21 Jul 2021 at 11:23, Krieger, Donald N. kriegerd@upmc.edu wrote:
External Email - Use CautionThanks, Bruce, and thanks for getting back so quickly.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Fischl, Bruce *Sent:* Wednesday, July 21, 2021 11:08 AM *To:* 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] shortest distance between two points along the gray/white boundary
Hi Don
By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Krieger, Donald N. *Sent:* Wednesday, July 21, 2021 10:53 AM *To:* 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] shortest distance between two points along the gray/white boundary
External Email - Use Caution *Dear experts,
I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with “white” parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?
Thanks - Don
Department of Neurological Surgery
University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1y9TwNUJxhn2KETyO_DnnzUNyhPeTNaE4Y_tAv_TyYgMrAk...
External Email - Use Caution
Hi Donald,
I recently needed exactly what you want, and I have an R implementation that can work directly on FreeSurfer brain surface meshes. It interfaces with the C++ Geodesic Distance implementation in VCGLIB [1] (via Rcpp).
You can see it in action here: https://secure-web.cisco.com/1tfXDPtqQ72pBui5okMYRp9IIoRdyiDkvL9nPHkqBjPsMFO...
If you are interested let me know, and I can write up a short example script that shows how to use it with FreeSurfer meshes. The package versions one needs are not on CRAN yet though.
Tim
[1] vcg.isti.cnr.it/vcglib/
On 07/21/2021 5:39 PM John Griffiths j.davidgriffiths@gmail.com wrote:
External Email - Use Caution
Don,
I have found the following library to be useful for this purpose
https://secure-web.cisco.com/1U3Y67JfA4BlNJYX4ut9RehuCYpVbRmTunPkJWXOMufx-L2...
See here specifically:
https://secure-web.cisco.com/1F0B-uHPcON288SnpntFlNmHKtJKwLNJDJW38TSBDx59rT-...
HTH,
john
On Wed, 21 Jul 2021 at 11:23, Krieger, Donald N. kriegerd@upmc.edu wrote:
External Email - Use CautionThanks, Bruce, and thanks for getting back so quickly.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Fischl, Bruce *Sent:* Wednesday, July 21, 2021 11:08 AM *To:* 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] shortest distance between two points along the gray/white boundary
Hi Don
By far the easiest way to do this is to find the locations of the points on the sphere then compute the length of the great circle arc connecting them, then correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for computing actual geodesics (the procedure about will give you like a 10% error)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Krieger, Donald N. *Sent:* Wednesday, July 21, 2021 10:53 AM *To:* 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] shortest distance between two points along the gray/white boundary
External Email - Use Caution *Dear experts,
I would like to compute the shortest distance along the gray/white boundary between two points on the boundary, i.e. between points with “white” parcellation regions. The distance need not be guaranteed to be minimized and the path need not be unique. Can you suggest an approach using the freesurfer tools?
Thanks - Don
Department of Neurological Surgery
University of Pittsburgh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1y9TwNUJxhn2KETyO_DnnzUNyhPeTNaE4Y_tAv_TyYgMrAk...
--
Dr. John D. Griffiths
Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto
Assistant Professor @ Department of Psychiatry & Institute of Medical Sciences, University of Toronto
http://secure-web.cisco.com/1MhotjZ7By4G-C6pnT5xuE07XqjGiirDO7XAIoHbDdqsbUg8...
Frontiers in Neuroinformatics & Frontiers in Computational Neuroscience joint Research Topic: “Neuroinformatics of Large-Scale Brain Modelling” *Eds. John Griffiths, Kelly Shen, Padraig Gleeson* *Now accepting submissions! * Abstract deadline 26 Feb 2021. Manuscript deadline 30 July 2021. See topic page here <https://secure-web.cisco.com/1vxWYKXpIcqvqPcQhURa7rBFb63OBJs3syVwxC_vhUbY2-Z1ZnpWir3T_iugLGuE-Avy__p-Yc1TqDf_YkiVwoVNzOT28DkY3kCk0frA6P4S0cM1-G6VKHXShLFV5mh8pvLOSzf2CCcv1qHdTKfs79I9u-jwYKjMV5CsPO6RWm9IwTTO4FSh50f-5TrhMVhhWdPbfnKOVUCgg3gwTJfCbUh7qI5wwOFtIjGtVMeg5yJgJW_83gFoxlB0om_gjT_uoc1IxloqmcJ93ShvkOWTSVQ/https%3A%2F%2Fwww.frontiersin.org%2Fresearch-topics%2F16641%2Fneuroinformatics-of-large-scale-brain-modelling> for more info <https://secure-web.cisco.com/1snCb_CkyTgCkguu5IZi5_l90oXKwjzwot55QVBSV1Vz4e7IE9n7-iqAnYpgfPbuZI8FYTtl8tWBnGx6g1lbNhog_En4jp8MPqXGKoemG5i9UPQ5r9MWJdQImt8N2vz9PloPo4ADveqkkQ8HX5r7gHsi2u_mXEtNuefwVT6JnuDi35NaLPNDWp3DoVEynCa8kp8In1bdsnezYEd7WF5qHE1Bbk8_uFdghCzhhPtXDAx0rQfW98kxTNHPnDSvQ6mNzPmzz4b5rOsahmK0aCKaAYA/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Virus-free. http://secure-web.cisco.com/1FLsZK8aFLg8apxHRwmPAe-znYgUMaRWUmhB4A9EKuIgQYAaYDId2gMAAvBtxkhz0HTuLUVluwUIV1WREUqxb_C1lRKWnHtHtiBuv0arU175C6MyTzdTFd1hSP4skRvzyEdIMf_UfbZOR9rUFgSSxbEWFoQziD2pxjriODaI2NE6j_qc9kmmwyE57eJXUF5Uw-6YOXOnOQ18jtFHBnilB1wg_-gD0kdQwB2_ubzBCZYMqFV_JEOHCTkziDxS6lylsbl-e4gteiYmgH-74NyaTGQ/http%3A%2F%2Fwww.avast.com <https://secure-web.cisco.com/1snCb_CkyTgCkguu5IZi5_l90oXKwjzwot55QVBSV1Vz4e7IE9n7-iqAnYpgfPbuZI8FYTtl8tWBnGx6g1lbNhog_En4jp8MPqXGKoemG5i9UPQ5r9MWJdQImt8N2vz9PloPo4ADveqkkQ8HX5r7gHsi2u_mXEtNuefwVT6JnuDi35NaLPNDWp3DoVEynCa8kp8In1bdsnezYEd7WF5qHE1Bbk8_uFdghCzhhPtXDAx0rQfW98kxTNHPnDSvQ6mNzPmzz4b5rOsahmK0aCKaAYA/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ygJnMFv7Z3MwVDw1sK6YpahhREymhcJNy4zqQyC3KeJbmZyFgc0FBd1pb6-ODND_Mnb_-8K7i3pbkyOuvMFR6tx9rAdSPykIkpkN4XqyBFcEcOK49Hdhd1kOI37mKya5hQO9TzHgoU_NwPJ9_4lbxguRZPmOD1XuPnatm1AHIaLkvnkKjU9hN-fxEWpOVOgsm6BoFv7owUCPQovFMrcfUXYi6ffyR_3I5VQRhev35SSVwTwYeQ7b6XVTgJiNaFofN3W5h25ujuR1VyOLz5oPWg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce -
John Griffiths -
Krieger, Donald N. -
Tim Schäfer