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/1tfXDPtqQ72pBui5okMYRp9IIoRdyiDkvL9nPHkqBjPsMFOsuKvfVIbV0SZWLMB7gMAkLZEsJ71V0TpEQcUWE8A2lwj3T4h4vE9PamJNhh4s5YR5_BSrzujio-GnRvKsdOggEkbnZpJ0D3ugiuQC_WjeiQ_u3wvkDfg3nOT0wVfx8V50qa_VzKu97-zuy5TithCscyF_MwdKxMdf51-UHnALY8SMKLVelGlf0TJEZWy45htTJohzoXW3h8azlxg9j3-zdq6W5XC3PLPYI_Cbd2w/https%3A%2F%2Fgithub.com%2Fzarquon42b%2FRvcg%2Fpull%2F19 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.davidgriffi...@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-L2LYyccGN07nwOp17bs4N9M2lOSMLzk7W7ZkJQjbT2SooMuk-PVSRpQj_nEtWq4F_JStrLxRmY2CYnkOjkCCWCySLA3VsXYMsjiZzP8HTnxrK3x8W9ojrkgmtrxVkcSFqGnVh3FRr5usERT9T52rkLOBe3HnJ4zqEQF6QZ8pKmUyJn_BpGXmqHBsow7nLdji7B7DdFZJ2BWd61J5Tydtm62Dp6PG0PHdZ07xOnXvmg/https%3A%2F%2Fgithub.com%2Ftneumann%2Fsplocs > > See here specifically: > > https://secure-web.cisco.com/1F0B-uHPcON288SnpntFlNmHKtJKwLNJDJW38TSBDx59rT-FrOR1fcsA1dIzn7YxdHKh0SJAf2A9Ay5qE5yCskFlGsx0faLygqjx1AihXNFgtn4UlODPYAmi5S09S2Y03pjrVCYHbi6TXIGnRfi0e-vpeqcWWt9NarBcjYcZi4YnbQe_F9M-V3IWJK2DQVgy8ngE8yOMSkEu9s5H2sJOAeMLAhsZZtNPF5mkojeDJ77Itc7cqhSGpcaCL73aL29MnKMCDH2U7wal43Dm0FUwnOw/https%3A%2F%2Fgithub.com%2Ftneumann%2Fsplocs%2Fblob%2Ff531884ed6ce522b083a610000dba2d61f54749d%2Fgeodesic.py%23L66 > > > HTH, > > > john > > > > > On Wed, 21 Jul 2021 at 11:23, Krieger, Donald N. <krieg...@upmc.edu> wrote: > > > External Email - Use Caution > > > > Thanks, Bruce, and thanks for getting back so quickly. > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > > freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu < > > freesurfer-boun...@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_TyYgMrAk7lZCO3lz0iEwggLwDWNxovFCopVIQ3fgVErLvGh-9H3MNB6ZLAAbgzQbEY4HypoQy44VNbPx2JFXgO0hvHiDLMWsAuGY8z-23s-jMQjR0qFGLcglgTGgXL2EBzWMFkb67dog81cggwjMC8cSWuMePd7ZxeOhlfQHBjGjfpQCB8gHIiT0UkJq2tWZN2frHnNQHirjngLgDOgwf1toMK12DGFm8-umcRT-HjEFrw7A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > -- > > 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-C6pnT5xuE07XqjGiirDO7XAIoHbDdqsbUg8qc22dbqNuqsXAmRpB77Fcy2D17tJ5z5VwJjvX06NuTYxlVHXI5ukcZJJpZAiCwqtTWyc22PdCB8ojNkJ9UEEfqbt5_NM_l7sNhxo-QdsDVB3ff6MnwSBRVOaqr2M1uWKP18aNJXWaNiZsBhmLf4KdnmpXRdaHITmo4g3w98ZusuXPW2dD8SNnwuFrq0oJuFxQiXLAUq3sKX_-1Iq_NkVtDfg_nfNz7XjaYKN14A/http%3A%2F%2Fwww.grifflab.com > > > ~~~ > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
