Re: [Freesurfer] shortest distance between two points along the gray/white boundary
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%2Ff531884ed6ce522b083a61dba2d61f54749d%2Fgeodesic.py%23L66 HTH, john On Wed, 21 Jul 2021 at 11:23, Krieger, Donald N. 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' > *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' > *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_uFdghCz
[Freesurfer] Call for submissions: Frontiers Research Topic on “Neuroinformatics of Large-Scale Brain Modelling”
External Email - Use Caution Dear all, We are excited to announce an upcoming Research Topic, jointly within Frontiers in Neuroinformatics and Frontiers in Computational Neuroscience, on “Neuroinformatics of Large-Scale Brain Modelling”. This Research Topic will document the various ways in which neuroinformatics approaches are being applied in large-scale brain modelling, informing readers on both established practices and emerging techniques. We seek Original Research, Review, Mini-Review, Hypothesis and Theory, Perspective, and Opinion articles that cover, but are not limited to, the following topics: - Ontologies, systems, and tools for definition and specification of large-scale neural models - New approaches to parameter optimization, parameter space exploration, and systematic tracking of simulation behaviour across parameter combinations - Informing neural models with genetic and multi-omic data from large-scale databases and individual patients/subjects - Systematic computational modelling studies on large numbers of subjects, and/or using large-scale open-access datasets (HCP, ABCD, etc.) - ‘Hybrid’ modelling schemes that combine mean-field with spiking network models - ‘Hybrid’ approaches to defining connectivity in large-scale brain models (e.g. supplementing tractography with microscopy data for higher-resolution subcortical connectivity structure) - Simulations using high-resolution neuroanatomical data from initiatives such as BigBrain, Allen Institute, etc. - ‘High-density’ (large number of regions; small parcels) connectome-based neural mass modelling - Other neuroinformatics challenges and solutions in large-scale brain simulations - Comparisons between detailed spiking/morphological simulations and neural mass model simulations - Comparisons between models based on high-resolution and low-resolution Allen atlas connectivities Full details can be found on the research topic webpage at: http://secure-web.cisco.com/1hZHhtpRj8gVeM6_xqJvzBhQrTxasC-rAndyi5BIYUI9fpW6OtXlCK1fYeuijHeRU2PSwMnY94n1PLhnf5hknF-0sGrl5PQcFNn6LaUYCYKrqP-zpaqfJaJJmXCmmryyWBfXHGsb9GbzGAzijItxcER9uUn5OMRnbmCyl0kI6avO-SdIsvCQFZ5QeWOKy14yyJ1XFQmmNphNWWNObmBo1sz1AFRXqzj95wU8SRI7Fx7JDvPooyhi4_QjBgNqBgQUStboaE9cGJOsShLQNMn1zfw/http%3A%2F%2Fwww.frontiersin.org%2Fresearch-topics%2F16641%2Fneuroinformatics-of-large-scale-brain-modelling If you are considering submitting, please submit an abstract by Fri 26 Feb 2021. Deadline for submission of full manuscripts is Fri 30th July 2021. We look forward to your hearing from you and sharing this exciting work with the community. Your Research Topic co-editors, John Griffiths Padraig Gleeson Kelly Shen -- 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/1pwPAJXsEnOnQ39gT0nUnGh5e4p1g6W7ky5JGDbxtq9fwToBn53YbWk4KPnWGzKBLuN8jiqvUD14NBExi0tf_D_TrOHi1e0PLaBD1YHmffWdx519LtBoEE7XrFWIFVIjcBomQKrozvv2Kyt473qDjiw32EBBtpWhKWHNekA6VLUY6MAzvd0Wri_gsancqqeAhyuD77-Khqv7EKQQQsZGBBWEmtILZvnw7dj89G6xIU2RJEiCf6CHyJH-KpVwDkJ3AbCvfPTbjMh87ibGXFyc8WQ/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/19SFFzRdJ8-1loA4fh3BCp7VXmgONFiJKfNWqjmJYsKgf2b6Moqh0Npnl7M2VHKas89jAFolUcu_0GMBeDOYFEct_aKoLaEdAtjHm_vcqvPfHW6SPcdHlkGHRKSAzGF_V_Ac_vnAN2QABEJIg2wXc60m3qokXiT7sEis0cirrAVZFy6w8tUxNrI5C21JXYtymooKSUSeKejsYtiYI0KnoyyQ2aDeZknKMiamm8hGustb1PDBSu1wSroC7t1zGQX7IZQ-2kV92-Pz4ROPS8BXg0w/https%3A%2F%2Fwww.frontiersin.org%2Fresearch-topics%2F16641%2Fneuroinformatics-of-large-scale-brain-modelling> for more info ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PhD and MSc Opportunities in Computational Neuroscience and Neuroimaging at the University of Toronto
External Email - Use Caution The Whole Brain Modelling Group (PI Dr. John Griffiths; www.grifflab.com) at the CAMH Krembil Centre for Neuroinformatics ( www.krembilneuroinformatics.ca) and University of Toronto is looking for PhD and MSc students with a strong background in computational neuroscience and/or neuroimaging. The focus of the Group’s work is computational models of large-scale brain activity, with particular emphases on neural dynamics as measured by M/EEG and fMRI, oscillations, brain stimulation (TMS, TDCS), neural plasticity, and macro-connectomics. The student shall conduct research in one or more of these areas. They will have the opportunity to shape the details of the project based on their specific interests, as well as to contribute to other ongoing projects on a range of topics, including: neuroinformatics of whole-brain modelling, mapping and modelling anatomical connectivity and microstructure with DWI in relation to ageing and stroke, and multi-scale modelling of the thalamocortical system in relation to sleep, pharmacological neuromodulation, and neuropsychiatric disease. The successful candidate should have, minimally, an undergraduate degree in neuroscience, engineering, physics, mathematics, psychology, or related area, and a demonstrable track record of research experience and interest in computational neuroscience and/or neuroimaging. Expertise in one or more modern scientific computing programming language (Python, Matlab, Julia, R, C++) is essential. The candidate should also have familiarity with one or both of: i) neuroimaging data analysis (s/d/fMRI and/or M/EEG), and ii) computational modelling using numerical simulations (particularly modelling of neural population activity with mean-field/neural mass/neural field techniques, either with custom implementations or with tools such as The Virtual Brain Platform or Dynamic Causal Modelling). Full details of the position and application instructions can be found at www.grifflab.com/positions/ For informal inquiries, please email Dr. John Griffiths at john.griffi...@camh.ca with the title “PhD in Whole Brain Modelling” in the subject line ( Note: students interested in a September 2020 start at the University of Toronto should get in touch immediately to leave time for approaching application deadlines ) -- Dr. John D. Griffiths Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto Assistant Professor @ Department of Psychiatry, University of Toronto www.grifflab.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Post-Doctoral Fellowship in Whole Brain Modelling
External Email - Use Caution Post-Doctoral Fellowship in Whole Brain Modelling The Whole Brain Modelling Group (PI Dr. John Griffiths; www.grifflab.com) at the Krembil Centre for Neuroinformatics, Toronto, is looking to hire a Post-Doctoral Fellow with a strong background in neuroimaging and/or computational neuroscience. The successful candidate shall spearhead the group's efforts in computational modelling of large-scale brain dynamics, with a particular focus on brain stimulation (TMS, TDCS), EEG, neural plasticity, and macro-connectomics. The fellow will have the opportunity to shape the details of the project based on their specific interests, as well as to contribute to other ongoing projects on a range of topics, including: neuroinformatics of whole-brain modelling, mapping and modelling anatomical connectivity and microstructure with DWI in relation to ageing and stroke, and multi-scale modelling of the thalamocortical system in relation to sleep, pharmacological neuromodulation, and neuropsychiatric disease. The successful candidate will have a PhD in neuroscience, engineering, physics, psychology, or related area, a track record for independent research, and a strong publication record. Strong programming skills and familiarity with neuroimaging data analysis (s/d/fMRI and/or M/EEG) are required; experience with computational modelling using numerical simulations (particularly modelling of neural population activity with mean-field/neural mass/neural field techniques) would be advantageous. Full details of the position and application instructions can be found at www.grifflab.com/positions/ For informal inquiries, please email Dr. John Griffiths at john.griffi...@camh.ca with the title “Post-Doctoral Fellowship in Whole Brain Modelling” in the subject line. -- Dr. John D. Griffiths Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto Assistant Professor @ Department of Psychiatry, University of Toronto www.grifflab.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] getting vertex-wise correspondences across subjects
Dear surfers, Could you please help me with the following analysis workflow: I am doing an analysis where I identify patterns on the ?h.orig surfaces. What I want to do now is to resample these patterns over vertices, such that I have vertex-wise correspondence across subjects. I believe this essentially requires the construction of and projection to a group template (although I'm aware this could be done with e.g. fsaverage). Here is where I'm at: cd(freesurfer dir) 1. Read ?h.orig surfaces; compute patterns (...some in-house stuff...) 2. Write patterns out to .mgh file Matlab save_mgh(pat,outfile,eye(4)); Python nibabel.MGHImage(pat[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 3. Generate group template make_average_subject --out avgsub --sd -subjects subj1 subj2 subj3 4. Register a single example subject to the new group template mris_register -curv subj1/surf/lh.sphere avgsub/lh.reg.template.tif subj1/surf/lh.sphere.reg.avgsub 5. Project the surface patterns identified above on to the new group template, so that the vertex values correspond across subjects, and can be averaged, statistically compared. etc. mri_surf2surf --srcsubject subj1 --srcsurfreg sphere.reg.avg_sub --trgsubject avg_sub --trgsurfreg sphere.reg --hemi lh --sval --tval /tmp/test_avgsub.mgh However this breaks down at mri_surf2surf, and I'm not particularly confident that the earlier parts are exactly right either. Could you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] subdividing consistently within aparc.annot
Would the Lausanne2008 template from the connectome mapping toolkit not do the trick? http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html On 3 October 2012 23:18, Satrajit Ghosh sa...@mit.edu wrote: hi bruce, is there a way to divide consistently (same number of regions and one to one correspondence - obviously not the exact same areas) across subjects within aparc regions? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Mr. John Griffiths, MSc PhD Candidate Centre for Speech, Language, and the Brain Department of Experimental Psychology University of Cambridge, UK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_surf2surf error - Return code 254
Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.**mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.**mgz --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.**mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_**smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/** CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom
[Freesurfer] downsampling white matter surface and converting to .tri
Dear FS peeps, I am trying to downsample a (white matter) surface with mri_surf2surf. I also want the output in .tri format. First problem is that mri_surf2surf doesn't let me output in .tri format mri_surf2surf --hemi lh --srcsubject subj1 --sval-xyz white --trgsubject subj1 --trgicoorder 4 --trgsurfval subj1_white_downsampled.tri --tfmt tri gives me ERROR: could not determine type of temp_surf_white.tri (that happens with the 'tfmt' flag or not) The command does work when the output is a .gii or .mgh file, but when I then try to convert those files to .tri format with mris_convert I get the error ERROR: MRISread: cannot read surface data from file subj1_white_downsampled.gii! ...which is also the error I get when trying to load the file into freeview as a surface. Any idea what I'm doing wrong here? If there is a better way to convert lh.white into a downsampled .tri file please do tell. Thanks very much, john (p.s. thanks to Dan, Doug, and Bruce for getting me to this point...) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] downsampling white matter surface and converting to .tri
Hi Bruce. That seems to help - this command runs with no errors mri_surf2surf --hemi lh --srcsubject CBU070282 --sval-xyz white --trgsubject CBU070282 --trgicoorder 3 --trgsurfval white_trgicoorder3 --tval-xyz But unfortunately the --trgicoorder flag doesn't seem to be doing anything; when I run mris_info on the outputs of this command it says 'nvertices' is the same as the original file, for whatever value of trgicoorder I use. The files are the same size as well. Any idea why this might be happening? Thanks, john On 8 December 2011 14:45, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John try adding --tval-xyz so that it knows you want to write out a surface. cheers Bruce On Thu, 8 Dec 2011, John Griffiths wrote: Dear FS peeps, I am trying to downsample a (white matter) surface with mri_surf2surf. I also want the output in .tri format. First problem is that mri_surf2surf doesn't let me output in .tri format mri_surf2surf --hemi lh --srcsubject subj1 --sval-xyz white --trgsubject subj1 --trgicoorder 4 --trgsurfval subj1_white_downsampled.tri --**tfmt tri gives me ERROR: could not determine type of temp_surf_white.tri (that happens with the 'tfmt' flag or not) The command does work when the output is a .gii or .mgh file, but when I then try to convert those files to .tri format with mris_convert I get the error ERROR: MRISread: cannot read surface data from file subj1_white_downsampled.gii! ...which is also the error I get when trying to load the file into freeview as a surface. Any idea what I'm doing wrong here? If there is a better way to convert lh.white into a downsampled .tri file please do tell. Thanks very much, ** john (p.s. thanks to Dan, Doug, and Bruce for getting me to this point...) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_surf2surf error - Return code 254
[ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2surf not working. Not sure what's going wrong there - the command I used was mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial /home/jdg45/lh.pial_converted.mgz For the original question - I was using a converted .mgz file because when I just give it the path to the 'lh.pial' file in the same directory it says it cant determine the file type - mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: ERROR: could not determine type of /work/imaging5/Freesurfer/CBU070282/surf/lh.pial Standard error: Is there a .xxx suffix for those files I should be using? Incidentally, the reason I'm doing this is that I want to downsample a surface file; someone suggested to me to use mri_surf2surf with the 'trgicoorder' flag. Is this a good way to downsample a surface? Thanks, john On 6 December 2011 19:02, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.**mgz --tval /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.**mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_**smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/**CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_surf2surf error - Return code 254
Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
