Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

recon-all sudden stop during Talairach
by Mikael Novén 28 Jun '16

28 Jun '16

Dear Freesurfer Developers, I'm attempting to process high resolution images on a new system and following https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I at first try to run downsampled (1x1x1 mm) images. recon-all suddenly stops during #@# Talairach with no error codes except for the "exited with ERRORS" message. I'm a bit clueless as to what could be wrong. The images are from a Philips 7T Achieva system and have been normalized using ANTS N4BiasFieldCorrectionImageFilter() before attempting recon-all (though uncorrected gives the same resulting error). I thought that there was a problem with the permissions so I changed the default using setfacl which seems to work but no change. OUTPUT: INFO: extension is mgz #-------------------------------------------- #@# Talairach tis 28 jun 2016 12:52:35 CEST /usr/local/freesurfer/subjects/106_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 106_1 exited with ERRORS at tis 28 jun 2016 12:52:36 CEST" BUILD-STAMP: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 OPERATING SYSTEM: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04 LTS Release: 16.04 Codename: xenial UNAME -A OUTPUT: Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Log file included. Thank you very much for your help. All the best, Mikael Novén

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Download FreeSurfer
by Damien Marie 28 Jun '16

28 Jun '16

This message contained a link to a web site whose IP address has recently been associated with malicious activity. Due to that activity the site is not accessible from within the Partners Network. The link has been modified in the message below. If you feel this is an error please contact the IS Service Desk and open a ticket with the network security - phs assignment group. IS Service Desk numbers BWH 617-732-5927 BWH-RICS 617-525-0848 DFCI 617-632-3399 FALK 617-983-7454 LCC 857-307-4150 MCL 781-416-8940 MGH 617-726-5085 NHP 617-643-2020 NSMC 978-354-2014 NWH 617-243-6001 PCHI 781-433-3757 PHH 617-726-0790 PHS 617-726-5085 SRH 617-952-5555 ********************************* Hello everybody, Storage servers are offline for downloading FreeSurfer from the wikipage. Does anyone know an alternate location for the distribution please? Best, Damien

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updated mri_convert file
by Olivia Cheung 28 Jun '16

28 Jun '16

Hi Freesurfer team, I would like to download a copy of the updated mri_convert but the link <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes> on the Release Notes webpage does not seem to work. Would you please fix that? I need the updated mri_convert because I'm getting the following error: "nifti1Read(): unsupported slice timing pattern 5" Thanks! Olivia

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retinotopy analysis documentation
by Francesca Strappini 28 Jun '16

28 Jun '16

Hello Freesurfers, Where can I find the documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Freesurfer/Freeview help
by Abbie McNulty 27 Jun '16

27 Jun '16

Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain, how should I proceed? The online tutorials have confused me especially since I am not sure if I am supposed to be using the terminal or the command window for a lot of the code commands. Any help would be appreciated. Thanks! Abbie McNulty -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

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Stuck on “CORRECTING DEFECT”
by Dan Loewenherz 27 Jun '16

27 Jun '16

Hi freeserver folks, First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :) My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message. Thanks so much! Dan ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824, ne=425736, g=343) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425 CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)

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Freeview nightly / dev / beta
by Vincent Koppelmans 27 Jun '16

27 Jun '16

Hello Freesurfer developers, I am looking for a version of Freeview that recognizes the -noquit flag. V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from "ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev>”. I am particularly interested in a Linux version. Would it be possible to open up access to the beta versions of Freeview to us endusers again? Thanks! - Vincent

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Re: [Freesurfer] visualizing statistical maps in FreeView
by Bruce Fischl 27 Jun '16

27 Jun '16

Hi Lars I'll leave this for Ruopeng. cheers Bruce On Mon, 27 Jun 2016, Lars Morten Rimol wrote: > > Hi Bruce, > > > > Yes, now it works (my guess is I loaded a single subject surface as template > before…) but I don’t find an FDR correction button in the Configure Overlay > interface. The fdr threshold can of course be calculated in Matlab but then > why not use tksurfer, which provides that functionality it in the > interface. Also: Unlike in tksurfer, the color bar doesn’t seem to reflect > the thresholding of the overlay…. > > > > > > Thanks! > > > > LMR > > >

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Qdec-correction for multiple comparison
by John Anderson 25 Jun '16

25 Jun '16

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License for data file?
by Matthew Brett 24 Jun '16

24 Jun '16

Hi, Over at our nibabel Python package, we've got stuck trying to work out what license we should give to a file we got from Freesurfer version 3.0.3: https://github.com/nipy/nibabel/pull/461 The file is `subjects/bert/surf/lh.inflated.nofix` from Freesurfer 3.0.3. It looks like this is a modified version of the original files from the tutorial dataset - which I think derive from here: https://web.archive.org/web/20070711224104/http://www.fmridc.org/f/fmridc/7… Is that right? What license should we give when we are distributing the `subjects/bert/surf/lh.inflated.nofix` in an archive we are using to test our software? Thanks a lot, Matthew

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