Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

freesurfer on debian
by Darren Weber 10 Nov '05

10 Nov '05

If freesurfer is adopting some kind of open-source license (hoorrah!), can we do away with the requirement for a license file? Are there any components/dependencies of freesurfer that are not open-source? Does anyone have detailed instructions for a) compiling freesurfer? b) installation of freesurfer on debian? Is anyone working on creating a debian package for freesurfer? For that matter, has anyone created any rpm packages for freesurfer? Debian already has a package for minc tools, see http://packages.debian.org/stable/science/minc-tools but this does not include all the MNI tools (eg, n3 and mritotal). Comments, suggestions all welcome. Thanks, Darren

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problems with spheres
by Thomas, Adam (NIH/NIMH) 10 Nov '05

10 Nov '05

I recently noticed that some of my subject's spherical surfaces appears to have several small, pyramid-like points on them. One example is shown here in tksurfer: http://fmrif.nimh.nih.gov/~adamt/sphere.jpg Looking at these points in more detail in suma shows that several triangles are folder on top of each other so that all the vertices are on the spheres surface, but some triangles are entirely overlapped by others. The spherical surface is here: http://fmrif.nimh.nih.gov/~adamt/rh.sphere.asc (11MB) And this is a close up of near node 141619 in suma: http://fmrif.nimh.nih.gov/~adamt/sphere_suma_zoom.jpg These distortions are causing us problems with subject averaging. Is there something we can do to fix or avoid them? Thanks, -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370

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how do you include parietal lobe in the cut?
by Joongnam Yang 10 Nov '05

10 Nov '05

Hi, I know how to cut the occipital lobe and flatten it. You cut calcarine and pick three points and another point to select the plane and do "cut plane". Would someone let me know how to extend the cut so that the cut can include part of the parietal lobe? The menu bar has "whole brain cut" and "occipital cut" only. Thanks. Nam.

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Re: [Freesurfer] mris_fix_topology
by Sasha Wolosin 10 Nov '05

10 Nov '05

Hi Bruce, yep, the cerebellum was attatched, so I guess that must have been the problem. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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directories needed for recon-all
by Goldman, Aaron (NIH/NIMH) 10 Nov '05

10 Nov '05

Hi, I just upgraded my freesurfer distribution (recon-all now says it's version 1.114), and am preparing to try out the creation process. Before I do that, I was wondering what I need to make sure my subjects directory contains for everything to work properly (for example, I remember the old version skipped a step if you didn't have the average7 directory in there). Also, do I need to make sure my average7, etc aren't obsolete versions? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

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mris_fix_topology
by Sasha Wolosin 10 Nov '05

10 Nov '05

Dear all, I ran into a problem with the mris_fix_topology step of recon-all. Below is the output of mris_fix_topology. Does anyone know what this might mean? Any help is greatly appreciated, Thanks, Sasha Fix Topology lh Wed Nov 9 23:53:11 EST 2005 /data/Sasha_subjects/0248_corffe/scripts mris_fix_topology 0248_corffe lh ************************************************************* Setting options ************************************************************* Topology Correction Parameters retessellation mode : greedy search ordering dependant retessellation: 0 initial patch selection : 0 use precomputed edge table : 0 smooth retessellated patch : 0 match retessellated patch : 0 verbose mode : 0 ************************************************************* reading input surface /data/Sasha_subjects/0248_corffe/surf/lh.qsphere... INFO: Volume /tmp/mritotal_24375/nu_8_dxyz.mnc cannot be found. INFO: found the orig volume info on /data/Sasha_subjects/0248_corffe/mri/filled in the surface data. before topology correction, eno=-1360 (nv=257430, nf=517668, ne=776458, g=681) using quasi-homeomorphic spherical map to tessellate cortical surface... Too many intersected faces for face 347232 (171859, 173622, 173623) No such file or directory reading T1 volume from T1... reading wm segmentation from wm... 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... ERROR: mris_fix_topology exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/sdb7 136908624 11451328 118388296 9% /data ------------------------------------------ recon-all exited with errors at Wed Nov 9 23:55:36 EST 2005 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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keeping wm edits
by Don Hagler 09 Nov '05

09 Nov '05

When I run recon-all with the -autorecon2-wm flag, my white matter edits get overwritten, presumably by aseg, even if I use the -keepwmedits flag. Is that the correct behavior or is this a bug? If instead of -autorecon2-wm I use -stage2, then the wm is untouched (as desired). For some reason though, it was then unable to find the pons and I had to use the -pons-xyz option to get it to work. Any idea why using -stage2 would produce this problem with finding the pons?

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View aseg labels on inflated average7
by Jonathan Wisco 09 Nov '05

09 Nov '05

Hi is there an aseg overlay for average7 and if so, where? If possible, I would like to see my significant areas overlayed on an aseg overlay. Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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Re: parcellating primate brain
by Mark Pinsk 09 Nov '05

09 Nov '05

I remember Oleg Gusyatin posted some time ago about wanting to make a macaque parcellation. Just wondering if that was ever done, and if so, would it be accessible to users by any chance :) ? I know I can use Caret, but we're all using freesurfer for human data here so I was just wondering. thx- mark Bruce, > > if you could outline the manual parcellation procedure (formats of > required files, size of the training set, etc.), I would do it with > help of an anatomist. > > -Oleg On Mon, 19 Jan 2004, Bruce Fischl wrote: > > > > > Hi Oleg, > > > > > > someone would need to manually parcellate a set of macaque brains > > (around > > > 10-15 should be sufficient). > > > > > > cheers, > > > Bruce > > >

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license
by Roberto Toro 07 Nov '05

07 Nov '05

Hi, I asked (twice, using rto(a)psychology.nottingham.ac.uk) for a license to use freesurfer the last week and haven't had any answer.... is this delay normal? thanks in advance! roberto This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer