Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30056 discussions

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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analyze format
by Sasha Wolosin 07 Nov '05

07 Nov '05

Dear all, When converting from analyze format is there any way to get mri_convert to read in orientation information from the analyze header file? 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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linking tksurfer and tkmedit
by Mark Pinsk 07 Nov '05

07 Nov '05

I just finished going thru the wiki's 'recommended' workflow with one of my subjects, which is just great ! It tells me to use tkmedit to check my wm and pial surfaces after autorecon2. I did and they looked pretty good (nothing caught my eye to have to fix). However when autorecon3 completed, I could easily see a couple little defects on the spheres. 1) should i try to fix those defects and re-do autorecon3 ? I imagine so, especially if I want to cut and flatten my surfaces. 2) how do i link tksurfer and tkmedit so that I may click on the sphere and see the corresponding location on the wm volume? I can't find that explained yet in the wiki. thx! Mark ps- using the latest dev version

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make_average_surface error
by Jane Aspell 07 Nov '05

07 Nov '05

Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell >make_average_surface --subjects jane kader anna ==================== make_average_surface ==================== input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject jane... The following must be revisited********************************** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD

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mris_anatomical_stats
by Jonathan Kaiser 05 Nov '05

05 Nov '05

I have an annotation file that covers the entire surface (each vertex has an annotation). When I run mris_anatomical_stats with the annotation file and sum the values from each annotation, I get a larger result for the surface area and a smaller value for the gray matter volume than if I run mris_anatomical_stats with just the surface (no annotation file specified on the command line). [cuneus:kentron] (nmr-dev-env) mris_anatomical_stats -a 2859_4_ct/label/rh.cmaparc.annot -b 2859_4_ct/ rh sum of each annotations' surface area: 112383 mm^2 sum of each annotations' gray matter volume: 375675 mm^3 [cuneus:kentron] (nmr-dev-env) mris_anatomical_stats 2859_4_ct/ rh total surface area = 98400 mm^2 total gray matter volume = 401366 mm^3 -Jon

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