Freesurfer

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30132 discussions

High resolution segmentation
by Jahfari, Sara 18 Apr '11

18 Apr '11

Dear Freesurfer crew, We would like to use freesurfer to do the high resolution parcellation of gray matter reported in Hagmann et all. 2008. This far I have used (looking also at previous postings on this matter) mris_divide_parcellation pp0672 rh aparc.annot 150 rh.split150.annot (but this creates a parcellation of long strips per region, that is not fully suited for what we want). mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot The make_face_parcellation looks very nice, but I have the following questions: 1. How can I convert the .annot file to an actual .mgz volume segmentation. ( I have tried mri_annotation2label but I am not sure how the — segbase should be specified) 2. Is there a way to match the aparc.annot labels to the ic3.annot parcellation (in the way that is done with mris_divide_parcellation) ( I have converted the both annot files to labels to look at the vertex numbers, but preferably I would like the eventual segmentation to contain label info’s per volume such as in aparc+aseg.mgz) Any help would be appreciated a lot. Thanks, Sara

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install tracula
by John Fredy 18 Apr '11

18 Apr '11

Hello all I am doing the tutorial about tracula ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but I can`t find the trac-all command in my system. I was running freesurfer 4.5, and now I am running freesurfer 5, but I can´t see the executable in any folder Thanks in advance John Ochoa

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Convert transforms from xfm to lta
by Matt Glasser 17 Apr '11

17 Apr '11

Is it possible to convert an .xfm to an .lta or alternatively to initialize mri_em_register with an .xfm that one has manually generated? It is not doing a very good job for me. Thanks, Matt.

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Non-linear Volumetric Registration
by Tetiana Dadakova 17 Apr '11

17 Apr '11

Dear list, Could you please recommend me the literature on non-linear volumetric registration used in FS? Also, is there a possibility to view talairach.m3z file? Thank you, Tanja.

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Re: [Freesurfer] install tracula
by Allison Stevens 15 Apr '11

15 Apr '11

Sorry, I meant not in 5.0. > > On Fri, Apr 15, 2011 at 19:29, Allison Stevens > <astevens(a)nmr.mgh.harvard.edu> wrote: >> John, >> Tracula is available in the soon to be released 5.1 but not in 5.1. >> Allison >> >> On Fri, 15 Apr 2011, John Fredy wrote: >> >>> Hello all >>> >>> I am doing the tutorial about tracula ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) but I can`t >>> find the trac-all command in my system. I was running freesurfer 4.5, and >>> now I am running >>> freesurfer 5, but I can´t see the executable in any folder >>> >>> Thanks in advance >>> >>> John Ochoa >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >> >> > > >

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Re: [Freesurfer] homologous left and right roi
by Prapti Gautam 15 Apr '11

15 Apr '11

Hi, I want to copy a label I've created on a region on the left hemisphere to the right (or vice versa) and was wondering if there has been any progress on the tools avaialable. Is there perhaps a beta version of the functionality that could be used? Thanks, Prapti ---------------------------------------------------------------------------- 5. Re: Homologous Right Left ROIs (Douglas N Greve) Message: 5 Date: Tue, 15 Mar 2011 11:22:13 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Homologous Right Left ROIs To: Lena Palaniyappan <Lena.Palaniyappan(a)nottingham.ac.uk> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4D7F8425.3030204(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Lena, we don't have tools released yet to do this. They should be available in the spring. dopug Lena Palaniyappan wrote: > Hi all > > I have a ROI label on left hemisphere ? I need to map this ROI onto > right hemisphere to get a homologous region (for testing hemispheric > differences). What is the best way for doing this? > > Cheers > Lena

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autostimdur vs noautostimdur
by Katie Bettencourt 15 Apr '11

15 Apr '11

I'm a bit confused about what the -autostimdur and -noautostimdur flags in mkanalysis-sess do. I've checked the help files, but the wording is a bit confusing, and when I run them on my event related design, I get different results depending on which flag I use, with the -noautostimdur being more of what I expect as far as results go. Also, they are only used in event related and AB designs, not blocked, correct? Katie

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sulcal depth
by Lugar, Heather 15 Apr '11

15 Apr '11

Is there a way to extract sulcal depth statistics for a group of subjects using a function like aparcstats2table for mean curve, thickness, volume, etc.? Thanks, Heather

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FreeSurfer ver 4.0 vs 5.0
by Keefe, Helen L 15 Apr '11

15 Apr '11

Hello Bruce and All, Here are some new questions to an ongoing issue. 1. What are advantages of version 5.0 over the former version? I have processed 82 scans so far in the former version and am debating whether to re-run them all in 5.0. We will eventually have a total of 560 scans, so we need to decide soon. 2. In version 5.0, when I run tksurfer $i lh pial -annotation aparc the corpus callossum is labeled as "none". Is there a way to have it be labeled correctly as itself in ver 5? Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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failing recon-all with freesurfer v5.0
by Saad Ramadan 14 Apr '11

14 Apr '11

Hi, I have upgraded to v5.0 assuming that I'll be in a better shape now. I issued this command: nohup recon-all -s ../NanditaGoodDataSetSubject5.0_run2 -i ./t1_svs.nii -autorecon-all & which failed after a while . I used nohup so that I can close shell with terminating the calculation. The tail of recon-all.log is show below (in red ). I do assume that I have no RAM problems as this computer is dedicated for such calculations. Any hint pls? Thanks #-------------------------------------------- #@# Smooth2 lh Wed Apr 13 17:48:03 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Apr 13 17:48:12 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.7 mm, total surface area = 85687 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 321 vertices thresholded to be in k1 ~ [-0.25 0.24], k2 ~ [-0.11 0.05] total integrated curvature = 0.502*4pi (6.303) --> 0 handles ICI = 1.4, FI = 9.5, variation=161.148 170 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.14 0.12] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Wed Apr 13 17:52:48 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm NanditaGoodDataSetSubject5.0_run2 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ NanditaGoodDataSetSubject5.0_run2/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 258 ] WARN: S lookup min: -0.547240 WARN: S explicit min: 0.000000 vertex = 126 #-------------------------------------------- #@# Sphere lh Wed Apr 13 17:53:01 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 4.62 hours scaling brain by 0.274... pass 1: epoch 1 of 3 starting distance error %20.44 pass 1: epoch 2 of 3 starting distance error %20.39 unfolding complete - removing small folds... starting distance error %20.32 removing remaining folds... final distance error %20.32 284: 0 negative triangles Linux cluster.bwh.harvard.edu 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NanditaGoodDataSetSubject5.0_run2 exited with ERRORS at Wed Apr 13 22:30:15 EDT 2011

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