Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

mne_setup_forward_model --- non-brain surface issue
by Suarez, Ralph O., 01 Jun '09

01 Jun '09

Hello everyone, I am having a problem using the command: mne_setup_forward_model --surf --ico 4 I get the following error: Surface outer skin is not completely inside surface outer skull (sum of solid angle = 1.16234e-15 * 4*PI) I have viewed these surfaces with tkmedit and noticed on the images exactly where the problem is, but I am not sure how to fix this problem. Any helpful suggestions would be greatly appreciated! Thank you, Ralph

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changing psubmit to qsub in rebuild script
by Kevin Scheibel 01 Jun '09

01 Jun '09

Hey All, The cluster that I submit jobs to uses qsub instead of psubmit, but I'm trying to preserve the way that rebuild_gca_atlas.csh runs. Here is the man page for qsub: http://gridengine.sunsource.net/nonav/source/browse/~checkout~/gridengine/do c/htmlman/htmlman1/qsub.html I guess I'm looking for the equivalent of psubmit's configuration settings in qsub. I.e. how would I write the following homologous command in qsub?: psubmit -l nodes=1:opteron -m $USER -c "$cmd" Kevin Scheibel k.scheibel(a)ucla.edu

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(repost) viewing sig.mgh files on the image volumes
by Nasim Maleki 01 Jun '09

01 Jun '09

Dear Freesurfers! I'm trying to transform and overlay the sig.mgh files on the 3D volumetric data. I use mri_surf2vol to convert sig.mgh and everything works fine up to the point that I try to view the overlay with tkmedit. There is no overlay on top of the main volume although it is successfully loaded and also when I use the 'configure functionaloverlay' interface in tkmedit I get the following error: Error: Error 18 in FunV-TclOISetSampleType: Invalid Parameter" Have I missed something? Thanks for your help in advance. Nasim P.S. I use FreeSurfer v4.3.0

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grey/white
by roberto toro 01 Jun '09

01 Jun '09

Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto

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volume comparisons
by Samantha Clark 01 Jun '09

01 Jun '09

Hi, I was wondering if there was a way to compare t1 or t2 maps between 2 subjects using the volume brain as opposed to the surface brain. To be specific I have two brains which are T1 maps. I want to see the differences in T1's between the two brains. How would i go about doing this. I hope i am clear in my question. --sam

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Re: [Freesurfer] A problem about average curvature value
by Zhangyuanchao 01 Jun '09

01 Jun '09

Thanks a lot! what do you mean by iterative smoothing, is it heat kernel smoothing? Attached is a paper about curvature of UCLA, in which I highlight some part of it. firstly, they average the mean curvature within 3mm, then obtain its absolute value, Then they further smoothed the absolute mean curvature using heat kernel smoothing. I do not know what is the difference between averaging and iterative smoothing. By the way, can I get the absolute value of a curv file using build-in function rather than load it into matlab and then write it back to binary files? yczhang Thanks --- 09年6月1日，周一, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 写道：发件人: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 主题: Re: [Freesurfer] A problem about average curvature value 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn> 抄送: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> 日期: 2009年6月1日,周一,下午10:36 Hi yczhang, yes, mris_average_curvature will do this on the surfae. It uses iterative averaging, but this converges to a Gaussian. Doug: can you post the formula that translates number of iterations into fwhm? thanks Bruce p.s. remember to include the -w switch otherwise it won't write out the results. On Mon, 1 Jun 2009, Zhangyuanchao wrote: > Is there any build-in function that I can average a curvature file with Radius of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv are smoothed in some way, is it smoothed simply by averaging the values? > > Thanks! > > Best Regards, > yczhang > > > ___________________________________________________________ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > http://card.mail.cn.yahoo.com/ ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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cortical thickness value of each pixel
by Feng-Xian 01 Jun '09

01 Jun '09

Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I can’t find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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A problem about average curvature value
by Zhangyuanchao 01 Jun '09

01 Jun '09

Is there any build-in function that I can average a curvature file with Radius of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv are smoothed in some way, is it smoothed simply by averaging the values? Thanks! Best Regards, yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Re: [Freesurfer] cortical thickness value of each pixel
by Bruce Fischl 01 Jun '09

01 Jun '09

oops, I meant "non cortical regions" On Mon, 1 Jun 2009, Feng-Xian wrote: > > Hi, > From your response, I thick that if I want to get the global thickness > statistics (mean +/- SD) without any regions where the thickness is 0, I > would consider these regions where the thickness is 0. But, I donÿÿt know > what can I do? Would you teach me? > > First, I get the global thickness statistics with all regions by the > following command: > mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > 155006 103166 299737 2.608 1.022 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 > /surf/lh.white > > Then, I get the global thickness statistics with some regions where the > thickness is 0 by the following command: > mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 155006 103166 0 0.000 0.000 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ > 0/surf/lh.white > > Thank you in advance! > > Feng-Xian > > > > > On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote >> that's right, but it will average over the whole surface including >> e.g. the callosum where the thickness is 0. If you specify the >> ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 >> Jun 2009, Feng-Xian wrote: >> >>> >>> Hi, >>> From your suggestion, I get the global thickness statistics (mean +/- > SD) >>> by the following command: >>> mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh >>> >>> Then, I get the following information: >>> table columns are: >>> number of vertices >>> total surface area (mm^2) >>> total gray matter volume (mm^3) >>> average cortical thickness +- standard deviation (mm) >>> integrated rectified mean curvature >>> integrated rectified Gaussian curvature >>> folding index >>> intrinsic curvature index >>> structure name >>> 155006 103166 299737 2.608 1.022 0.121 0.041 2632 >>> > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 >>> /surf/lh.white >>> >>> So, I think 2.608 & 1.022 is the global thickness statistics (mean +/- > SD) >>> for this subject. Do I have something wrong? >>> >>> Thank you in advance! >>> >>> Feng-Xian >>> >>> >>> >>> On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote >>>> Hi Feng-Xian, >>>> >>>> the ?h.thickness files in each subject's surf dir contain the vertex- >>>> wise thickness, and mris_anatomical_stats will compute the average. >>>> Make sure to give it -l ?h.cortex.label so it only computes them >>>> over the cortial region of the surface >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Mon, 1 Jun 2009, Feng-Xian wrote: >>>> >>>>> >>>>> Hi, >>>>> I want to calculate the global thickness statistics (mean +/- SD) for >>> all >>>>> my subjects. And, I could calculate the global thickness statistics by >>> some >>>>> information about cortical thickness values of each pixel. But I canÿÿt >>> find >>>>> any files regarding cortical thickness values of each pixel. >>>>> Could you suggest me how to calculate the global thickness > statistics >>> or >>>>> tell me where to get the file regarding cortical thickness values of > each >>>>> pixel? >>>>> >>>>> Thank you in advance! >>>>> >>>>> Feng-Xian >>>>> >>>>> >>>>> ------------------------------------------------- >>>>> Chang Gung University Mail Server Web Mail system >>>>> By Chang-Gung University Information Center >>>>> (http://www.cgu.edu.tw/ic/) >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>> >>> >>> ------------------------------------------------- >>> Chang Gung University Mail Server Web Mail system >>> By Chang-Gung University Information Center >>> (http://www.cgu.edu.tw/ic/) >>> >>> >>> > > > ------------------------------------------------- > Chang Gung University Mail Server Web Mail system > By Chang-Gung University Information Center > (http://www.cgu.edu.tw/ic/) > > >

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Re: [Freesurfer] cortical thickness value of each pixel
by Bruce Fischl 01 Jun '09

01 Jun '09

use -l lh.cortex.label or rh.cortex.label to exclude the non-zero regions On Mon, 1 Jun 2009, Feng-Xian wrote: > > Hi, > From your response, I thick that if I want to get the global thickness > statistics (mean +/- SD) without any regions where the thickness is 0, I > would consider these regions where the thickness is 0. But, I donÿÿt know > what can I do? Would you teach me? > > First, I get the global thickness statistics with all regions by the > following command: > mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > 155006 103166 299737 2.608 1.022 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 > /surf/lh.white > > Then, I get the global thickness statistics with some regions where the > thickness is 0 by the following command: > mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 155006 103166 0 0.000 0.000 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ > 0/surf/lh.white > > Thank you in advance! > > Feng-Xian > > > > > On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote >> that's right, but it will average over the whole surface including >> e.g. the callosum where the thickness is 0. If you specify the >> ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 >> Jun 2009, Feng-Xian wrote: >> >>> >>> Hi, >>> From your suggestion, I get the global thickness statistics (mean +/- > SD) >>> by the following command: >>> mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh >>> >>> Then, I get the following information: >>> table columns are: >>> number of vertices >>> total surface area (mm^2) >>> total gray matter volume (mm^3) >>> average cortical thickness +- standard deviation (mm) >>> integrated rectified mean curvature >>> integrated rectified Gaussian curvature >>> folding index >>> intrinsic curvature index >>> structure name >>> 155006 103166 299737 2.608 1.022 0.121 0.041 2632 >>> > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 >>> /surf/lh.white >>> >>> So, I think 2.608 & 1.022 is the global thickness statistics (mean +/- > SD) >>> for this subject. Do I have something wrong? >>> >>> Thank you in advance! >>> >>> Feng-Xian >>> >>> >>> >>> On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote >>>> Hi Feng-Xian, >>>> >>>> the ?h.thickness files in each subject's surf dir contain the vertex- >>>> wise thickness, and mris_anatomical_stats will compute the average. >>>> Make sure to give it -l ?h.cortex.label so it only computes them >>>> over the cortial region of the surface >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Mon, 1 Jun 2009, Feng-Xian wrote: >>>> >>>>> >>>>> Hi, >>>>> I want to calculate the global thickness statistics (mean +/- SD) for >>> all >>>>> my subjects. And, I could calculate the global thickness statistics by >>> some >>>>> information about cortical thickness values of each pixel. But I canÿÿt >>> find >>>>> any files regarding cortical thickness values of each pixel. >>>>> Could you suggest me how to calculate the global thickness > statistics >>> or >>>>> tell me where to get the file regarding cortical thickness values of > each >>>>> pixel? >>>>> >>>>> Thank you in advance! >>>>> >>>>> Feng-Xian >>>>> >>>>> >>>>> ------------------------------------------------- >>>>> Chang Gung University Mail Server Web Mail system >>>>> By Chang-Gung University Information Center >>>>> (http://www.cgu.edu.tw/ic/) >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>> >>> >>> ------------------------------------------------- >>> Chang Gung University Mail Server Web Mail system >>> By Chang-Gung University Information Center >>> (http://www.cgu.edu.tw/ic/) >>> >>> >>> > > > ------------------------------------------------- > Chang Gung University Mail Server Web Mail system > By Chang-Gung University Information Center > (http://www.cgu.edu.tw/ic/) > > >

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Freesurfer June 2009