Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Segmentation fault during -cortribbon flag in autorecon2
by Andreas Engvig 02 Jun '09

02 Jun '09

Hi, We've been encountering the following error when re-running 43 healthy subjects through both the recon-all -all stream and through the recon-all -long stream. The error seem to occur quite random with regards to the subjects: " #@# Cortical ribbon mask Tue Jun 2 03:09:13 CEST 2009 /work/220791.d/2039B.long.2039A/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2039B.long.2039A SUBJECTS_DIR is /work/220791.d WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. Segmentation fault " We've used Freesurfer v.4.1. The scans have previously been run in fs. 4.05. After the error occurs, I've tried to rerun the subjects just through this step. They usually complete the step after 1-2 subsequent reruns. However, this is quite time consuming - any suggestions how to solve this? We use centOS4 64bit. I run the subjects on our computing cluster which allocates 2,1 GB of memory for each subject. I've seen the error addressed on the list earlier, but I couldn't find any obvious solution. Thanks! Best regards Andreas Engvig Center for the Study of Human Cognition University of Oslo PB 1094 Blindern 0317 Oslo Cell: +47 988 58 770

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smoothing sulc
by qwfy1234567 02 Jun '09

02 Jun '09

Hi, I want to use sulc measure to make group analysis, before making analysis,I have to smooth the sulc measure. Should I smooth it directly or I first get the absolute value,then I smooth it? you know sulc has both positive and negative value? Best, Gang

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-- ROI label map activation
by Suarez, Ralph O., 01 Jun '09

01 Jun '09

Hello all, I am interested in doing ROI analysis of MEG activation using the standard Freesurfer atlas labels. My goal is to quantify the amount of MEG activation in a specific ROI for comparisons between other ROIs, and other subjects. So, ultimately I need to extract quantifiable MEG activation exclusive to a given atlas region. I am a bit confused as how this can be done. Can anyone point me in the right direction? Any suggestion or advice that anyone is willing to offer would be greatly appreciated. Thanks, Ralph

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Option --fwhm with command mri_nu_correct.mni
by Ed Gronenschild 01 Jun '09

01 Jun '09

Hi I tried to use option --fwhm 0.1 with mri_nu_correct.mni and noticed that this is incorrectly interpreted as option --distance 0.1. This script reads if($#FWHM) set cmd = ($cmd -distance $FWHM); whereas this should be if($#FWHM) set cmd = ($cmd -fwhm $FWHM); Is it possible to correct the mri_nu_correct.mni script? Ed

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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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