Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Regression: Activation as a function of condition
by Adam Nitenson 11 Jan '11

11 Jan '11

Hello Freesurfers, We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load. I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis (STABLE 4) that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 19
by Bevil R. Conway 11 Jan '11

11 Jan '11

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not have access to email. For issues concerning my laboratory, please contact my lab manager, Rosa Lafer-Sousa (rlaferso(a)wellesley.edu) Thank-you and I'll be in touch when I get back. Bevil

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Re: [Freesurfer] what is subcortical volume?
by Douglas N Greve 10 Jan '11

10 Jan '11

Yes, it is accurate. Why do you think it's not? There's lots of validation stuff on the wiki. The subcortical gray matter structures are given below. Left_Thalamus) Right_Thalamus) Left_Thalamus_Proper) Right_Thalamus_Proper) Left_Caudate) Right_Caudate) Left_Putamen Right_Putamen Left_Pallidum) Right_Pallidum) Brain_Stem) Left_Hippocampus) Right_Hippocampus) Left_Amygdala) Right_Amygdala) Left_Accumbens_area) Right_Accumbens_area) Left_VentralDC) Right_VentralDC) Left_Substancia_Nigra) Right_Substancia_Nigra) Left_Cerebellum_Cortex) Right_Cerebellum_Cortex) Eisenstein, Sarah wrote: > Thank you for your response. However, is this considered an accurate estimation of subcortical volume? As far as I know, Freesurfer is unable to estimate some deep subcortical structure volumes. So what is subcortical volume (as given by Freesurfer aseg.stats) composed of? > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, January 10, 2011 4:39 PM > To: Eisenstein, Sarah > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] (no subject) > > The aseg.stats file takes into account partial voluming which is not > taken into account when you simply sum up the subcortical structures > because some of those structures will be partially volumed with white > matter. > > doug > > Eisenstein, Sarah wrote: > >> Hello, >> >> >> >> What goes into the calculation of subcortical volume? We have tried >> adding volumes of individual subcortical areas but the total does not >> equal the subcortical volume provided by aseg. Is the subcortical >> volume calculation accurate? >> >> >> >> Thanks, >> >> >> >> Sarah Eisenstein >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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(no subject)
by Eisenstein, Sarah 10 Jan '11

10 Jan '11

Hello, What goes into the calculation of subcortical volume? We have tried adding volumes of individual subcortical areas but the total does not equal the subcortical volume provided by aseg. Is the subcortical volume calculation accurate? Thanks, Sarah Eisenstein

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redraw failed: no gl window open error
by juli＠nmr.mgh.harvard.edu 10 Jan '11

10 Jan '11

Hello, I am working in freesurfer-Linux-centos4_x86_64-stable-v4.0.5-20081003. The issue I am having started several days ago when I was trying to create overlap of thresholded stats maps using mri_binarize and mri_concat (from sig.mgh files). When I was attempting to load the concatenated file I was getting an error "surfer: ### redraw failed: no gl window open" and in the tk window I am getting just an average recon without any overlay map. Also, now I am unable to load any of the GLMs I have ran previously. Going by the previous posts as well as http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems, I have tried the following: - setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride prior to running freesurfer - NVidia driver update - setenv doublebufferflag 1 - I have also checked my xorg.conf file (attached) Depth is set to 24. If you could point me in any other direction to fix/undo this issue I would greatly appreciate it. Thank you in advance, Juli

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Error FsFast Tutorial
by Fernanda Palhano 10 Jan '11

10 Jan '11

Hi, I am trying to run the FsFast tutorial, but I am getting the following error: Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -aparc+aseg tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat [Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tksurfer-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -hemi lh -aparc tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. $Id: tksurfer-sess,v 1.15.2.1 2010/07/14 16:08:04 greve Exp $ Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 Mon Jan 10 15:08:15 BRT 2011 /Applications/freesurfer/bin/tksurfer list odd-v-0 con/map odd-v-0 /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii maplist /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii mri_concat /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii --o /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat I checked all the mgh files in fb1-analysis-study and any of them have register.dof6.dat, there is only register.dat. Where can I obtain these file? Thanks in advance, Fernanda Palhano

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 13
by Bevil R. Conway 10 Jan '11

10 Jan '11

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64 bits Mac
by Ed Gronenschild 10 Jan '11

10 Jan '11

Hi, The Mac OSX 10.6 version offers the possibility to run in 64 bits mode (by pressing simultaneously the 6 and 4 keys during startup). I was wondering if Freesurfer can be used in 64 bits mode? In other words: does it use the 64 bits or does it run only in compatibility mode and in fact in 32 bits mode? Ed

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Group analysis, contrasts
by Per Selnes 10 Jan '11

10 Jan '11

I'm trying to set ut a freesurfer group analysis. In my fsgd file there are four groups/classes and 2 variables, like so: GroupDescriptorFile 1 Title Class Class1 Class Class2 Class Class3 Class Class4 SomeTag Variables Variable1 Variable2 Input subj1 Class1 49 1 Input subj2 Class2 50 2 Input subj3 Class3 51 3 Input subj3 Class4 52 4 Input... I'm a bit puzzled as to how I should set up the contrasts. With DODS, there should be a matrix of 12 regressors, and I want to model how thickness varies with Variable2, ignoring the effects of Variable1 and Class. Should my contrast be 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 or 0 0 0 0 0 0 0 0 1 1 1 1 or something completely different? I have tried both contrasts, and they yield identical (and plausible) results. Kind Regards, Per Selnes

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"segfault error" after reinstallation of ati videocard driver
by Alexander Lebedev 09 Jan '11

09 Jan '11

Dear Freesurfer users and developers, I sent a message to you yesterday ("unable to download FS"). The matter is that I have got "segfault error" after reinstallation of ati videocard driver. First of all I would like to say that I am a newbie in FS and the last thing i want to do is to disturb you by trifles. But honestly I tried my best to find a solution (as well as ".xdebug_tkmedit") and I keep being stuck at running tkmedit. I am providing a bug report. Would you be so kind to help me in solving this problem? -- Best Regards, Alexander Lebedev. I.P. Pavlov State Medical University, 197022, Lev Tolstoy str. 6/8, Saint Petersburg, Russian Federation. tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: alexander.vl.lebedev

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