Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

which volume to edit?
by Yang Liu 11 Jan '11

11 Jan '11

Hi Freesurferers, I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time. For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works. So, which one should I work on? brian.mgz or brainmask.mgz? Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it. How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently. Thank you. Yang

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Invitation to connect on LinkedIn
by Stefan Du Plessis via LinkedIn 11 Jan '11

11 Jan '11

LinkedIn ------------Stefan Du Plessis souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Stefan Accepter l'invitation de Stefan Du Plessis http://www.linkedin.com/e/-qq80um-git9d09s-34/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Stefan Du Plessis http://www.linkedin.com/e/-qq80um-git9d09s-34/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ SAVEZ-VOUS que présenter vos compétences sur LinkedIn augmente votre crédibilité professionnelle et peut vous amener des propositions de postes ou de missions ? Répondre à des questions de la rubrique Réponses vous permet de faire valoir votre expertise auprès d'une communauté mondiale de professionnels. http://www.linkedin.com/e/-qq80um-git9d09s-34/abq/inv-24/ -- (c) 2010, LinkedIn Corporation

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surface area vs. areal expansion
by Ecker, Christine 11 Jan '11

11 Jan '11

Dear FreeSurfer experts, I would like to compare surface area in a vertex-by-vertex fashion across two subject groups. There has been some discussion already on the mailing list and it seems that areal expansion is a better measure than simply surface area for doing so. I also remember reading that when the data is converted from native space to a template (e.g. fsaverage), the values are automatically transformed to areal expansion measures, which have been used previously in some genetic studies (e.g. Rimol et al. (2010) or Joyner et al. (2009)). Please could you let me know if the output of –qcache (e.g. lh.area.pial.fsaverage.mgh) contains the area values (i.e. average area across triangles touching vertex) or areal expansion values - I believe these values are also compared in qdec. Many thanks, Christine

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a segfault error after reinstallation of ati videocard driver on CentOS 5.5 x86_64
by Alexander Lebedev 11 Jan '11

11 Jan '11

Dear Freesurfer users, Has anybody tried to run FS with ati video cards? I am asking because I am completely stuck with it... At the beginning everything was good except the bad brain displaying with "$rh pial" command (FS displays only a small piece of it). I decided to reinstall my videocard driver - and now I cant start even "$tkmedit" getting a "segfault error". I am providing you my report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.32.1.el5 x86_64 --------------------------------------------------------------------- 1) subject name: bert 2) the entire command-line executed: [root@localhost subjects]# setenv FREESURFER_HOME /usr/local/freesurfer [root@localhost subjects]# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl [root@localhost subjects]# tkmedit bert orig.mgz 3) the error message generated: =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : ================================================= I have also attached my "xdebug_tkmedit" and "xorg.conf" files. Any help would be very appreciated... Thank you beforehand. -- Sincerely Yours, 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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contrasts using DODS
by Jose Luis Cantero Lorente 11 Jan '11

11 Jan '11

Hello, -  we are analyzing cortical thickness data from three groups and want to study whether there are between-group differences after removing the effects of three covariates. We are assuming different intercepts and different slopes (DODS) and would like to be sure that the contrasts performed for the ANOVA and for the post hoc comparisons are correct: ANOVA 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 e.g., post-hoc analysis for testing group1 > group2 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 I would appreciate your help with this matter. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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intensity values of original T1 rounded to next integer
by Micheli, C. 11 Jan '11

11 Jan '11

Dear Freesurfers The command: mri_convert orig.mgz conv.mgz --conform generates a conform volume but the intensity values are rounded to the next integer. Do you know how to avoid this? Best Cristiano

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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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