Freesurfer March 2009

freesurfer@nmr.mgh.harvard.edu

73 participants
100 discussions

making ROIs
by Gabriel Go.Es. 17 Mar '09

17 Mar '09

hello i'm trying to make a ROI wich not coincides with the FS parcellation, i've click the surrounding area, then click in custom fill buttom, i've tried all options, and each time all the brain gets white and then purple, wich i think that means it's not making the roi, i've tried clicking in make closed path and make path, then custom fill buttom and still can't make that single ROI i'm sending the images step by step Regards Gabriel _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

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Reminder: Please Respond to Rutvik's Invitation
by Rutvik Desai 13 Mar '09

13 Mar '09

Rutvik Desai wants you to join Yaari! Is Rutvik your friend? <a href="http://yaari.com/?controller=user&action=mailregister&friend=1&sign=YaariKR…">Yes, Rutvik is my friend!</a> <a href="http://yaari.com/?controller=user&action=mailregister&friend=0&sign=YaariKR…">No, Rutvik isn't my friend.</a> Please respond or Rutvik may think you said no :( Thanks, The Yaari Team ____ If you prefer not to receive this email tell us <a href="http://yaari.com/?controller=absn&action=addoptout&email=freesurfer@nmr.mgh…">here</a>. If you have any concerns regarding the content of this message, please email abuse(a)yaari.com. Yaari LLC, 358 Angier Ave, Atlanta, GA 30312 YaariKRC845XHS519XFL703GTA571

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tkregister2 error
by jake＠nmr.mgh.harvard.edu 13 Mar '09

13 Mar '09

Hi, I can't seem to open a window in tkregister2. Any help would be appreciated, thanks! [striatum:mri] (nmr-std-env) tkregister2 --targ orig.mgz --mov /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr --reg /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat tkregister_tcl /usr/local/freesurfer/stable4/lib/tcl/tkregister2.tcl target volume orig.mgz movable volume /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr reg file /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.9 2009/02/13 21:37:03 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.004 0.010 -0.024 -0.800; 0.122 -0.056 1.003 -1.403; -0.009 0.998 0.056 6.038; 0.000 0.000 0.000 1.000; float2int = 2 --------------------------------------- INFO: loading target orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /space/amaebi/35/users/ablood/R01_Botox/CD_R01BTX_ctrl2_sess2/bold/020/fmcsm4.bhdr INFO: bvolumeRead: min = 0, max = 1508 INFO: changing move type to float Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 5.000 -75.000; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 2 INFO: making tkreg matrix compatible with round ---- New registration matrix -------- 1.004 0.010 -0.023 0.769; 0.123 -0.056 1.002 -3.866; -0.008 0.998 0.056 4.482; 0.000 -0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.004 0.010 -0.023 0.769; 0.123 -0.056 1.002 -3.866; -0.008 0.998 0.056 4.482; 0.000 -0.000 0.000 1.000; Determinant -1.01103 subject = CD_R01BTX_ctrl2_sess2_recon Zoom Factor = 2, SQR() = 4 FOV = 256 Opening window CD_R01BTX_ctrl2_sess2_recon Can't create a context! register: ### tkoInitWindow(name) failed [striatum:mri] (nmr-std-env) ===================================================== BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090311 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_ctrl2_sess2_recon/mri

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analyze convert
by Gabriel Go.Es. 12 Mar '09

12 Mar '09

hello everybody i'm trying to convert a FS average to *.img, when i use mriconvert with one subject i put the rawavg.mgz, but in the average subject this file does not exist, so how can i make it? to convert the Fs average to an *.img Regards Gabriel Diferentes formas de estar en contacto con amigos y familiares. Descúbrelas. Descúbrelas. _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

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analize convert
by Gabriel Go.Es. 12 Mar '09

12 Mar '09

hello everybody i'n trying to convert a FS average to *.img, when i use mriconvert with one subject i put the rawavg.mgz, but in the average subject this file does not exist, so how can i make it? to convert the Fs average to an *.img Regards Gabriel _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

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Aparcstats question
by Nathan Dankner 12 Mar '09

12 Mar '09

I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure? Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance, Nathan

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A question about symmetry between two hemispheres
by carl＠nmr.mgh.harvard.edu 11 Mar '09

11 Mar '09

Hi Lars, In the interim you might want to take a look at thread below about this issue where I discuss some admittedly imperfect approaches pending doug's tool carl schwartz On 3/11/09 3:32 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: Not yet. I have some experimental software to do this but it is not ready for release. "Soon". doug Lars M. Rimol wrote: > Hi, > This is perhaps a tricky problem. I have created a lh STG label using > "custom fill" and the "up to functional threshold" option and > retrieved the data from those vertices. This label is just a minor > portion of the entire STG parcellation. Now I would like to compare to > the homologous area in the right hemisphere. Short of using the > annotation labels and thereby chosing the entire parcellation, is > there any way to get the vertex numbers for "the same" area in the > right hemisphere? > > > Thank you! > > > -- > yours, > LMR > ------------------------------------------------------------------------ >>>>>>>>>>>>>>>>> ---------------------------- Original Message ---------------------------- Subject: [Freesurfer] A question about symmetry between two hemisphere From: carl(a)nmr.mgh.harvard.edu Date: Mon, January 19, 2009 12:35 am To: freesurfer(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- hi yczhang, see also my reply on Dec 2 2008 to frederic.andersson(a)univ-tours.fr re similar question -- search freesurfer archives on "comparing hemispheres" Ultimately to look at the symmetry question properly, we will need Doug's tool. In the interim, below is one, admittedly imperfect approach. Suppose you have a cluster of thickness difference (or bold signal) in one hemisphere between 2 groups. Create your own average subject (to increase accuracy of visualization (but fs average would work as well). Then hand-draw the analogous cluster in the other hemisphere. To do so, you would need to determine the min and max values that occur in x, y, z in talairach space and additional control points as required for the cluster or region where the primary finding occurs . Then flip the sign on the x coordinates and hand draw the cluster in the opposite hemisphere, guided by the tal coodinates. Determine the variable of interest (mean thickness, mean bold signal, etc) in the "mirror" cluster. Input that variable into a glm/anova (outside of freesurfer) where side, group, variable of interest and test for whether there is a side x variable interaction, suggestive of a truly lateralized finding. Remember that the test statistic/significance level for the PRIMARY hemisphere finding is not appropriate to report as it is inherently biased (it is defined as the region where there is a significant between group difference. It is the "mirror" contra-lateral and the presence or absence of a side x variable interaction that is the focus. You might also be able to simply analyze the mirror cluster alone without putting the other side into the anova since it, unlike the primary finding cluster, is not a biased metric. best, carl schwartz >>>>>>>>>>>> no, the vertex index is essentially arbitrary and you can't use it to compare left and right. Doug had some tools for this, but I'm not sure whether they are ready for primetime yet. cheers, Bruce On Sun, 18 Jan 2009, Zhangyuanchao wrote: > Dear Expert, > > I want to exame the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi, I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region. > > > > For example, > > ID=1000, > For the left hemisphere, the vertex 1000 corespond to 'medial_wall'; what about the vertex 1000 on the right hemisphere? Is it also corespond to the same anatomical region "medial_wall" so that we can compare their cortical thickness of vertex 1000 on both left and right hemisphere to exame the symmetry property. > > > Thanks a lot! > yczhang >

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Are accurate volumes necessary for accurate surfaces?
by Jeff Sadino 11 Mar '09

11 Mar '09

Hello Surfers, I want to do a study on the cortical thickness for some new subjects. As I understand the Recon process, the surface files get their information from the volume files. If I want to increase the accuracy of my thickness files, do I first need to manually check the accuracy of the volume segmentations? Thank you, Jeff _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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qcache error
by Dankner, Nathan (NIH/NIMH) [F] 11 Mar '09

11 Mar '09

Hello All, While running qcache on a subject, I received this error: ERROR: number of vertices in [subj path]/surf/rh.thickness does not match surface (152261,152724)ERROR: reading curvature file This has only happened with this one particular scan. Is this something that can be resolved? Thanks in advance, Nathan

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homologous lh and rh labels
by Lars M. Rimol 11 Mar '09

11 Mar '09

Hi, This is perhaps a tricky problem. I have created a lh STG label using "custom fill" and the "up to functional threshold" option and retrieved the data from those vertices. This label is just a minor portion of the entire STG parcellation. Now I would like to compare to the homologous area in the right hemisphere. Short of using the annotation labels and thereby chosing the entire parcellation, is there any way to get the vertex numbers for "the same" area in the right hemisphere? Thank you! -- yours, LMR

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Freesurfer March 2009