Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

clusterwise multiple comparison correction
by Elizabeth O'Hare 19 Mar '09

19 Mar '09

hello, i am working through the group analysis and multiple comparisons corrections tutorial using my own data. according to the tutorial, after running this command: mri_glmfit --y lh.thickness.10.mgz --glmdir LH_MRT_agecovar.glmdir -- fsgd matrixT_FSGD --surf fsaverage lh --fwhm 10 --C MRT_agecovar.mtz -- sim mc-z 100 1.3 mc-z.negative --sim-sign neg i should find CSD files in the LH_MRT_agecovar.glmdir/csd directory. my problem is that there is no /csd directory made as a result of the command that i run. there are also no CSD files in the contrast subdirectory. there is one CSD file (located at the same level as my glmdir) called: mc-z.negative-MRT_agecovar.mtz.csd but this file does not contain any CWP information. i'm running version 4.1.0 on fedora 10 any help would be much appreciated. thanks! libby

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merging rh and lh surfaces
by slew＠nmr.mgh.harvard.edu 19 Mar '09

19 Mar '09

Hi, I would like to have a single surf file that composed of both right and left pial surf. Is there a way to do it in freesurfer? Best. seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Follow-up Question -- Multiple Comparison - Clusterwise Correction
by Devdutta W 18 Mar '09

18 Mar '09

Hi Doug, This is a follow up question regarding display issue from mri_glmfit-sim. The issue as you explained was that the original annotation was not being cleared. You suggested a short-term as well as a long-term fix. The temporary fix was deleting "-annot aparc" from mri_glmfit-sim. As a more permanent fix, you emailed me a modified copy of mri_surfcluster. 1. My question is when re-running mri_glmfit-sim with the new mri_surfcluster do I still need to delete "-annot aparc" from mri_glmfit-sim? In other words, are both of these needed or will using the modified mri_surfcluster alone solve the problem? 2. Another question: Is there any way to convert the previous "bad" .annot file to "good" .annot file so we can view it without having to run mri_glmfit-sim again? We ran it with 5000 iterations and it took over 10 days. If there is a way we can get the same results without having to re-run it, I would very much like to know about it. Thank you for your help so far. Devdutta On Tue, Mar 17, 2009 at 12:26 PM, Devdutta W <devdutta.w(a)gmail.com> wrote: > Hi Doug, > Thanks for your help. A followup question to your last email: the short > term fix that you mentioned earlier, do I need to make that fix in addition > to copying the new mri_surfcluster file in the binary dir? Or has that been > fixed already? > > Thanks, > Devdutta > > > On Mon, Mar 9, 2009 at 4:41 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > > wrote: > >> >> Try copying this: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfclust… >> >> into your $FREESURFER_HOME/bin directory (make a backup first), and then >> re-run. >> >> doug >> >> >> Devdutta W wrote: >> >>> We are using Red Hat Enterprise Linux 5. >>> Thanks for your help. I'll try that out. >>> >>> On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> I think I've found the problem in that the original annotation at >>> a vertex is not being cleared if a cluster is not there. >>> >>> The short term fix is to delete " --annot aparc" from >>> mri_glmfit-sim at line 353. I'll email when I have a longer term >>> fix. What platform are you using? >>> >>> doug >>> >>> Devdutta W wrote: >>> >>> When I load mc-z.abs.2.sig.cluster.mgh, if the "Draw filled >>> labels" button is toggled on, it looks no different from >>> before. Toggling the "show overlay" button doesn't do anything. >>> If the "Draw Outlined labels" button is toggled on, the >>> outlines of the colored regions can be seen (including the >>> outlines of the clusters). This time, toggling the overlay >>> button on-off shows the clusters. >>> >>> On Mon, Mar 9, 2009 at 2:12 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >>> >>> /what does it look like when you load >>> mc-z.abs.2.sig.cluster.mgh >>> as an overlay?/ >>> >>> >>> >>> Devdutta W wrote: >>> >>> Nick, Sita, >>> The average subject is created from our data, perhaps >>> that's >>> why it looks different. We were having problems getting >>> freesurfer to recognize our average subject. So we linked >>> fsaverage to our average subject. I didn't see a >>> button (or a >>> tool) to toggle on-off the annotation. The overlay >>> button is >>> there but toggling it doesn't do anything. >>> There indeed are clusters mixed in with the >>> annotations. But >>> from the documenation, it seems that the command we are >>> using >>> is /supposed/ to show clusters (but only the clusters, >>> not the >>> the annotations). And that is the question I am trying >>> to get >>> answered. >>> >>> Here is the command we are using: >>> /tksurfer fsaverage lh inflated -annot >>> mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray/ >>> I am running this command from the appropriate folder and >>> fsaverage is linked to our average subject. We are >>> using the >>> following documentation: >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh…<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh…> >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> > >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> > >>> < >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highligh… >>> >\_glmfit\-sim) >>> >>> Thanks, >>> Devdutta >>> >>> >>> >>> On Mon, Mar 9, 2009 at 12:09 PM, Nick Schmansky >>> <nicks(a)nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>>>> wrote: >>> >>> Devdutta, >>> >>> What version of freesurfer is being used? The fsaverage >>> subject you >>> show doesnt look right. Also, I see what appear to >>> be clusters >>> mixed in >>> with the annotations. The summary files output by >>> the multiple >>> correction step will tell you how many and the size >>> of the >>> clusters. >>> You should be able to toggle on-off both the >>> annotation and the >>> overlay >>> independently. >>> >>> I am cc'ing Sita, as she may be able to help you on >>> this (I >>> will have >>> limited email contact this week). >>> >>> Nick >>> >>> >>> On Mon, 2009-03-09 at 11:21 -0500, Devdutta W wrote: >>> > Forgot to attach the images, again. >>> > >>> > >>> > On Mon, Mar 9, 2009 at 11:20 AM, Devdutta W >>> <devdutta.w(a)gmail.com <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com <mailto:devdutta.w@gmail.com>> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> >>> >>> >>> > wrote: >>> > Hi Nick, >>> > Can you shed some light on why this might be >>> happening? I >>> > will attach the two picture again in case >>> you weren't >>> able to >>> > view them last time. I tried what I >>> thought you >>> meant by >>> > "turn off annotation display" and I have >>> stated what >>> happened >>> > in my previous email (please see below) >>> > >>> > * If I don't include the -annot >>> option in >>> tksurfer it >>> > only displays the fsaverage, >>> naturally. >>> > * If I toggle off the button that >>> says "show >>> labels", it >>> > looks like it is just the >>> fsaverage as well. >>> > * If I toggle on the "Draw outlined >>> labels" >>> button it >>> > shows the same regions as before >>> except >>> they are >>> > merely outlined, not filled. >>> > Any help you can give me will be appreciated. >>> > >>> > Thanks, >>> > Devdutta >>> > >>> > >>> > On Wed, Mar 4, 2009 at 10:36 AM, Devdutta W >>> > <devdutta.w(a)gmail.com >>> <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> >>> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> wrote: >>> > Nick, >>> > I confess, I am not exactly sure >>> what you >>> mean by >>> > "turn off annotation display". I >>> tried a few >>> > things. >>> > >>> > * If I don't include the -annot >>> option in >>> > tksurfer it only displays the >>> fsaverage, >>> > naturally. >>> > * If I toggle off the button >>> that >>> says "show >>> > labels", it looks like it >>> is just the >>> > fsaverage as well. >>> > * If I toggle on the "Draw >>> outlined >>> labels" >>> > button it shows the same >>> regions >>> as before >>> > except they are merely >>> outlined, >>> not filled. >>> > These were the only ones that I could >>> think of. Is >>> > that what you meant or was it >>> something >>> else that I >>> > missed? >>> > >>> > Thanks, >>> > Devdutta >>> > >>> > >>> > On Tue, Mar 3, 2009 at 7:12 PM, Nick >>> Schmansky >>> > <nicks(a)nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu> >>> <mailto:nicks@nmr.mgh.harvard.edu >>> <mailto:nicks@nmr.mgh.harvard.edu>>>> wrote: >>> > What is displayed if you >>> turn off the >>> > annotation display? >>> > >>> > The threshold in the >>> simulation >>> is used to >>> > determine whether clusters >>> > are found or not. A >>> threshold of 2 >>> indicates >>> > a p-value of 0.01 >>> > (1/(10^2), 3 is 0.001, >>> etc. The >>> threshold >>> > referred to in the tksurfer >>> > display is just for color >>> thresholding. >>> > >>> > Nick >>> > >>> > >>> > On Tue, 2009-03-03 at >>> 17:17 -0600, >>> Devdutta W >>> > wrote: >>> > > Forgot the attachments >>> earlier. >>> Here they >>> > are now >>> > > >>> > > On Tue, Mar 3, 2009 at >>> 5:11 PM, >>> Devdutta W >>> > <devdutta.w(a)gmail.com >>> <mailto:devdutta.w@gmail.com> >>> <mailto:devdutta.w@gmail.com <mailto:devdutta.w@gmail.com >>> >> >>> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com> <mailto:devdutta.w@gmail.com >>> <mailto:devdutta.w@gmail.com>>>> >>> >>> >>> > > wrote: >>> > > Hi Freesurfers, >>> > > More questions >>> about this >>> analysis. >>> > > 1) Referring to the >>> documentation, >>> > we used the following >>> > > command: >>> > > tksurfer >>> fsaverage lh >>> inflated - >>> > annot mc- >>> > > >>> z.abs.2.sig.ocn.annot >>> -fthresh 2 - >>> > curv -gray >>> > > >>> > > The >>> documentation says we >>> should see >>> > an image as shown in >>> > > Figure 1 (attached). >>> But what we >>> > see is Figure 2 (also >>> > > attached). Can >>> somebody explain >>> > this? >>> > > >>> > > 2) When running the >>> simulation >>> does >>> > it matter what threshold >>> > > we use? For >>> example, >>> can we use a >>> > threshold of 2 or 3 >>> > > (instead of 4 as >>> shown in >>> > documentation) when running >>> > > mri_glmfit-sim? >>> And do >>> we have to >>> > use the same threshold >>> > > while displaying the >>> clusters >>> after? >>> > > >>> > > Thanks for any help. >>> > > >>> > > Devdutta >>> > > >>> > >>> > > >>> > >>> _______________________________________________ >>> > > Freesurfer mailing list >>> > > >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >>> >>> > > >>> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > >>> > >>> > >>> > >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >

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avg ROI
by Gabriel Go.Es. 18 Mar '09

18 Mar '09

I have created a ROI in an average subject, how can i transpose that ROI to each subject? i mean, use it like a mask to make some statistics on each subject 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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LABORATORY RESEARCH ASSISTANT - JOB POSTING
by Jean Augustinack 18 Mar '09

18 Mar '09

LABORATORY RESEARCH ASSISTANT POSITION AT MGH IN CHARLESTOWN MA Laboratory technician wanted for correlation studies in histological/pathological Alzheimer's disease and ex vivo structural magnetic resonance imaging. New Position Minimum requirement: Bachelor's Degree or higher Preferred degree: B.S. Degree in biological science Strong interest in basic research. Ability to work as a team. Responsibilities: The applicant will assist and support research using histological tissue processing in normal human and Alzheimer's disease brain samples, as well as standard lab techniques that include immunohistochemistry, and microscopy and quantitative analysis of brain areas involved in memory and several other areas. The applicant should be self-motivated, hard-working, conscientious, and independent, with the ability to learn new techniques. Some basic knowledge of Unix/Linux will be helpful. Experience with histology staining procedures and/or microscopy a plus. Interested parties should send a CV and contact information for three references to: jean(a)nmr.mgh.harvard.edu

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Changing from 1.4x1.4x1.4 mm slices to 1x1x1
by Jeff Sadino 18 Mar '09

18 Mar '09

Hello, I am analyzing some subjects from several years ago when we had a protocol that called for slices 1.4x1.4x1.4mm. I am also including in the study more recent scans with a protocol for 1x1x1mm slices. I am using freesurfer 3.0.5. I am wondering if the different slice dimensions will cause differences in the analysis. As I read on a previous post, freesurfer resamples all its input data into 1mm isovolumetric voxels anyways, so I should be ok? Regards, Jeff Sadino _________________________________________________________________ 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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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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