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30088 discussions

Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView
by Emad Ahmadi 03 Mar '14

03 Mar '14

> Hi Bruce, > > Thank you for your response. I just want to draw manually the region of the new label on the images of few subjects. > > What I am about to do is to define a new label for the trigeminal nerve sensory nucleus (just roughly as the region that the nerve enters the brainstem); I just need to label it manually for all subjects. > > Best, > Emad > > > > On Mar 3, 2014, at 11:32 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Emad >> >> do you mean draw one manually or add it so it is automatically labeled in new subjects? If the latter it requires manually labeling a training set and rebuilding a classifer, etc..., so it is far from trivial >> >> cheers >> Bruce >> >> >> On Mon, 3 Mar 2014, Emad Ahmadi wrote: >> >>> Hello, >>> I want to define a new label in aparc+aseg.mgz (to mark certain brainstem >>> structures); I would appreciate it if you help me with how I have to do it. >>> Lots of thanks, >>> Emad >>> Emad Ahmadi, MD >>> ----------------------------------------------- >>> Postdoc Research Fellow >>> Department of Radiology >>> Massachusetts General Hospital >>> Harvard Medical School >>> 25 New Chardon Street, Suite 400 >>> Boston, MA 02114 >>> Tel: 617 726 5237 >>> Email: emad(a)nmr.mgh.harvard.edu >>> >> >> >

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Re: [Freesurfer] Group Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 03 Mar '14

03 Mar '14

Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos > That's great. Thanks a lot for your help, Doug! > > >> >> Those are the same things. The way you control for age is to compute a >> value for both groups at the same age (eg, age=0). If you demean the >> age, then the difference will be at age=meanage. With DOSS, the >> difference is always the same regardless of age (which makes it more >> interpretable) >> doug >> >> >> On 02/25/2014 03:00 PM, pfotiad(a)nmr.mgh.harvard.edu wrote: >>> Hi Doug, >>> >>> Thank you for your response. >>> Concerning scenario 2, I believe I have some hard time understanding >>> the >>> term intercept. If I'm not mistaken the intercept represents the >>> cortical >>> thickness at "age 0." The resulting clusters by using a design matrix >>> of >>> [1 -1 0 0] will give me the areas where the intercept is significantly >>> different between the Diseased group and the healthy group. >>> >>> Are those clusters the same clusters that have a different mean >>> regional >>> cortical thickness in Diseased versus Healthy subjects after >>> controlling >>> for age, or are those two completely different things? >>> >>> >>> Thanks again, >>> Panos >>> >>>> On 02/25/2014 02:07 PM, pfotiad(a)nmr.mgh.harvard.edu wrote: >>>>> Hi FS community, >>>>> >>>>> I had a few questions regarding my understanding of the group >>>>> analysis >>>>> in FS: >>>>> >>>>> 1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No >>>>> Covariates, and my contrast matrix is [1 -1], do the resulting >>>>> clusters >>>>> (if any) show the regional significant differences between the two >>>>> groups >>>>> by comparing just the means of the values that I am comparing? For >>>>> instance, if I'm comparing cortical thickness between a diseased and >>>>> a >>>>> control group, is this going to give me the clusters where the >>>>> Diseased >>>>> subjects' (no age included in the fsgd file, just the two groups) >>>>> mean/regional cortical thickness differs significantly from the >>>>> controls'? >>>>> In other words, is a 50 yo subject's mean/regional cortical thickness >>>>> going to be treated the same as a 80 yo subject's? >>>> Yes, just a simple two-group t-test. >>>>> 2) Now suppose that I would like to control for age. Then I'm >>>>> assuming >>>>> that I need to create an fsgd file with two Groups (One Factor/Two >>>>> Levels) >>>>> and One Covariate (age). Similarly, if I would want to visualize the >>>>> differences in the regional values of cortical thickness between the >>>>> two >>>>> groups but after they have been controlled/adjusted for age, what >>>>> contrast >>>>> matrix should I use? Normally I would use [0 0 1 -1] but this will >>>>> give >>>>> me >>>>> the significant differences in the age slopes not the mean values, >>>>> unless >>>>> I am missing something here. >>>> Correct, that will give you the difference in age/thickness slopes. >>>> You >>>> could do [1 -1 0 0] to give you the difference in intercepts. A better >>>> way, is to first look for differences in the slopes. If you do not >>>> find >>>> any, then rerun with DOSS with a contrast of [1 -1 0]. By using a >>>> DOSS, >>>> the difference in intercept is always constant regardless of age (as >>>> opposed to DODS). >>>> doug >>>>> Thanks in advance for your help and sorry for the lengthy message. >>>>> >>>>> Best, >>>>> Panos >>>>> _______________________________________________ >>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >

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WM vol as measure
by Yang, Daniel 03 Mar '14

03 Mar '14

Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I want to test the WM regions that is most strongly positively correlated with a given factor. Thanks! Daniel

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Re: [Freesurfer] Freeview crashes xterm
by Venkataraman, Archana 03 Mar '14

03 Mar '14

My apologies, I meant the X server crashes, not the xterm. Thanks. - Archana > -----Original Message----- > From: Venkataraman, Archana > Sent: Monday, March 3, 2014 1:19 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Freeview crashes xterm > > Hi, > > I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the > installation was successful and the paths are set correctly. However, my > xterm crashes when I try to launch freeview. Strangely, the program works > as expected when launched remotely via NX. Has anyone encountered this > problem before? > > Thanks. > > - Archana

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fsgd plots > 2 Class
by dgw 03 Mar '14

03 Mar '14

Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but I included the error below just in case). Should I just read in the thickness file in matlab/python and pull the data out from there (I assume it each frame is an input ordered respectively to the fsgd)? Thanks, Dan Is all of the data ingdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd Could not find XAxis tag in file. Using default one. �NggdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named marcie.nmr.mgh.harvard.edu by dwakeman Mon Mar 3 13:06:37 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

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Freeview crashes xterm
by Venkataraman, Archana 03 Mar '14

03 Mar '14

Hi, I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the installation was successful and the paths are set correctly. However, my xterm crashes when I try to launch freeview. Strangely, the program works as expected when launched remotely via NX. Has anyone encountered this problem before? Thanks. - Archana

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Re: [Freesurfer] Problematic dilated ventricles
by Victor Kovac 03 Mar '14

03 Mar '14

Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz > > then run: > > recon-all -make all -s MPS1036-1 > > you should be all set > > Bruce > > > > On Mon, 9 Dec 2013, Victor Kovac wrote: > > I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you >> for looking into MPS2002-3 -- it is quite the brain. And somehow, with all >> those morphological abnormalities, this subject has an IQ of 130. Very >> strange. >> Thanks, >> Victor >> >> >> On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> which one? I'm still messing with MPS2002-3 in my spare time >> On Mon, 9 Dec 2013, Victor Kovac wrote: >> >> Hi Bruce, >> Is there a way for you to send the subject(s) you >> analyzed to me? I know >> it's too big for email, but could you possibly >> upload it to GoogleDrive? >> >> Thanks! >> Victor >> >> >> On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> p.s. the other thing I did was run the graph >> cut skull >> stripping, which removed a bunch of extraneous >> stuff >> On Wed, 4 Dec 2013, kovac081(a)umn.edu wrote: >> >> Hey! >> >> Victor Kovac (kovac081(a)umn.edu) has uploaded >> some files >> for you at the Martinos Center FileDrop: >> >> -> MPS2002-3.zip (292.12 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=55xjt9pflsi> >> -> MPS2017-1.zip (264.15 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=ak4v31bzu4p> >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here are the two subjects with ventriculomegaly that >> are causing >> the worst issues. The worst segmentation in >> MPS2002-3 is in the >> superior frontal (slices 150-180) and parietal >> (slices 50-95) >> cortical areas; this may be due to the numerous >> dilated >> Virchow-Robin spaces in his brain, which is another >> neuropathological feature of this disease. >> >> Thanks! >> Victor >> >> Please be aware, your upload will expire on December >> 31st. If >> you'd like to download these files, feel free to use >> the link >> below: >> >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep >> >> Cheers, >> The NMR Team >> >> >> >> >> >> The information in this e-mail is intended only for >> the person to whom >> it is >> addressed. If you believe this e-mail was sent to >> you in error and the >> e-mail >> contains patient information, please contact the >> Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the >> e-mail was sent to you >> in error >> but does not contain patient information, please >> contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> >> >>

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Fw: Re: error in mri_glmfit-sim when using --bg and doss
by charujing123 03 Mar '14

03 Mar '14

Hi doug and others, I am sorry for pasting files in my first contrast directory, if it can help me desolve the question: cache.th23.abs.pdf.dat mc-z.abs.2.sig.cluster.summary mc-z.neg.3.sig.cluster.summary mc-z.pos.3.sig.cluster.summary cache.th23.abs.sig.cluster.mgh mc-z.abs.2.sig.masked.mgh mc-z.neg.3.sig.masked.mgh mc-z.pos.3.sig.masked.mgh cache.th23.abs.sig.cluster.summary mc-z.abs.2.sig.ocn.annot mc-z.neg.3.sig.ocn.annot mc-z.pos.3.sig.ocn.annot cache.th23.abs.sig.masked.mgh mc-z.abs.2.sig.ocn.mgh mc-z.neg.3.sig.ocn.mgh mc-z.pos.3.sig.ocn.mgh cache.th23.abs.sig.ocn.annot mc-z.abs.2.sig.voxel.mgh mc-z.neg.3.sig.voxel.mgh mc-z.pos.3.sig.voxel.mgh cache.th23.abs.sig.ocn.mgh mc-z.abs.3.pdf.dat mc-z.neg.3.y.ocn.dat mc-z.pos.3.y.ocn.dat cache.th23.abs.sig.voxel.mgh mc-z.abs.3.sig.cluster.mgh mc-z.neg.pdf.dat mc-z.pos.pdf.dat C.dat mc-z.abs.3.sig.cluster.summary mc-z.neg.sig.cluster.mgh mc-z.pos.sig.cluster.mgh cnr.mgh mc-z.abs.3.sig.masked.mgh mc-z.neg.sig.cluster.summary mc-z.pos.sig.cluster.summary F.mgh mc-z.abs.3.sig.ocn.annot mc-z.neg.sig.masked.mgh mc-z.pos.sig.masked.mgh gamma.mgh mc-z.abs.3.sig.ocn.mgh mc-z.neg.sig.ocn.annot mc-z.pos.sig.ocn.annot gammavar.mgh mc-z.abs.3.sig.voxel.mgh mc-z.neg.sig.ocn.mgh mc-z.pos.sig.ocn.mgh maxvox.dat mc-z.abs.3.y.ocn.dat mc-z.neg.sig.voxel.mgh mc-z.pos.sig.voxel.mgh mc-z.abs.2.pdf.dat mc-z.neg.3.pdf.dat mc-z.pos.3.pdf.dat mc-z.pos.y.ocn.dat mc-z.abs.2.sig.cluster.mgh mc-z.neg.3.sig.cluster.mgh mc-z.pos.3.sig.cluster.mgh sig.mgh Thanks. All the best. Rujing Zha 2014-02-22 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-22 10:18 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDF…, I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-21 23:49 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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How to define a new label for aparc+aseg.mgz in FreeView
by Emad Ahmadi 03 Mar '14

03 Mar '14

Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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aligning/quality of CT
by Borzello, Mia 02 Mar '14

02 Mar '14

Hi Freesurfers, In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've done a coregistration and am looking at it in tkmedit and the quality of the image isn't so good. Thanks, Mia

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