Freesurfer March 2014

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Hippocampus segmented file in tkmedit.
by Saurabh Thakur 04 Mar '14

04 Mar '14

How to create only Hippocampus segmented file in tkmedit. aseg.mgz. for Hippocampus file. Please cheers Saurabh Thakur,

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shrink the white matter surface
by charujing123 04 Mar '14

04 Mar '14

Hi all, I got a thin pial thickness when I got a default recon-all -all, which can be got in the attachment. Now I want to get a appropriate result by shrinking the whiter susface. Would you please tell me what option I should add when I run "recon-all -s subject -all -??" Thanks. All the best. Rujing Zha 2014-03-04 charujing123

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How to create a figure for a scientific article
by charles laidi 03 Mar '14

03 Mar '14

Dear Freesurfers, I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2 I would like to create a figure for my article. However, I'm not able to find a way to highlight only cerebellar cortex / white matter with freeview, instead of having every label of other subcortical structures in different colors. I would like to have only the cerebellum colored. Could this be done with freeview ? Thanks a lot, Charles

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Re: [Freesurfer] hippocampal subfields
by Gregory Kirk 03 Mar '14

03 Mar '14

Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: > Dear Gabor, > the segmentation benefits to some extent from higher resolution data, > but produces decent estimates of the subfields at 1x1x1. We are working > on a new atlas that will incorporate much more detail, and will more > effectively take advantage of high-resolution images. > Kind regards, > Juan Eugenio Iglesias > > On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: > > Dear all, > > > > > > 1. Which is the suggested resolution for hippocampal subfields > > segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 > > and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields > > segmentation really work with 1.0*1.0*1.0 resolution? > > 2. The article "Automated Segmentation of Hippocampal Subfields from > > Ultra-High Resolution In Vivo MRI." suggested on Freesurfer's page > > uses FOV=448. We are unable to set up the matrix to achieve 0.38mm > > resolution using this FOV. Is there any other suggested article to set > > up our measurements? > > > > Thanks, > > > > -- > > Gabor Perlaki > > > > _______________________________________________ > > 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 > > > 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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hippocampal subfields
by Gabor Perlaki 03 Mar '14

03 Mar '14

Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article "Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI<https://surfer.nmr.mgh.harvard.edu/pub/articles/VanLeemputHippocampus2009.p…>." suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki

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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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Freesurfer March 2014