Freesurfer

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30132 discussions

visualize defects using tkmedit
by Benjamin Kay 18 Oct '12

18 Oct '12

It is possible to visualize topological defects in tksurfer by loading the curvature from surf/?h.defect_labels. Is there any way to visualize these defects in tkmedit? I am having trouble seeing how the defects are related to wm.mgz, etc., in tksurfer, and it would be very helpful if there were a way to see the defects in tkmedit.

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Re: [Freesurfer] Mixed-effects models for longitudinal data analysis in Freesurfer
by Douglas N Greve 18 Oct '12

18 Oct '12

Is training a within subject factor or between? If between, then you can do it as a two group design as I described in a post yesterday. doug On 10/17/2012 08:04 PM, Harry Hallock [hhal5293(a)uni.sydney.edu.au] wrote: > Hi Doug, > > Is it possible to add an extra factor to this repeated measures fsgd format, such as training and non-training. As ideally we are also trying to find interactions between groups and time. > > Cheers, > Harry > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, 17 October 2012 4:29 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mixed-effects models for longitudinal data analysis in Freesurfer > > If you want to do a repeated measures ANOVA with more than two time > points, I've put a page together here: > > http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > > doug > > > On 10/15/2012 08:24 PM, Harry Hallock [hhal5293(a)uni.sydney.edu.au] wrote: >> Hi Martin, >> >> If you could make available that lme toolbox link, that would be great! >> Thanks for the help. >> >> Cheers, >> Harry >> ------------------------------------------------------------------------ >> *From:* jorge luis [jbernal0019(a)yahoo.es] >> *Sent:* Tuesday, 16 October 2012 8:16 AM >> *To:* Martin Reuter; Harry Hallock [hhal5293(a)uni.sydney.edu.au] >> *Cc:* freesurfer(a)nmr.mgh.harvard.edu >> *Subject:* Mixed-effects models for longitudinal data analysis in >> Freesurfer >> >> Hi Harry >> >> As Martin said, longitudinal linear mixed-effects models (lme) are the >> recommended tool for analyzing longitudinal data obtained from the >> Freesurfer longitudinal image processing pipeline. The increase in >> power can be dramatic. Coming up there is a paper about this subject. >> We are working on making our lme tools available and easy to use but >> in the mean time, if you are interested, I can make available a link >> for you to download our Matlab-based lme toolbox. >> >> Best >> -Jorge >> >> >> ------------------------------------------------------------------------ >> *De:* Martin Reuter<mreuter(a)nmr.mgh.harvard.edu> >> *Para:* Harry Hallock<hhal5293(a)uni.sydney.edu.au>; Douglas N >> Greve<greve(a)nmr.mgh.harvard.edu>; >> "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> >> *Enviado:* Domingo 14 de octubre de 2012 21:06 >> *Asunto:* Re: [Freesurfer] 3 Factor glm group analysis >> >> Hi Harry. >> >> I have some scripts to compute a slope into the time thickness or >> volume (linear fits) and then run a standard glm on that . >> >> However, we recommend to run a linear mixed effects model >> (external software). We are working on making that available. >> >> Best Martin >> >> Harry Hallock<hhal5293(a)uni.sydney.edu.au> wrote: >> >> Thanks Doug! >> >> If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction? >> >> Harry >> ------------------------------------------------------------------------ >> >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, 10 October 2012 1:10 AM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] 3 Factor glm group analysis >> >> Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 >> group analysis (search for "paired" on our wiki). >> doug >> >> >> >> On 10/09/2012 12:45 AM, hhal5293(a)uni.sydney.edu.au wrote: >> >> Hello, We are currently doing a longitudinal Group >> Analysis using FreeSurfer, and were wondering if there is >> a way to run a 3 factor design (time is 2 levels, group is >> 2 levels, subject is 10 levels) using the mri_glmfit >> model, as i want to test the time by group interaction? Is >> there a way of writing this model in an FSDG file? If we >> can't do this using mri_glmfit, is it possible to do this >> using QDEC? Regards, Harry >> ------------------------------------------------------------------------ >> 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> ------------------------------------------------------------------------ >> >> 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. >> >> >> >> >> ------------------------------------------------------------------------ >> >> Freesurfer >> mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> -- >> Sent from my phone, please excuse brevity. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. >> >> >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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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Repeated measures ANOVA fsgd file
by Caroline Jiang 17 Oct '12

17 Oct '12

Hi, I'm trying to set up my fsgd file for repeated measures ANOVA with two groups and 6 time points (0, 1, 2, 3, 4, 5) by following the example from here: http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova Does this look correct for the fsgd file? Subject 2 is missing time points 2 and 5. GroupDescriptorFile 1 Title RepeatedMeasures Class Group1 Class Group2 Variables TP0-vs-TP1 TP0-vs-TP2 TP0-vs-TP3 TP0-vs-TP4 TP0-vs-TP5 Input subject1_tp0 Group1 1 1 1 1 1 Input subject1_tp1 Group1 -1 0 0 0 0 Input subject1_tp2 Group1 0 -1 0 0 0 Input subject1_tp3 Group1 0 0 -1 0 0 Input subject1_tp4 Group1 0 0 0 -1 0 Input subject1_tp5 Group1 0 0 0 0 -1 Input subject2_tp0 Group1 1 1 1 1 1 Input subject2_tp1 Group1 -1 0 0 0 0 Input subject2_tp3 Group1 0 0 -1 0 0 Input subject2_tp4 Group1 0 0 0 -1 0 Input subject3_tp0 Group2 1 1 1 1 1 Input subject3_tp1 Group2 -1 0 0 0 0 Input subject3_tp2 Group2 0 -1 0 0 0 Input subject3_tp3 Group2 0 0 -1 0 0 Input subject3_tp4 Group2 0 0 0 -1 0 Input subject3_tp5 Group2 0 0 0 0 -1 I'm interested in the overall group effect [1 -1 0 0 0 0 0 ], overall time effect, and group-x-time interaction. Is this the correct contrast for the overall time effect? 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 What would be the contrast for group-x-time interaction? Thanks! Caroline

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calculate percent from two different mgh files
by Knut J Bjuland 17 Oct '12

17 Oct '12

How can I dived a gamma.mgh with another gamma.mgh to get new mgh structure? Is there any Freesurfer Matlab function that I should use. I am able to use Matlab to calculate the difference for vol. n=size(gamm.vol(2)) for i=1:n; test=gamma.mgh.vol(i)/gamma.mgh(i) end I am trying to follow this howto at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html. Knut J

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topology fixer removes connected white matter
by Benjamin Kay 17 Oct '12

17 Oct '12

I'm puzzling over why freesurfer is not including a chunk of white matter in the final surface and how I can fix it. The culprit appears to be the topology fixer. If you look at the attached screenshots, you can see that the offending bit of left frontal lobe is well-connected to the rest of the brain in wm.mgz (and, for completeness, filled.mgz). The yellow surface, which corresponds to lh.smoothwm.nofix, includes the desired white matter. Thus, neither tessellation nor smoothing would seem to be the problem. The green (white matter) and red (pial) surfaces from lh.orig exclude the desired white matter. Thus, I'm assuming the topology fixer is cutting off what it perceives to be a defect... but I can't figure out why or how to fix it. Although I will try, I do not expect that filling in the few missing white matter voxels or adding control points in that region will have any effect. Any other ideas?

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Editing Pial Surface
by Jonathan Holt 17 Oct '12

17 Oct '12

I'm wondering about how to best approach two similar problems with pial surfaces. In one case I'd like to extend it and in the other I'd like to reduce it (for lack of a better term) These first two images are from a brain in which I'd like to extend the surface. http://i.imgur.com/ziDQd.png http://i.imgur.com/i0sX3.png In this case focus on the bottom left and right corners of the cortex. You can see, especially in the second image (with aseg.mgz loaded), the pial surface cuts off part of the cortex on both sides. Interestingly, the pial surface seems to adhere to the aparc.mgz file, which is loaded and pretty clear in the first image, where the left out parts of the cortex are just labelled as 'none'. http://i.imgur.com/aUKiG.png http://i.imgur.com/4BRwv.png In the second case I want to edit the pial surface so it follows that gyrus toward the midline in the left hemisphere. In this case I've tried control points, specifically along the gyrus, and autorecon2-cp. I also tried to edit the parcellation along the gyrus for several slides followed by autorecon2 & 3. This didn't help anything, so I'm a bit stuck. You can see this brain follows the same trend as the last in which the pial surface follows the aparc.mgz, and the aseg.mgz seems more or less correct. Thanks and any help would be awesome! jon

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Talairach Failure Detection
by Daniel Ferreira 17 Oct '12

17 Oct '12

Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file. 2) Anyway, I tried also -notal-check to see if something changed in spite Talairach failed, but it fails also (off course). 3) I used -use-mritotal but I still get the same. However, this time processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck. Please, any idea? Thanks a lot Daniel #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/subjects/N001511_d2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Changes to Sub-cortical Structures after adding WM control points
by Mark Fletcher 17 Oct '12

17 Oct '12

Dear FreeSurfers, After adding WMCP to a number of my subjects (which corrected the problem), I retrieved to cortical and subcortical volumes from my subjects using the "aparcstats2table". I had used "aparcstats2table" before and after adding the control points. Accurately, the regions I wanted to change, did change in volume. However, the subcortical volumes post WMCP changed a lot as well? Some regions changed more than 20% after adding WMCP to other regions? Is this normal? Should I go with the original "subcortical" segmentation volumes, or the new ones? Is this part of the known bug in version 5.1.0 mentioned in the release notes about "running recon-all" a second time? Please advise? Sincerely , Mark Fletcher

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Supratentorial volume vs brain segmentation volume
by Kwan, Justin 17 Oct '12

17 Oct '12

Dear Freesurfer experts, What is the difference between the supratentorial volume and brain segmentation volume? Does the supratentorial volume include CSF and ventricle volume? Thank you very much for your help. Best, Justin Justin Kwan, MD Assistant Professor Department of Neurology University of Maryland School of Medicine 110 South Paca Street, 3rd Floor Baltimore, MD 21201

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Functional labels from freesurfer
by ffmpeg ffmpeg 17 Oct '12

17 Oct '12

Hello! I was told that Freesurfer should generate labels for functional areas of the brain (for example, visual zones - V1, V2, etc.) when doing reconstruction (recon-all -autorecon-all). But the the label/ directory in output contains only these files: aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label which contain only anatomical labels. What could be wrong? If freesurfer does not generate those labels, is there some way to obtain them? (Obviously, I could create such labels by hand, but the result would be probably messy and imprecise.) Best wishes, Platon Pronko

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