Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

error while compiling utils
by Kim, Daniel 19 Oct '12

19 Oct '12

Hi Freesurfer users, I'm trying to compile utils on my Ubuntu 10.04 64 bit machine and I am getting a considerable amount of error while compiling afni.c - I am using gcc-4.4.3, g++-4.4.3 for compilers - I have successfully installed VXL and MNI as per the developer's guide (I am not building any GUI apps) - Had to add "-I/usr/src/linux-headers-2.6.32-43/include" under CFLAGS in utils/Makefile since without it, it would spit out error message saying it cannot find <linux/compiler.h> - under the utils folder, "make" gives an error along the lines of "expected specifier-qualifier-list before ‘size_t’" (attaching error log file) - tried using older compiler gcc-3.3, g++3.3 but problems seems worse I'm a bit stuck here and hoping that someone has had experience similar to this who can lend me some help? Thanks very much! cheers Danny Kim Children's Brain Mapping Centre BC Children's Hospital

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Cortical thickness percent difference surface maps script in matlab feedback wanted.
by Knut J Bjuland 18 Oct '12

18 Oct '12

Dear Freesurfer expert I have produce a script to make percent difference in cortical thickens using information from the mailing list. Could you please take look if this script is correct, or if there is a better way to do it? function [ out ] = diff_map( difference, average ) %percent difference Summary of this function goes here % This function takes two gamma.mgh from group differences 1 -1 and divide % with gamma.mgh from 0.5 0.5 to produce a new mgh with percent % difference between two groups. % Copyright Knut Jørgen Bjuland <knutjbj(a)hotmail.com> % Freesurfer license mat=fast_vol2mat(difference.vol); n=size(mat); for i=1:n(2), mat(i)=difference.vol(i)*100/average.vol(i); end out=difference; out.vol=fast_mat2vol(mat,out.volsize); end

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downsampling surface in native space
by Franz Liem 18 Oct '12

18 Oct '12

Dear FS experts, I would like to downsample a subject's white surface to arrive with a smaller number of vertices in order to feed the surface into FSL's surface tracking. I tried to map the fsaverage6 onto the single subject: mri_surf2surf --hemi lh --srcsubject fsaverage6 --sval-xyz white --trgsubject s01 --trgsurfval white.ico6 --tval-xyz --trgicoorder 6 If I load it into tksurfer, the surface now looks (as expected) much coarser. However, the number of vertices is still ~ 130k. Furthermore, it would be great if vertex x would spatially correspond in all subjects. Any advice is much appreciated, Cheers, Franz

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Cortical thickness percent difference surface maps howto
by Knut J Bjuland 18 Oct '12

18 Oct '12

Hi Is it possible to generate surface maps for the percent difference in cortical thickness between 2 groups within with Freesurfer 5.1? Could you please give link to how to use Matlab to compute the differences as described in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html? Cheers Knut J

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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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Freesurfer October 2012