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30089 discussions

error finding data on bourget
by qtnguyen＠nmr.mgh.harvard.edu 19 Oct '12

19 Oct '12

Dear Freesurfer experts, I'm trying to run structural reconstruction for two subjects DODASD016 and DODASD017. DODASD016 was scanned last Wed Oct 10 and last week I was able to findsession DODASD016, run dcmdir-info-mgh, and run recon-all using pbsubmit. However, after this was done I was unable to unpack the Bold & DTI Data from Bourget. We believe that the recon-all didn't work and when we tried to re-run: (for DODASD016) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 (and for DODASD017) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 ...I got the error message "ERROR: finding data" Can you help me resolve this issue? Or can you direct me to someone who can help? Thank you! Trang

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local GI calculation Error
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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withe matter of cortical Lables
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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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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