Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

Re: [Freesurfer] mri_segstats error
by Douglas N Greve 16 May '11

16 May '11

And do you have write permissions? Can you touch stats/aseg.stats doug Fernanda Palhano wrote: > Yes. > > [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] > fernandapalhano% ls > aseg.stats lh.aparc.a2009s.stats lh.supramarg.stats > rh.aparc.a2009s.stats wmparc.stats > lh.aparc.a2005s.stats lh.aparc.stats > rh.aparc.a2005s.stats rh.aparc.stats > > Fernanda > > On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does the stats directory exist? > doug > > Fernanda Palhano wrote: > > Hello, > > I'm trying to use mri_segstats to obtain some subcortical > volume stats. When running the command line both in the > tutorial data or in my own data, I have the follow error: > ERROR: could not open stats/aseg.stats for writing > > [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] > fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum > stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid > 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in > mri/norm.mgz --in-intensity-name norm --in-intensity-units MR > --etiv --subject 004 > Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt > > $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats > --pv mri/norm.mgz --ctab-default --excludeid 0 > --brain-vol-from-seg --brainmask mri/brainmask.mgz --in > mri/norm.mgz --in-intensity-name norm --in-intensity-units MR > --etiv --subject 004 > sysname Darwin > hostname Fernanda-Palhanos-Mac-Pro.local > machine i386 > user fernandapalhano > atlas_icv (eTIV) = 1792580 mm^3 (det: 1.086761 ) > ERROR: could not open stats/aseg.stats for writing > > Any ideas? > > Thanks, > Fernanda > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@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> > > > > 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. > > -- 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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mri_segstats error
by Fernanda Palhano 16 May '11

16 May '11

Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3 (det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda

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two questions
by Ilana Hairston 16 May '11

16 May '11

Hi there, First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the distribution of negative and positive z values is not necessarily normal. i.e., the range of negative values maybe be 0 to -5, and the range of positive values 0 to +3. 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. 3. Is there a way to set FDR separately for positive and negative values? thanks ilana Ilana Hairston hairstonster(a)gmail.com ************************* Our ignorance is not so vast as our failure to use what we know. —M. King Hubbert, peak oil prophet

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[Major Upgrade] - iSurf Brainview 3.0.0
by Pedro Paulo de Magalhães Oliveira Junior 16 May '11

16 May '11

Today it was released the version 3.0.0 of iSurf Brainview, it's a major version release for IPad, IPhone and IPod Touch. Major New Features - Quiz for Brain structures (you can take a Quiz with 10 random questions about structure locations. The current database has more than 40 questions) - Select the brain structure by name - You have a list of available structures. Minor Changes - Visual Improvements - Memory usage improvement - Paper of Destrieux, C. - Versioning As usual suggestions and feedbacks are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… A personal note: Some residents in Radiology of our med school found the quiz challenging. I think it can be a very good tool to teach neuroanatomy in MRI --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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sliver problem with tksurfer over VNC
by Diederick Stoffers 16 May '11

16 May '11

Hi all, I am experiencing the infamous sliver problem in tksurfer over VNC. I tried solving it by installing VirtualGL, but it doesn't work, I get the following error message: [VGL] WARNING: VirtualGL attempted and failed to obtain a Pbuffer-enabled [VGL] 24-bit visual on the 3D X server :0. If the application [VGL] subsequently fails, then make sure that the 3D X server is configured [VGL] for 24-bit color and has accelerated 3D drivers installed. Window type not found! My xorg.conf shows 24 bit color depth. I am running Scientific Linux 5.4 on a Dell PE R905 with embedded ATI ES1000 video controller. It might be that the ATI ES1000 doesn't support hardware acceleration, it is a rack server. Does anybody have experience with this issue? Pointers? Cheers, Diederick

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Load normalized thickness into Matlab
by René Besseling 16 May '11

16 May '11

Dear all, I'd like to analyse some Freesurfer outputs in Matlab. I know it is possible to load ./surf/lh.thickness into Matlab using read_curv, but is it also possible to load normalized (and smoothed) thickness maps, i.e. thickness maps registered to fsaverage, for vertex-wise comparison? I thought these normalized maps would be called something like ./surf/lh.curv.fwhm10.fsaverage, but I only find files like ./surf/lh.curv.fwhm10.fsaverage.mgh (note the .mgh extension) which dont work with read_curv. Am I missing something? Best regards, René

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Re: [Freesurfer] discrepancy between p-values computed from t.nii and those stored in sig.nii
by Pablo Polosecki 16 May '11

16 May '11

Hi Doug, I know I'm reviving an old question. It seems to me that the variance of the errors estimated the way you are proposing below (i.e. using the residuals provided by selxavg3-sess) is biased in the sense that the residuals are not whitened (i.e. they are not independent becasue there is a temporal correlation), and that I could make an incorrect inference because of that. Am I right? If so, could you perhaps suggest a way of correcting for that? Thank you very much, Pablo On Fri, Nov 12, 2010 at 11:03 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > wrote: > > The residuals are not saved by default, but you can tell selxavg3-sess to > save them by adding the -svres flag. By variance I mean the temporal > variance of the mean waveform of the residuals. The t that you want is given > by: > > t = ces/sqrt(rvar * C'*inv(X'*X)*C) > > where ces is the average ces over the ROI, the rvar is the variance > described above, X is the design matrix, and C is the contrast matrix. Both > of these are in the X.mat matrix. > > doug > > Pablo Polosecki wrote: > >> Oh, thank you. I am a little bit lost now. Could you clarify a little bit >> more for me? Could you tell where the residuals are stored? >> By variance of the residuals you mean variance across voxels in the ROI? >> What is the efficiency of the contrast? >> >> >> On Thu, Nov 11, 2010 at 12:15 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> That's actually not the right way to do it either. You need to get >> the residuals for the ROI, average the residuals, compute the >> variance of the average residual. Then divide this by the >> efficiency for the contrast, then take the sqrt() of this number. >> This is the standard error of the ces. Then compute the average >> ces over the ROI. The t is then the average ces/standard error. >> >> doug >> >> Pablo Polosecki wrote: >> >> Well, that is bad (beacuse there is a bug) and good (because >> now it is known) at the same time. >> I wanted to estimate a p-value for a group of voxels of >> interest for a certain contrast in my analysis. Instead of >> averaging the p values for these voxels, I thought it would >> make more sense to calculate the average t statistic for the >> voxels and then estimate the p-value for the group of voxels >> myself using tcdf function in matlab. So, I guess I need the t >> values for that, unless I can think of a workaround, which so >> far I couldn't. >> Best, >> Pablo >> >> On Thu, Nov 11, 2010 at 11:57 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> Hi Pablo, you have found a bug in FSFAST in which the values in >> the t.nii file are actually the sqrt of the p-values. I >> have fixed >> it in our code base and it will be in the next version. Do you >> actually need the t-values? >> >> thanks! >> >> doug >> >> Pablo Polosecki wrote: >> >> I understand the X.mat contains the variable DOF which >> tells >> me the degrees of freedom for the analysis, right? In >> my case >> it is 5915. This is what I get when I load X.mat into a >> structure named 'x': >> >> x = >> >> DoSynth: 0 >> UseFloat: 0 >> SynthSeed: -1 >> flac0: [1x1 struct] >> runflac: [1x21 struct] >> X: [6048x133 double] >> DOF: 5915 >> rfm: [1x1 struct] >> yrun_randn: [] >> RescaleFactor: 5.6510 >> ErrCovMtx: 0 >> acfseg: [1x1 struct] >> acfsegmn: [6048x1 double] >> nrho1segmn: 0.1456 >> W: [6048x6048 double] >> >> >> >> On Thu, Nov 11, 2010 at 11:35 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: >> >> what is your dof? >> >> Pablo Polosecki wrote: >> >> Oh, sure. It is: >> >> >> t.vol(test_voxel_number) >> >> ans = >> >> -0.6368 >> >> >> On Thu, Nov 11, 2010 at 10:25 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: >> >> sorry, I meant what is the actual value of >> the t in >> t.vol(test_voxel_number)? >> >> Pablo Polosecki wrote: >> >> Firstly, thank you for the quickyresponse. >> >> t.vol is the t-volume, loaded from t.nii >> using >> the MRIread >> function (i.e. t=MRIread('t.nii');). >> test_voxel_number >> is just >> some voxel of the volume that I'm using as an >> example >> in this >> sanity check (I set it to 4000 in the sample >> code but it >> could have been anything else). I'm using >> -(abs(t.vol(test_voxel_number) >> )) because that is how I think the p-value is >> calculated from >> the t-statistic is a 2 tailed test. (See for >> instance the >> matlab code of the built-in ttest.m function >> where you >> have p >> = 2 * tcdf(-abs(tval), df) with df being the >> degrees of >> freedom.) Still if I used the >> alternative you >> sugggest, >> without the minus sign, I get: >> >> >> my_pval=-log10(2*tcdf((abs(t.vol(test_voxel_number))), >> x.DOF)) >> >> my_pval = >> >> -0.1690 >> >> While I still have the stored p-value of >> >> stored_pval = >> >> -0.4055 >> >> >> Thanks again! >> On Thu, Nov 11, 2010 at 10:02 AM, >> Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: >> >> what is t.vol(test_voxel_number)? Why >> do you use >> -(abs(t.vol(test_voxel_number))) >> instead of >> +(abs(t.vol(test_voxel_number)))? >> >> doug >> >> Pablo Polosecki wrote: >> >> Dear experts, >> >> For different reasons I found >> myself double >> checking the >> relationship between t-values in t.nii >> and p-values >> stored in >> sig.nii. If I use the following >> matlab code I >> thought >> that I >> should get the values of my_pval and >> stored_pval >> to be the >> same (except perhaps for the sign): >> >> >> cd(fullfile(basedir,session,'bold',anal,contrast)) >> x=load('../X.mat') >> t=MRIread('t.nii'); >> sig=MRIread('sig.nii'); >> test_voxel_number=4000; >> >> my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))), >> x.DOF)) >> stored_pval=sig.vol(test_voxel_number) >> >> >> >> However I get: >> stored_pval = >> >> -0.4055 >> >> my_pval = >> >> 0.2804 >> >> Am I doing something wrong here? My >> FreeSurfer >> version >> is 4.5 >> Thank you! >> >> -- Pablo Polosecki >> Graduate Fellow >> Laboratory of Neural Systems >> The Rockefeller University >> 1230 York Avenue, Box 9 >> New York, NY 10065 >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >> <mailto: >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@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 >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@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> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> < >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> < >> http://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> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> 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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@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> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> < >> http://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> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@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> >> <http://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> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@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> >> <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> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@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> >> >> >> > -- > 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 > >

2 1

mri_surfcluster and the color table
by Elisa Golfinopoulos 16 May '11

16 May '11

Hi, I am trying to use an annotation file that was created from a parcellation scheme developed in my lab with mri_surfcluster. However, it's unclear to me how I can set the corresponding color table for this annotation file either locally or globally. mri_surfcluster doesn't seem to have a --ctab or --colortable argument. Is there a way to set the color table as an environment variable and would this be an appropriate workaround or is it the case that the color table is a fixed setting for mri_surfcluster? Your help is greatly appreciated. Cheers, Elisa -- Elisa Golfinopoulos Speech Laboratory Cognitive and Neural Systems Boston University Phone: 617.353.6181

2 3

visualization after cluster correction
by Jacobs H (NP) 16 May '11

16 May '11

Hi FreeSurfers, This is more a visualization question. I did the cortical thickness analyses on my data and compared my two groups statistically. After that I ran the mri_glmfit-sim to correct for multiple comparisons using the cluster correction. When I visualize the results, each cluster has its own color. However, I would like to present the original sig.mgh file (where each vertex has received a significance value according to the color table) minus the clusters that did not survive the correction. How should I do that? Thank you very much! Best regards Heidi [cid:327214308@11052011-0AC8] Heidi Jacobs, MSc. PhD student Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Alzheimer Center Limburg Division Cognitive Neuropsychiatry and Clinical Neurosciences h.jacobs(a)maastrichtuniversity.nl <mailto:h.jacobs@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 Note: the email addresses have changed! [cid:327214308@11052011-0ACF] Please consider your environmental responsibility before printing this e-mail.

3 2

.mgh to .label ??
by Ritobrato Datta 16 May '11

16 May '11

Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri

2 1

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Freesurfer May 2011