Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

2 1

[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

1 0

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

1 0

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

3 2

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

surfsace of specific broadman's area
by Oya, Hiroyuki (UI Health Care) 15 May '11

15 May '11

Dear all, I like to create a surface rendering restricted to some area (selected from aparc.annot.a2009s.ctab files)? Any suggestion would be appreciated. Best, Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

1 0

creating roi
by 李俏俊 13 May '11

13 May '11

dear all, i want to get ROI in the naive space (for example STG) using freesurfer,i check the email list and find that command mri_extract_label may help, so i try it as follow, mri_extract_label aparc+aseg.mgz 1030 outli.mgz but i do not get the ROI i expect. do anyone know how can i get the ROI in naive space ？by other commands?by other software? many thanks~ qjli -- best wishes -------------------------------------------------- CCM计算医学中心 www.ccm.org.cn 中国科学院自动化研究所 Institute of Automation, Chinese Academy of Sciences --------------------------------------------------

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer