Re: [Freesurfer] Question about LME modle

Hi Lanbo lme_lowessPlot shows a time plot of the lowess regression curve for each group in your study (two groups in this case). The curve for each group is a smooth estimate of the trend in the mean response over time for that group. This is only used for visualization purposes and can help

Re: [Freesurfer] lme_mass_RgGrow problem

The spatiotemporal lme model is more advanced than the traditional vertex-wise lme but it's also more difficult to setup with the current scripts. So I'd suggest you simply use the easier traditional vertex-wise lme:1-Read your label eg.: lhcortex =

Re: [Freesurfer] LME: contrast questions

and time). Time squared, if considered, would be just a fixed effect. Best-Jorge De: Jordi Pegueroles <jo...@pegueroles.cat> Para: jorge luis <jbernal0...@yahoo.es> CC: Freesurfer <freesurfer@nmr.mgh.harvard.edu> Enviado: Lunes 28 de noviembre de 2016 11:34 Asunto:

Re: [Freesurfer] LME: contrast questions

Hi Jordi You have implicitlyincluded the reference group in your statistical model by includingan intercept term and a time variable: group0 intercept: ß1group0 time: ß2group1 intercept:ß1+ß3group1 time: ß2+ß4group2 intercept:ß1+ß5group2 time: ß2+ß6 >From here you canquickly see that your

Re: [Freesurfer] LME for functional data, 3 factors

interests. Best-Jorge De: Laura Rueda Delgado <laura.ruedadelg...@kuleuven.be> Para: jorge luis <jbernal0...@yahoo.es>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 14 de abril de 2016 11:23 Asunto: Re: [Freesurfer] LME fo

Re: [Freesurfer] Extract random effects (LME) for correlation

Hi Joseph Not sure what youare trying to accomplish but if the beta coefficient for the timevariable is significant then that means that the slope of change overtime is significantly different from zero. Anyway, I think you canestimate subject-specific slopes using lme_mass_rfx which has as

Re: [Freesurfer] LME for functional data, 3 factors

Hi Laura In the wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModelswe recommended to order the columns of the design matrix in thefollowing way: Column 1: theintercept term (which is a column of ones) Colum 2: the timecovariate if it varies across subjects (eg. time from

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo Yes, too many locations at which the estimation algorithm didn't converge is problematic. That might mean that having two random effects is not appropriate for your data. You should try to run the command with just a single random effect for the intercept term: lhstats =

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo The error you are getting is because in your Matlab setup you can only request a maximum of 4 matlab parallel workers and by default lme requests 8. So you just need to modify your command like this: lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4); Please make sure that

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

Hi Matthieu The easiest for you is to follow these steps: 1-Read your label eg.: lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');  2-Read the data file eg.: [lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); 3-Fit a vertex-wise lme model with random effects for the

Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?

I would say that you can do that only if your data is continous (preferably close to normally distributed). Binary data or any non-continous data requires a different approach (eg. Generalized Estimating Equations). Best-Jorge De: Martin Reuter Para:

Re: [Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (LME) Models

Please change the subject of your message to "Problem installing installing Freesurfer on Mac ". -Jorge De: pablo najt Para: "freesurfer@nmr.mgh.harvard.edu" Enviado: Miércoles 16 de septiembre de 2015 3:32 Asunto: [Freesurfer]

Re: [Freesurfer] A mixed effect model approach in within subject dataset

Hi Pablo I think you can useLME to analyze your data by ordering the rows of your design matrixappropriately. You can consider all subjects belonging to the samefamily as if they were a single subject in a longitudinal analysis.You can put in your design matrix all subjects belonging to

Re: [Freesurfer] lme_realizedPower

Hi Fabio I think (I'mnot a dedicated statistician) you cannotconclude to any extent that the cortical thickness in the two groupsis the same. You can only say that there wasn't enough evidence ofdifferences between the two groups in terms of your measurements. I don't understandwhat you mean

Re: [Freesurfer] advice/question regarding your LME toolbox for freesurfer

Hi Sara For those analysis Iwent through the following steps: First considered afull model for both the mean and the covariance and selected the bestmodel for the covariance: 1- Fitted a fullmodel (model1) including intercept, time and time squared as bothfixed effects and random effects.2-

Re: [Freesurfer] Fw: longitudinal statistics LGI

: Freesurfer support list freesurfer@nmr.mgh.harvard.edu CC: jorge luis jbernal0...@yahoo.es Enviado: Jueves 26 de marzo de 2015 10:50 Asunto: Re: [Freesurfer] Fw: longitudinal statistics LGI Hi Jorge, I have read the previous posts and applied it for my analysis which is longitudinal study go

Re: [Freesurfer] lme_mass_RgGrow

Hi Jordan Regions produced bylme_mass_RgGrow are not directly related to how the mean responsechange over time. The command just attempts to discover regions ofvertices with very similar lme covariance parameter estimates. Thenwe assume the underlying temporal covariance matrix is the

Re: [Freesurfer] longitudinal statistics LGI

(lhstats_winner, CM); 5-Saveresults eg.: fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); -Jorge De: Jon Alan Wieser wie...@uwm.edu Para: jorge luis jbernal0...@yahoo.es; Freesurfer support list freesurfer@nmr.mgh.harvard.edu CC: Krista Lisdahl Medina krista.med...@gmail.com

Re: [Freesurfer] Fwd: comparing lme models

effects then you can perform statistical inferences (F-test)to determine whether your age^2 term is significant. If notsignificant you can drop it from the model. -Jorge De: Lars M. Rimol lari...@gmail.com Para: FS maling list freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal Rusiel

Re: [Freesurfer] longitudinal statistics LGI

p { margin-bottom: 0.1in; line-height: 120%; }Hi Jon I guess that whenyou say “we have continuous data as to the amount of drug usage”you actually mean that the amount-of-drug-usage is a continuousvariable that changes over time for each subject. So yes you can keepthis variable as a

Re: [Freesurfer] LME Models

Hi Karishma The Matlab LME toolbox is only intended for univariate and mass-univariate analyses and not for multivariate analysis. However the recently developed spatiotemporal model can be modified to work with multivariate data (instead of regions of voxels there will be multiple variables

Re: [Freesurfer] longitudinal analysis and linear mixed effects models

Hi Emma As Martin said not having a control group (or placebo group in which subjects don't receive any treatment) is not a good study design. In your case you will need to use LME because it looks like you are expecting some sort of non-linear change for the mean response over time

Re: [Freesurfer] how to choose the best random effect in LME models

Hi Fabio If you want to compare a lme model including only a single random effect for the intercept term against the same model but including only a single random effect for the slope term all you need to do is to choose the one with higher maximum likelihood after model fitting. However if

Re: [Freesurfer] LME Longitudinal QDEC Table

Hi Elijah This is  happening because the columns of your Qdec table file are separated by tabs or something else. You need to use simple spaces instead or properly modify fReadQdec to support tabs. This is something I need to fix on github: https://github.com/NeuroStats Best -Jorge

Re: [Freesurfer] Patch that adds parapool support to lme_mass_F, lme_mass_fit_EMinit, lme_mass_fit, lme_mass_fit_init. lme_mass_fit_Rgw

Hi Knut Thank you very much for your contribution. I'll take a look at it and apply the patches as soon as I have  time (probably next weekend) on github: https://github.com/NeuroStats Best -Jorge De: Knut J Bjuland knut.j.bjul...@ntnu.no Para: jorge luis

Re: [Freesurfer] LME Longitudinal QDEC Table

'); Best -Jorge De: Elijah Mak fk...@medschl.cam.ac.uk Para: jorge luis jbernal0...@yahoo.es CC: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Lunes 14 de julio de 2014 9:35 Asunto: Re: [Freesurfer] LME Longitudinal QDEC Table Hi Jorge, Many

Re: [Freesurfer] LME Longitudinal QDEC Table

Sorry, you need to do: M = Qdec(2:end,:); Best -Jorge De: jorge luis jbernal0...@yahoo.es Para: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Lunes 14 de julio de 2014 10:06 Asunto: Re: [Freesurfer] LME Longitudinal QDEC Table Hi

Re: [Freesurfer] freesurfer lme matlab tools

Hi  Melinda The eleventh column age should be age-at-baseline so it's a time-independent covariate. If you have only two time-points then you should use the vertex-wise lme model with a single random effect for the intercept term: 1-Read your label eg.: lhcortex =

Re: [Freesurfer] Linear Mixed Models in FS?

fix this issue on github:https://github.com/NeuroStats this weekend. Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: jorge luis jbernal0...@yahoo.es CC: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 19 de junio de 2014 5:01 Asunto

Re: [Freesurfer] Linear Mixed Models in FS?

Hi LMR If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main

Re: [Freesurfer] Linear Mixed Models in FS‏

: Lars M. Rimol lmr1...@hotmail.com Para: jorge luis jbernal0...@yahoo.es CC: Ørjan Bergmann orjan.bergm...@gmail.com Enviado: Lunes 16 de junio de 2014 8:25 Asunto: RE: Linear Mixed Models in FS‏ Hi Jorge, I have a couple of questions which I hope you can assist us with. We have run some

Re: [Freesurfer] LME Matlab toolbox

Hi Victor As explained in the wikifs_read_surf.m andfs_read_Y.m depend on Freesurfer's scripts so you need to have installed Freesurfer software package and included the Freesurfer's matlab subdirectory in your Matlab's search path. Best -Jorge El Martes 13 de Mayo de 2014 4:40, Victor

[Freesurfer] lme and survival (time-to-event) analysis tools on github

Hi everyone Just wanted to point out that all the technology required to implement the statistical methods used in our last paper: Event time analysis of longitudinal neuroimage data. Neuroimage. doi: 10.1016/j.neuroimage.2014.04.015. is available on github: https://github.com/NeuroStats I

Re: [Freesurfer] per voxel regressor in LME toolbox?

The lme toolbox allows you to have different regression models across locations. If there is a missed data value at some location (vertex/voxel) for a given time-point for a given subject then you can exclude the corresponding row of the full design matrix at that location using the parameter

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure (lme_mass_FDR2): Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006).

Re: [Freesurfer] LME advice

Hi Eric   I don’t see any fundamental problem with this analysis. It looks like a regular lme computation. The p-value is essentially zero (to the extent of numeric precision). Even under the null hypothesis p-values distribute uniform(0,1). When signal is present in the data the distribution of

Re: [Freesurfer] comparing models

Hi Eric The longitudinal lme model is no different from cross-sectional models when it comes to testing the significance of a covariate. You just simply use an F-test with the contrast [0 0 0 0 0 1] to test the last covariate in the first model. You can then drop the last covariate if the test

Re: [Freesurfer] Linear Mixed Effects Models

Hi Eric The meaning of the variable ni is explained in the header of each script that have it either as an input or output. But you can also download the sample data from the wiki page (ftp://surfer.nmr.mgh.harvard.edu/pub/data/long_mixed_effects_tools-data.tar.gz)  where you will find instances

Re: [Freesurfer] LME model

Hi Sean An important issue in the LME model concerns the centering of the times of measurement. It changes the interpretation of both the mean response and the variance of the random effects. If tij represents time since baseline then the subject-specific intercept coefficient ß1+b1i 

Re: [Freesurfer] Fwd: Problems with longitudinal analysis

Hi Knut There are a few confusing things in your question post. First, it seems that your attached images are depicting p-values. We usually use -log10(pvalue) format for visualization in tksurfer. The sig.mgh file saved by lme should be in that format. However we didn't use tksurfer to build

Re: [Freesurfer] To believe non-convergence?

Hi Sean I'm not sure what is going on. Can you please run the simpler univariate analysis at some random locations? Eg. At location 1000 of your mask (assuming you have to random effects for intercept and time): [stats, st]= lme_fit_FS(X, [1 2], Y(:, mask(1000)), ni); If your mask is

Re: [Freesurfer] To believe non-convergence?

that  lme_mass_fit_vw ran for. Many thanks, Seán On 4 December 2013 18:22, jorge luis jbernal0...@yahoo.es wrote: Hi Sean I'm not sure what is going on. Can you please run the simpler univariate analysis at some random locations? Eg. At location 1000 of your mask (assuming you have to random effects

Re: [Freesurfer] To believe non-convergence?

You are correct. Buena suerte! :-) -Jorge Sent from Yahoo Mail on Android ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

[Freesurfer] Rv: Fwd: Re: LME Guide + Developer Build

Hi Vivian The error you are getting means that the number of elements of your contrast vector is not the same as the number of columns of your design matrix. I think you're trying to apply the contrast matrix shown in the wiki page example to the sample dataset that we distribute with lme.

Re: [Freesurfer] Problems with LME-Setup

I think it is CM.C = [0 1 0 0]  if you want to test if the slope is significantly different from 0. I also would say that for a dataset with only two time points the results of lme will not probably be very different from what you already got from mri_glmfit. lme is designed for more complex

Re: [Freesurfer] LME toolbox for VBM-style data?

Hi Sean If you can load the 3D VBM data into Matlab as a matrix Y(nm x nv, nm total number of VBM maps and nv total number of voxels) then you can use lme_mass_fit_vw to fit a voxel-wise lme model (the region-wise approach is not yet implemented for euclidean 3D data). You should ask to the

Re: [Freesurfer] lme issues + failure to converge

Hi Cathy If you only have three groups in your data (Control subjects, High risk patients, Ill patients) then you should drop the “Controls versus all others and controls*time interaction” terms from your design matrix. Otherwise it is ill-conditioned. One way to check your design matrix is

Re: [Freesurfer] Centos vs. Ubuntu

For a workstation machine I prefer Ubuntu rather than Centos. There are available drivers for graphic cards in Ubuntu that make the experience with graphic tools (eg. tksurfer) much better than it is with Centos. In addition, by default  every developer tool (eg. the GNU compilers, debugger and

Re: [Freesurfer] Fwd: Sample size estimation from LME models

Hi Nicolas The common random effects design matrix expression  means that all subjects in your prospective study are expected in advance to have the same random effects design matrix (Zi). If you assume a linear trajectory over time and a two-year study with repeated measurements every six

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

help and patience. --Francois From: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Reply-To: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Date: Thursday, March 28, 2013 5:36 PM To: Francois Lalonde flalo...@mail.nih.govmailto:flalo...@mail.nih.gov, freesurfer

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

in your longitudinal analysis).  I guess they would contribute to specifying group differences at the level of the intercept? --Francois From: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Reply-To: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Date: Wednesday, March 27

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

Hi Francois If you want to test the model with three random effects including intercept, time, and time*time as the random effects then you should use [1 2 3] (these are the columns corresponding to those covariates in X). Actually, for the example in the wiki page we first tested [1 2 3] but

Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Hi Alex The cmd  [detvtx,sided_pval,pth] = lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0); only takes a few seconds to finish. Please check if  Y, Beta2, fstats.pval,fstats.sgn, sided_pval all have the same number of columns. Best -Jorge De:

Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah   The linear mixed effects (LME) estimation procedure deals with missing data and variable timing across subjects by specifying the time interval since baseline for each scan. You will have a different number of rows for each subject in your design matrix depending on how many time

Re: [Freesurfer] LME - contrast

Hi Alex Certainly, for such a simple design matrix, only two repeated measures per subject with a small inter-subject variability in between-scan time interval and a very small number of subjects with a single time point the results from both procedures should not be very different.

Re: [Freesurfer] LME matlab toolbox - smooth error

Hi Yolanda This is one of a few scripts in LME that requires an extra Matlab toolbox (maybe the only, besides the statistic toolbox). As it is documented in its header you are require to have the curve fitting toolbox installed to run it successfully. Best -Jorge

Re: [Freesurfer] issue about LME Matlab tools

Hi Ting Just use the default procedure. We limited the number of iterations for the estimation procedure to 20 for the mass-univariate analysis. If the model for the covariance is correct, that is to say, you have correctly specified the set of random effects that is supported by your data then

Re: [Freesurfer] Longitudinal analysis - contrast

- is this a simple numerotation of subjects, like: 01 02 03 04 ... ? Yes, it is. Best -Jorge De: Alex Hanganu al.hang...@yahoo.ca Para: Jorge Luis Bernal-Rusiel jbernal0...@yahoo.es CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Enviado: Viernes 7 de diciembre de 2012

Re: [Freesurfer] Longitudinal analysis - contrast

...@yahoo.ca Para: Martin Reuter mreu...@nmr.mgh.harvard.edu CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Rusiel jbernal0...@yahoo.es Enviado: Jueves 6 de diciembre de 2012 16:45 Asunto: Re: Re: [Freesurfer] Longitudinal analysis - contrast Hello Martin, Thanks for your

Re: [Freesurfer] Longitudinal analysis - contrast

-Jorge De: Alex Hanganu al.hang...@yahoo.ca Para: jorge luis jbernal0...@yahoo.es CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 5 de diciembre de 2012 13:50 Asunto: Re: [Freesurfer] Longitudinal analysis - contrast Hi Jorge, thanks

Re: [Freesurfer] Longitudinal analysis - contrast

code. Sorry, but this is what he have at this point. Best -Jorge De: Alex Hanganu al.hang...@yahoo.ca Para: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Russiel jbernal0...@yahoo.es Enviado: Miércoles 5 de diciembre de 2012 18:20 Asunto

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Alex   I think that your design is very simple and so will be to use our lme tools. There is an example of a mass-univariate analysis on the wiki at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics. However, the analysis there is much more complex (because of the more complex

Re: [Freesurfer] Repeated measures ANOVA fsgd file

Hi  Caroline If your longitudinal study is unbalanced over time (ie. the timing of the serial measurements is different across subjects) and with such a relatively high amount of repeated measures (6) it is very likely that you will need a longitudinal linear mixed effects (lme) model  to

[Freesurfer] 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

Re: [Freesurfer] Paired t-test with independent samples

A paired t-test is a special case of a repeated measures ANOVA with a single within-subject factor and two levels. You should use it when the measurements in one group are correlated with the measurements in the other group and there is a within-subject effect that persists across paired

[Freesurfer] A doubt with the group analysis of longitudinal data

Hi all I have some longitudinal data ready for the group analysis but I have a doubt: Can I simply use the following command to resample all left hemisphere thickness maps onto the fsaverage surface (as in traditional cross-sectional analyses)? mris_preproc --fsgd fsgd.txt --target fsaverage

Re: [Freesurfer] Cortical Normalization Questions

I think we must be careful about including noisy large scale measurements as global nuisance covariates in the General Linear Model (GLM). The GLM assumes that the independent variables are measured almost without error (eg. see http://en.wikipedia.org/wiki/Errors-in-variables_models).  For

Re: [Freesurfer] question about Cluster-wise Correction for Multiple Comparisions

Those vertices with p-value lower than 0.0001 are used to form the clusters for the cluster-wise correction. If  the signal in your SPM is weak but extended you should use a permissive cluster-forming p-value (eg 0.01). On the other hand, if your signal is strong and very localized you should

Re: [Freesurfer] Matlab and FS {Disarmed}

escribió: De: Carolina Valencia cvalen...@linkdx.com.co Asunto: Re: [Freesurfer] Matlab and FS Para: jorge luis jbernal0...@yahoo.es CC: freesurfer@nmr.mgh.harvard.edu Fecha: jueves, 7 de julio, 2011 15:30 Hi Jorge, Thanks for your reply,  I installed Octave in the Ubuntu machine, Should I

Re: [Freesurfer] Matlab and FS

  Hi Carolina   There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore,

[Freesurfer] New Random Field Theory tool specifically for Freesurfer-based data analyses

of smoothing in cortical thickness analyses which is based on a hierarchical RFT-FDR multiple comparison correction (Neuroimage 52, 158-171). Cheers Jorge Luis Bernal Rusiel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Bonferroni multiple comparison correction

. Cheers Jorge Luis --- El vie, 20/11/09, Jonathan DuBois jonathan.m.dub...@gmail.com escribió: De: Jonathan DuBois jonathan.m.dub...@gmail.com Asunto: [Freesurfer] Bonferroni multiple comparison correction Para: freesurfer@nmr.mgh.harvard.edu Fecha: viernes, 20 de noviembre, 2009 18:37 When

[Freesurfer] About corrected t-statistics and p-values

Hello freesurfer experts I would like to know how to get in freesurfer corrected p-values and t-statistics for the FDR analysis and corrected t-statistics for the clusters in the cluster size inference by permutation testing. In advance thank you very much Jorge Luis

Re: [Freesurfer] Gaussian random field correction

of simulations) with those from freesurfer permutation testing and I think it is a very good alternative. Cheers Jorge Luis Bernal Rusiel Phd Student. Laboratory of functional Neuroscience. University of Pablo de Olavide. Seville. Spain --- El lun, 6/7/09, Jürgen Hänggi j.haen

Re: [Freesurfer] RE: fdr thresholds in tksurfer compared to Nichol's function

Use the fast_fdrthresh matlab function provided in the fsfast/toolbox directory in freesurfer. It gives the same results as tksurfer. Cheers Jorge Luis Bernal Rusiel Phd Student Laboratory of Functional Neuroscience. University of Pablo de Olavide. Seville. Spain --- El jue, 25/6/09, Lars

[Freesurfer] About cluster thresholding

in the surfaces Para: jorge luis [EMAIL PROTECTED] CC: freesurfer@nmr.mgh.harvard.edu Fecha: domingo, 29 junio, 2008 5:22 Hi Jorge, yes, the area of a vertex is 1/3 of the area of all triangles that it is a member of, and it should sum to the area of the surface. The average subject has

[Freesurfer] About the area of the vertices in the surfaces

Hello all I have some questions: I would like to know how freesurfer computes the vertex’s wise areas? eg. thouse in lh.area. It should be expected that the sum of the areas of all the vertices across a surface equals the total surface area? To be much specific: Can I compute the area of an

[Freesurfer] Estimating the difference in cortical thickness between two groups

Hello all We are comparing the cortical thickness of two groups with the following fsgd file: GroupDescriptorFile 1 Title Thickness-subj Class contr Class modif Input subj1 contr Input subj2 contr Input subj3 contr Input subj4 contr ... Input subj36 modif Input subj37 modif Input subj38

[Freesurfer] About the average subject

Hello all Hello all We are planning to perform a cross-sectional study involving two population of subjects. I think we have to choice one among two possibilities : 1-Make a single average subject for both populations and resample all the subject to this average for the statistical analysis.

[Freesurfer] About Gaussian Random Field Theory on fsaverage

Thank you Bruce and Moo Chung I will try with those tools I have another question: If I want to use GRFT on smooth thickness spms over the fsaverage subject , should I use the fsaverage white matter total surface area which is 70394.7 mm2 or the group average surface area which is 86444.7 mm2?

[Freesurfer] About the hippocampal surface smoothing tools

Hello Bruce We are also very interested in your hippocampal surface smoothing tools. Can you provide us with the beta version of your software? I advance Thank you Jorge --- Bruce Fischl [EMAIL PROTECTED] escribió: Hi Kim, we do have some tools for smoothing the hippocampal

[Freesurfer] Problems with make_average_subject

Hello all I am trying to build an average subject under FS X86-64 v4.0.1 and I get the follow: [EMAIL PROTECTED] ~]$ make_average_subject --subjects subj1 subj10 subj11 --out subjavr limit: descriptors: No se puede %s: %s: No se puede %s el límite %s el límite [EMAIL PROTECTED] ~]$ The

RV: Re: [Freesurfer] Spherical ROIs areas in the fsaverage

is necessary to align folds cheers, Bruce On Wed, 12 Sep 2007, jorge luis wrote: Hello all I have made changes in the thickness values in some regions of a left hemisfere of a subject surface after mapped it onto the fsaverage sphere. The changes were made to have areas close to these in the left colum

[Freesurfer] Spherical ROIs areas in the fsaverage

Hello all I have made changes in the thickness values in some regions of a left hemisfere of a subject surface after mapped it onto the fsaverage sphere. The changes were made to have areas close to these in the left colum of the following table: My area Freesurfer number of vertices

[Freesurfer] Freesurfer and Gaussian Random field theory

Hello all I have computed and smoothed some thickness maps using Freesurfer. Next I would like to make inference using Gaussian Random Field theory (GRFT). How can I do it in Freesurfer? If it is not implemented in freesurfer , is there any thing that I have to take into account when applying

[Freesurfer] Doubt in thickness computation

Hello all In Neuroimage Han. et all ( 2006) it is said about Freesurfer automatic thickness computation : For each point on the gray/white surface, the shortest distance to the pial surface is first computed. Next, for each point on the pial surface, the shortest distance to the gray/white

[Freesurfer] Question about aseg.mgz

Hello all Are the norm.mgz and aseg.mgz volumes already aligned to talairach standard space ? I have read on the freesurfer tutorial that the transformation is computed and stored in transforms/talairach.ita but it is no applied to the initial volume. I would like to get the segmentation

[Freesurfer] Conversion to Minc Line OBJ

Hello all I would like to convert a freesurfer triangular surface (ASCII or binary) to Minc Line OBJ file format. I know how to convert to Minc Polygons OBJ file format, but it is not useful for my application. I need a conversion to the Lines OBJ format. Any help is welcome In advance thank

[Freesurfer] Problems with surface topologies

Hello all I have the freesurfer automatic hippocampus segmentation for some subjects. It seems that the segmentation is not bad. I have produced the binary masks (after labels generation in tksurfer)with the following command: mri_label2vol --label label/lefthipoca.label --temp mri/orig.mgz

[Freesurfer] Cortical ROIs analysis

Hello all I have a question: How to threshold a thickness statistical parametric map by using FDR just in one specific label of the fsaverage cortical surface parcelation? In advance thank you a lot Jorge __ LLama Gratis a

Re: [Freesurfer] Doubts with region areas on the fsaverage sphere

areas on fsaverage. The total surface area of the average will be wrong (inevitable with the way that fsaverage is computed). However, there is a correction, and our tools take this into account. doug jorge luis wrote: Hello all I have made deep changes in 9 regions of a left

[Freesurfer] About the FDR button

Hello all I am using the genome interface to XWindows in Linux Centos 4 X86-64. I have a problem with the freesurfer interface for FDR correction in tksurfer. The Configure Overlay Display window is to large for the screen and the FDR button is hide down. I have proved to change the display

[Freesurfer] Spherical coordinates

(it should be the same for all vertices). jorge luis wrote: Hello all I would like to know what kind of coordinates (RAS, Talairach, Spherical) are saved in the AsCII file resulting from: mris_convert lh.sphere.reg lh.sphere.reg.asc I could not find correspondence among

[Freesurfer] Doubt on spherical coordinates

Hello all I would like to know what kind of coordinates (RAS, Talairach, Spherical) are saved in the AsCII file resulting from: mris_convert lh.sphere.reg lh.sphere.reg.asc I could not find correspondence among the resulting coordinates and those that are shown in Tksurfer. If

[Freesurfer] How to get subcortical segmentation for the average subject

Hello all. How can I get a subcortical segmentation for the average subject (the result of make_average_subject)? There is no aseg.mgz file on the corresponding directory I hope it can be used for VOI analysis of functional data. Any help is welcome. In advance Thank you

[Freesurfer] Problems runing a complete freesurfer analysis under Centos4 X86-64

Hello all I have a Dual core Intel Pentium 3.0Gz machine with 2GB RAM and two SATA2 Hard Disks (300 GB and 80GB, respectively). I have successfully installed Linux Centos4 X86-64 (on the 80 GB disk) and the corresponding freesurfer version. I have run several freesurfer commands

[Freesurfer] Why I would need Boundary Shift Integral or IPCA for computing whole-brain atrophy rates?

Hello all I have seen in the articles: -Freeborough, P.A., Fox, N.C., 1997. The boundary shift integral: an accurate and robust measure of cerebral volume changes from registered repeat MRI. IEEE Trans. Med. Imaging 16, 623- 629. - Kewei Chen et. all. An automated