Your inputs have been very helpful. Looking at the examples on LME webpage, the contrast for both univariate and mass-variate creates 3 rows with 14 columns for univariate and 17 for mass-variate analysis. My understanding is that 3 rows have been created because there are 4 groups being analyzed and applying that rationale to my data would mean that the contrast for my analysis would require 2 rows since I comparing 3 groups. Is my logic correct here?
So, for my analysis if I want to include two random effects, namely, intercept and time_from_base_scan, which are given in Column 1 and 2, respectively, the contrasts based on M having 6 columns would as follows: CM.C = [1 1 ; 1 1] zeros(2,4)]; or CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0] Mayank On Mar 7, 2018, at 3:33 PM, Diers, Kersten /DZNE <kersten.di...@dzne.de<mailto:kersten.di...@dzne.de>> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi, let me just mention that my previous comments were directed at the design matrix X and not necessarily at the QDEC table. In that sense, it is possible, but not necessary to modify the QDEC table prior to loading it into Matlab. Alternatively, one might do these modifications within Matlab, although this would require some additional manual coding. For the present analysis, however, the current qdec table looks fine. About question 1: If I understood correctly, you have so far loaded the (modified) QDEC table and stored the extracted information within the matlab variable 'M'. In addition to that you'd also need to sort the data within each subject according to time, and load 'Y', 'lhcortex' and possibly 'lhsphere'. For a description of all of these steps please see the "mass-univariate" section of the example data analysis on the tutorial page. About question 2: Just to be precise, I assume that for this particular case the matlab variable 'M' contains the following four columns: time-from-baseline, age-at-baseline, group2, group3; where 'group2' and 'group3' indicate memberships in groups 2 and 3, respectively. Then, a design matrix can be created as follows: X = [ones(length(M),1) M M(:,1).*M(:,3) M(:,1).*M(:,4)]; Then the order of the columns of X is: intercept, time-from-baseline, age-at-baseline, group2, group3, time-from-baseline*group2, time-from- baseline*group3. Let's keep in mind that the order of columns in X is important for the formulation of contrasts at a later stage (and is different from the tutorial example). Again, this procedure and the matrices M and X are specific for this particular analysis scenario and cannot necessarily be generalized to others. Best regards, Kersten -----Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu<mailto:mkaus...@mcw.edu>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Wed, 7 Mar 2018 15:48:36 +0100 I have made the suggested edits and would appreciate if you could take a look at the qdec.table.dat file attached to this conversation. After going over the univariate example on the Freesurfer LME webpage, I had a couple of questions. 1. How will data be loaded into Matlab? More specifically, what would be the step(s) after the line M = Qdec2num(Qdec);? 2. Given that column named time_base_scan would be multiplied with column named group2 as well as group3, what will be the equation for creating the design matrix? X = [ones(length(M),1) M M(:,).*M(:,)]; Mayank On Mar 7, 2018, at 7:14 AM, Diers, Kersten /DZNE <Kersten.Diers@dzne. de> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi Mayank, I may have a few more general considerations before commenting on the number and kind of random effects. In the current design matrix, column 2 (time from baseline) and column 5 (visit) will be quite redundant. It is one of the advantages of the LME model to be able to deal with unevenly spaced observation intervals and also with possibly missing visits. In that sense, all temporal information is already contained within column 2, and I cannot see a good reason to additionally include column 5. It may even complicate things, due to the redundancy. If you have 3 groups, you will need two columns in the design matrix to indicate group membership (assuming that an intercept column is also present). Choose one group (say, group 1) as the reference group, which will not explicitly be coded, and then use one of the two group columns to indicate if a person belongs to group 2 (1=yes, 0=no), and the other to indicate if a person belongs to group 3 (1=yes, 0=no). Please don't code group membership numerically as 1, 2, 3 in a single column, as this will impose a linear relation between group membership and outcome measure (similar to linear regression). I am not sure about the current meaning of column 6, which multiplies age and time-from-baseline. It would be more important, in my eyes, to multiply time-from-baseline and group membership. Considering my second comment, this will also result in two colums. These will indicate whether or not the effect of time will differ between groups, and this (=different longitudinal trajectory) is often the primary interest in longitudinal studies. As far as I can see, your overall design is somewhat similar to the univariate example on the Freesurfer LME webpage, except that you have fewer groups and fewer covariates. As it does not matter for the design matrix whether or not the overall study is univariate or mass- univariate (as in your case), one suggestion would be that you construct your design in a similar way as in the given example. I hope that I have understood your design correctly, otherwise let me know. Best regards, Kersten -----Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Tue, 6 Mar 2018 19:22:57 +0100 I have tabulated the columns for easier comprehension. Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 intercept time of each scan from base scan for a given subject age at first scan for a given subject group (1, 2, or 3) visit (1,2 3, or 4) Column 2 * Column 3 Thanks again. Mayank On Mar 6, 2018, at 12:05 PM, Kaushal, Mayank <mkaus...@mcw.edu<mailto :m kaus...@mcw.edu>> wrote: Changing the Matlab directory worked. Thanks for all your inputs, Kersten. Sorry to prolong the conversation but if possible, I would appreciate input on whether my thought process regarding the LME analysis is on the right track. I am looking to compare cortical thickness between 3 groups over multiple visits. The design matrix created by me X = [ones(length(M),1) M M(:,1).*M(:,2)]; Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 intercept time of each scan from base scan age at first scan group (1, 2, or 3) visit (1,2 3, or 4) Column 2 * Column 3 Presently, I am running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1) as a test run. However, I would like to include Columns 1, 4, and 5 as random effects for LME analysis and if possible even include Column 2 as a random effect to have 4 random effects. lhstats = lme_mass_fit_vw(X,[1 4 5],Y,ni,lhcortex,[],1) or lhstats = lme_mass_fit_vw(X,[1 2 4 5],Y,ni,lhcortex,[],1) Now, I would like to know if having 3 or possibly 4 random effects would be too many random effects. Mayank On Mar 6, 2018, at 8:57 AM, Diers, Kersten /DZNE <Kersten.Diers@dzne. de <mailto:kersten.di...@dzne.de><mailto:kersten.di...@dzne.de>> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ The LME toolbox will create a text file ('parfor_progress1.txt') in Matlab's present working directory to indicate its progress in processing each vertex. To create this file it needs to have write permissions in Matlab's present working directory. I speculate that your present working directory in Matlab is the root directory '/' where the toolbox cannot create a file. The solution would be to not run the scripts from '/', but to set the Matlab working directory to another directory where you have write permissions. Best regards Kersten -----Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu<mailto:mkaus...@mcw.edu><ma il to:mkaus...@mcw.edu>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mai lt o:freesurfer@nmr.mgh.harvard.edu>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:fr ee sur...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Tue, 6 Mar 2018 15:17:31 +0100 After downloading version 6.0. and running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1), I received the following errors. Error using parfor_progress (line 17) Do you have write permissions for /? Error in lme_mass_fit (line 155) fn = parfor_progress('init',nv); Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); Thoughts? Mayank On Mar 6, 2018, at 7:08 AM, Diers, Kersten /DZNE <Kersten.Diers@dzne. de> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Yes, my understanding is the same. The LME toolbox can in a way be regarded as a post-processing add-on to Freesurfer. The only interface with Freesurfer are the read/write functions, everything else is to the best of my knowledge independent of Freesurfer. So I cannot see any problems in using the newer version of the LME toolbox with data from Freesurfer 5.3. Needless to say, this does not affect the usual recommendation, which is that Freesurfer versions should not be mixed in general. Best, Kersten ------Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu<mailto:mkaus...@mcw.edu>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mai lt o:freesurfer@nmr.mgh.harvard.edu>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:fr ee sur...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Mon, 5 Mar 2018 20:47:36 +0100 The version string I have been using: $Revision: 1.1.1.1 $ $Date: 2012/02/02 11:25:52 $ So, it appears that I do indeed have the older version. I am running Matlab 2017a, which is a relatively newer version. Before I proceed with using LME toolbox from a freesurfer 6.0, I would appreciate your input on the following. My understanding is that LME toolbox is used for statistical analysis and is independent of the freesurfer version performing the actual cortical thickness analysis. So, in theory, if I import cortical thickness data processed in version 5.3, I should still be able to run the LME toolbox from a version 6.0. So, can I input the files processed by freesurfer 5.3 (files that have been processed till mris_preproc and mri_surf2surf) and simply use the LME toolbox from a version 6.0 to perform the statistical analysis? Mayank On Mar 5, 2018, at 1:29 PM, Diers, Kersten /DZNE <Kersten.Diers@dzn e. de> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi, thanks for the additional information. I believe that we are dealing with a version issue now. Specifically, I have so far been testing with an LME toolbox from a Freesurfer 6.0 version on Matlab R2016a. In that sense, there is no need for a separate download of the LME scripts, since they are already included within the freesurfer directory (e.g. 'freesurfer/matlab/lme'). It is primarily the 'lme_mass_fit.m' script, which throws the current error. Could you please check your version of this script (type 'help lme_mass_fit.m')? Within my 5.3 installation, the version string is: % $Revision: 1.1.2.2 $ $Date: 2013/02/23 21:08:10 $ Within my 6.0 installation, the version string is: $Revision: 1.3 $ $Date: 2016/04/08 19:39:24 $ Unfortunately, the version string of the 'lme_mass_fit.m' script within a toolbox that I just downloaded from the LME website is the most ancient one: % $Revision: 1.1.1.1 $ $Date: 2012/02/02 11:25:52 $ When I use the 1.1.1.1 version instead of the one that is included within Freesurfer 6.0, I can replicate the problem reported in your current mail. With the 1.3 version I have no issues. As far as I know, the 'lme_mass_fit.m' script was updated to accommodate the changes in Matlab's way of doing the parallel processing. In older Matlab versions this was done using the 'matlabpool' command, but this was replaced by 'parpool', which is - to my knowledge - the only way of running parallel processing with recent Matlab versions. The LME toolbox was originally only tailored to the 'matlabpool' command, but has later been adapted to also include the 'parpool' command. Assuming that you are using a relatively recent Matlab version, the use of earlier vs. later versions of the toolbox would explain our respective observations. All in all, I currently see no way of getting an older version of the LME toolbox to run with a current Matlab version - except from modifying the code itself. So my suggestion would be to just use the newer LME toolbox that is shipped with Freesurfer 6.0. Let us know if I am mistaken or if there are further issues. Best regards, Kersten -----Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu<mailto:mkaus...@mcw.edu>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mai lt o:freesurfer@nmr.mgh.harvard.edu>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:fr ee sur...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Mon, 5 Mar 2018 16:34:14 +0100 Thanks for the quick response Kersten. I tried all the potential suggestions mentioned in your post but still no luck. Here’s the summary: lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1) Undefined function or variable 'matlabpool'. Error in lme_mass_fit (line 124) if (matlabpool('size') > 0) Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],2) Undefined function or variable 'matlabpool'. Error in lme_mass_fit (line 123) if (prs==1) || (matlabpool('size') ~= prs) Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); The "automatically create a parallel pool" was already deselected in my case. Also, I am using freesurfer 5.3 with LME toolbox downloaded from the freesurfer website. Mayank On Mar 5, 2018, at 9:12 AM, Diers, Kersten /DZNE <Kersten.Diers@d zn e. de> wrote: ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi, you might try supplying an additional command-line argument while calling the 'lme_mass_fit_vw' function: lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1) This will tell Matlab to use only one worker. Further documentation on this additional argument can be obtained by typing 'help lme_mass_fit_vw' at the Matlab prompt. To get this working with my Matlab installation, I additionally had to deselect the "Automatically create parallel pool (if one doesn't already exist) when parallel keywords (e.g., parfor) are executed." option. This can be found in Matlab's preferences menu (--> see the Parallel Computing toolbox section). As an alternative, using two workers might also be an option in your case: lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],2) To get this alternative approach working, I did not have to change the Matlab preferences. Hope this helps, Kersten -----Original Message----- From: "Kaushal, Mayank" <mkaus...@mcw.edu<mailto:mkaus...@mcw.edu>> Reply-to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mai lt o:freesurfer@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesur...@nmr.mgh.harvard. ed u> <freesur...@nmr.mgh.harvard.ed<mailto:freesur...@nmr.mgh.harvard.e d> u> Subject: [Freesurfer] Running Linear Mixed Effects (LME) Model Date: Sun, 4 Mar 2018 23:56:03 +0100 Dear Freesurfer Community, Running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); gives the following error, Starting parallel pool (parpool) using the 'local' profile ... Error using parpool (line 104) You requested a minimum of 8 workers, but the cluster "local" has the NumWorkers property set to allow a maximum of 2 workers. To run a communicating job on more workers than this (up to a maximum of 512 for the Local cluster), increase the value of the NumWorkers property for the cluster. The default value of NumWorkers for a Local cluster is the number of cores on the local machine. Error in lme_mass_fit (line 137) parpool(prs); Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); I am running Matlab on a personal MacBook Pro, 2.4 GHz Intel Core i5, 8 GB 1600 MHz DDR3. I have researched the forum on how to stop the function from trying to initiate parallel processing but so far haven’t been able figure out how to overcome this. Any help would be much appreciated. 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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_ co mplianceline&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r =R qvEwdmcEg_aWsE7PBL80w&m=JtHeh4F36Zz1ELE7LnYzZXcblTZGl5bubrruLBAzfrw&s =4 RDz2B3bkbGv045ePFVlaXOUhwU-3UOmzh11Xp8sYJc&e= . 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@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har vard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV 0iqFn3z4pVFYPQkjgspw4Y&r=RqvEwdmcEg_aWsE7PBL80w&m=GVM70MOA7CO9xz- DDMXn5Uq1e-YXiQbvHQnZkzH2lg8&s=Kjem-y9X16SRBARNZVRJ4zsVrtJ7BUt- PTmhkGvra68&e= 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_ complianceline&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y &r=RqvEwdmcEg_aWsE7PBL80w&m=GVM70MOA7CO9xz-DDMXn5Uq1e- YXiQbvHQnZkzH2lg8&s=xNpiFQrEL4qVzqqt4k7lDdv81WoNgalrePcN7qcKFz4&e= . 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@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har vard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV 0iqFn3z4pVFYPQkjgspw4Y&r=RqvEwdmcEg_aWsE7PBL80w&m=GVM70MOA7CO9xz- DDMXn5Uq1e-YXiQbvHQnZkzH2lg8&s=Kjem-y9X16SRBARNZVRJ4zsVrtJ7BUt- PTmhkGvra68&e= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=RqvEwdmcEg_aWsE7PBL80w&m=1elXGyZpDg3IRcgSYzJpahq0VVW7QvAExb-XcfwTDvs&s=O1jhLDwl3YQyJYlVNH-s7AxkIR7dip7Ix8nzlCAarWE&e= 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIGaQ&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=RqvEwdmcEg_aWsE7PBL80w&m=1elXGyZpDg3IRcgSYzJpahq0VVW7QvAExb-XcfwTDvs&s=xGZe-oGipT8llmP0DLD_KiYI97V81Ejc_0BRpcrQnk0&e= . 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@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.
