Hi Bruce, Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows:
Talairach.xfm file: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = However, the talaraich.xfm file generated by the non-paralellizing machine is the following: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = 1.088816 -0.036409 -0.059575 1.880753 0.047590 1.030018 0.245325 -4.493217 0.029937 -0.211744 1.231518 94.663368; Anna On Thu, Oct 22, 2015 at 6:00 PM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. normalization of hippocampal volume (geschwind2013) > 2. Postdoctoral Opportunity: Multimodal MRI registration and > analysis (Frederic Andersson) > 3. Re: A mixed effect model approach in within subject dataset > {Disarmed} {Disarmed} (jorge luis) > 4. Re: Sulcal depth units (Bruce Fischl) > 5. Re: mris_expand - problem reading thickness file? (Bruce Fischl) > 6. Re: How to compute the measures on the average brain? > (Bruce Fischl) > 7. Re: Talairach_afd error (Bruce Fischl) > 8. Re: How to compute the measures on the average brain? > (Douglas N Greve) > 9. Re: normalization of hippocampal volume (Douglas N Greve) > 10. Re: per analysis with covariates (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Oct 2015 17:18:21 +0900 > From: geschwind2013 <neurof...@gmail.com> > Subject: [Freesurfer] normalization of hippocampal volume > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <27af7eca-e1b4-4337-bb2c-4cbe4109f...@gmail.com> > Content-Type: text/plain; charset=euc-kr > > Hi, FS Experts, > > I?m using version 5.3 and have performed hippo-subfields analysis. > > To perform the statistics, shall I get the normalized volumes of each > hippo-subfields? > or just to do correction for ICV is enough ? > > thanks.. > > Hyon > > > ------------------------------ > > Message: 2 > Date: Thu, 22 Oct 2015 15:30:14 +0200 > From: Frederic Andersson <anders...@univ-tours.fr> > Subject: [Freesurfer] Postdoctoral Opportunity: Multimodal MRI > registration and analysis > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <6e3a85f5-c942-49d0-bbe0-4c51c4e8e...@univ-tours.fr> > Content-Type: text/plain; charset="utf-8" > > Postdoctoral Opportunity: Multimodal MRI registration and analysis > > Context and methodology > This postdoctoral position will focus on the registration of ex-vivo onto > in-vivo MR data. Based on some recent advances extending the combined > volume and surface registration, efficient approaches can be provided for > dealing with this issue. However, these methods need to be validated and > several open theoretical questions are related to this problem and will be > investigated during this postdoctoral work. The theoretical results > obtained will be tested and used on real human data in a larger framework > aiming at tractography validation (French National Research Agency Grant > ANR 2014, collaborative study Inserm U930, Universit? de Tours, Neurospin > and Martinos Center). > > Applicant profile > Candidates should have a strong background in image registration and MR > imaging, a good publication record, and strong experience in c++ and matlab > coding. Proficiency in English is required, as well as scientific writing > skills. > Applicants should send a CV, including list of publications and a > description of previous research experience, as well as the names and > emails of two academic referees to: Clovis Tauber ( > clovis.tau...@univ-tours.fr <mailto:clovis.tau...@univ-tours.fr>) and > Christophe Destrieux (christophe.destri...@univtours.fr <mailto: > christophe.destri...@univtours.fr> ) > > Conditions > Starting date: January 2016 (adjustable) > Contract: 2 years > Location: Imaging and Brain unit, INSERM U930, Tours. > Salary: related to experience > > References > G.M. Postelnicu, L. Z?llei, B. Fischl: Combined Volumetric and Surface > Registration, IEEE Transactions on Medical Imaging 28 (4), April 2009, p. > 508--522 > Zemmoura I, Serres B, Andersson F, Barrantin L, Tauber C, Filipiak I, > Cottier JP, Venturini G and Destrieux C 2014 FIBRASCAN: a novel method for > 3D white matter tract reconstruction in MR space from cadaveric dissection > Neuroimage 103 106?118 > Serres B, Zemmoura I, Andersson F, Tauber C, Destrieux C and Venturini G > 2013 Brain Virtual Dissection and White Matter 3D Visualization Stud. > Health Technol. Inform. 184 392--396 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/ed70621d/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 22 Oct 2015 13:45:28 +0000 (UTC) > From: jorge luis <jbernal0...@yahoo.es> > Subject: Re: [Freesurfer] A mixed effect model approach in within > subject dataset {Disarmed} {Disarmed} > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: "pablon...@hotmail.com" <pablon...@hotmail.com> > Message-ID: > <1841220171.2266406.1445521528699.javamail.ya...@mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hi Pablo > > If you havethoroughly checked that everything is properly setup so that > theordering of the design matrix's rows is in proper correspondence withthe > ordering of the image data matrix's rows and it is also in > propercorrespondence with the ordering of the entries in vector ni > (eachentry of this vector has the number of subjects belonging to the > samefamily) and the design matrix has enough covariates to describe > yourdata then the analysis should be correct. > > Bear in mind thatyou are not analyzing longitudinal data for which a > proper imageregistration pipeline exists in Freesurfer and there is a > clearwithin-subject correlation between cortical thickness values > acrosstime points at the same surface vertex. Instead you are > analyzingfamily data in which you are trying to model vertex-wise > correlationsacross different subjects. Although in principle there should > bewithin-family correlation the image registration procedure (and > imageprocessing pipeline in general) as well as individual variation > couldhave introduced a lot of noise in your data making the > vertex-wisewithin-family correlations rather weak. This makes it hard for > theLME estimation procedure to converge and give precise parameterestimates. > > Best-Jorge > > > > De: pablo najt <pablon...@hotmail.com> > Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Enviado: Jueves 22 de octubre de 2015 1:15 > Asunto: Re: [Freesurfer] A mixed effect model approach in within subject > dataset {Disarmed} {Disarmed} > > <!--#yiv0632092676 .yiv0632092676hmmessage > P{margin:0px;padding:0px;}#yiv0632092676 > body.yiv0632092676hmmessage{font-size:12pt;font-family:Calibri;}-->Hello > again,I have now also run the model with 2 random effects and it is > definitively worst. The final line says:Algorithm did not converge at > 79.5859 percent of the total number of locations. > Any suggestion if I should trust in the model with 1 random effect? I know > you Martin had doubts, so I am wondering what Jorge thinks of it.ThanksPablo > > To: freesurfer@nmr.mgh.harvard.edu > From: mreu...@nmr.mgh.harvard.edu > Date: Wed, 21 Oct 2015 08:55:04 -0400 > Subject: Re: [Freesurfer] A mixed effect model approach in within subject > dataset {Disarmed} {Disarmed} > > Hi Pablo, > > 23% still seems a lot, but may be OK (maybe Jorge can comment on that)? > > If you want to do a model comparison (2 random vs 1) take a look at the > wiki. It describes how to do that. > > Best, Martin > > On 10/21/2015 01:19 AM, pablo najt wrote: > > <!--#yiv0632092676 .yiv0632092676ExternalClass .yiv0632092676ecxhmmessage > P {padding:0px;}#yiv0632092676 .yiv0632092676ExternalClass > body.yiv0632092676ecxhmmessage {font-size:12pt;font-family:Calibri;}--> > Martin, Doing the changes in the matrix allowed me to run the command. The > command with just one random effect for the intercept term give me the > following output: > Aproximate percentage of fitted locations: 100% Summary: Algorithm did > not converge at 23.407 percent of the total number of locations. Total > elapsed time is 116.2184 minutes. > > Is this ok? Is there anything I should check? Should I also try two > random effects as well? Thank you Pablo > To: freesurfer@nmr.mgh.harvard.edu > From: mreu...@nmr.mgh.harvard.edu > Date: Tue, 20 Oct 2015 09:06:53 -0400 > Subject: Re: [Freesurfer] A mixed effect model approach in within subject > dataset {Disarmed} {Disarmed} > > Hi Pablo, > > the zero columns could be outside the cortex and then this would be fine. > Do > min(sum(lhY(:,lhcortex))) > if you get 0 you have at least one location where the column is all zero > (as we should not have any negative values, you can test that with > min(lhY(:)) > Now even if you still have a column of 0 , then that vertex is > problematic, but who cares about a single vertex. If you do a region > approach, it will be part of a region anyway. so you should check how often > you get 0 columns (inside cortex). > > About your M: I would subtract 1 from gender (to have 0 and 1) > Also you only need 2 columns for the groups: keep only column 3 and 4. A > HC is someone who has 0 in both. > > Best, Martin > > > > On 10/20/2015 04:37 AM, pablo najt wrote: > > <!--#yiv0632092676 .yiv0632092676ExternalClass .yiv0632092676ecxhmmessage > P {padding:0px;}#yiv0632092676 .yiv0632092676ExternalClass > body.yiv0632092676ecxhmmessage {font-size:12pt;font-family:Calibri;}--> > Dear ?FS experts, I am following up on an issue I am having when trying to > run linear mixed effects model. I keep getting 'Algorithm did not > converge'. So far I have changed the preprocessing steps following > literally from the wiki as in message below. Also I tried to use only one > random effect for the intercept. Also I have checked that?sum of vectors of > (ni) is equal to the number of rows in (X). > As none of the above worked I started to have concerns about the > dimensions of my lh.thickness_sm10.mgh. ?When I load in matlab in working > space says 'too many variables'. Is this ok? ? ? > > Also, when I open 'lhY' variable it shows a column of Zeros every nine > columns as below. Is this alright? > ? ? > > Perhaps this is fine but I would like to check on anything that is > creating this problem. For matrix 'M' I created a matlab script that loads > a matrix with intercept (all ones), HC (ones to HC otherwise zero), U_PT > (relatives of patients ones otherwise zero), PT (patients one otherwise > zero), gender, age (see below). The three columns for groups do not > match?the qdec.table.dat which have only one column for groups (HC, U_PT, > PT). However the?order of the rows is identical in M and qdec.table.dat > ? ? > > ?Please let me know if this should be set differently. Thank you Pablo > > > To: freesurfer@nmr.mgh.harvard.edu > From: mreu...@nmr.mgh.harvard.edu > Date: Mon, 19 Oct 2015 09:00:57 -0400 > Subject: Re: [Freesurfer] A mixed effect model approach in within subject > dataset {Disarmed} > > Hi Pablo, > > since you did not run this through the longitudinal stream, you won't > have a base ( or subject-template), also you won't have <tpid>.long.<base> > directories, so the first command should fail. For that you simply replace > the --qdec-long with --qdec and use the same table. Should work. The > second command is fine (it just smoothes the thickness stack). > > Best, Martin > > On 10/19/2015 06:51 AM, pablo najt wrote: > > <!--#yiv0632092676 .yiv0632092676ExternalClass .yiv0632092676ecxhmmessage > P {padding:0px;}#yiv0632092676 .yiv0632092676ExternalClass > body.yiv0632092676ecxhmmessage {font-size:12pt;font-family:Calibri;}--> Hi > Jorge and FS experts, I have run again the analysis and still get the > convergence problem. I am assuming the issue has to do with the > preprocessing steps, as I had doubts on how to follow from the instructions > if I am not using qdec and have a cross sectional design. > Instructions on lme in the wiki for preprocessing specify the following: > mris_preproc --qdec-long qdec.table.dat --target study_average --hemi > lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s > study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh > --fwhm-trg 10 --cortex --noreshape My data -as I explained below- is > cross section but I want to treat it as longitudinal as I want to analyse > subjects belonging to the same family.? Here is my 2 main questions:? 1) > for preprocessing should I follow instructions as it would be longitudinal > data? 2) Although my design does not allow using qdec (3 groups) do I still > create a qdec table and follow literally the two instructions above ? > Thank you Pablo > > ____________________________________________________________________________________________________________________________________ > > Date: Fri, 16 Oct 2015 16:24:36 +0000 > From: jbernal0...@yahoo.es > To: freesurfer@nmr.mgh.harvard.edu > CC: pablon...@hotmail.com > Subject: 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 = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4); > If the result still have too many non-convergence locations then > something might be wrong with the ordering of the design matrix and its > correspondence with the ordering of the ni vector or the ordering of the > image data etc... You will need to check it thoroughly. > Cheers -Jorge > > > > > > > De: pablo najt <pablon...@hotmail.com> > Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Enviado: Viernes 16 de octubre de 2015 1:43 > Asunto: Re: [Freesurfer] A mixed effect model approach in within subject > dataset {Disarmed} > > <!--#yiv0632092676 .yiv0632092676ExternalClass > #yiv0632092676ecxyiv7275178360 body.yiv0632092676ecxyiv7275178360hmmessage > {font-size:12pt;font-family:Calibri;}--> Thanks you for the replies. Jorge > and FS experts, I have run the analysis and first double checked that the > sum of vectors of (ni) is equal to the number of rows in (X). Both are 140 > which is the number of my subjects. The analysis gave the following > 'error'(?) below: I looked up a previous thread coming across this. At that > case you recommended Would you recommend this afain> > > Aproximate percentage of fitted locations: 100% Warning: matlabpool > will be removed in a future release. To query the size of an already > started parallel pool, query the 'NumWorkers' property of the pool. To > check if a pool is already started use 'isempty(gcp('nocreate'))'.? > Warning: matlabpool will be removed in a future release. To shutdown a > parallel pool use 'delete(gcp('nocreate'))' instead.? Parallel pool > using the 'local' profile is shutting down. ?? Summary: Algorithm > did not converge at 90.0637 percent of the total number of locations. > Total elapsed time is 550.1023 minutes. > > Also almost all the time the screen showed the following message: > 144114: Algorithm did not converge. Initial and final likelihoods: > -38.3408-1.5708i,-241.4153-1.570796i. Location 144113: Algorithm did > not converge. Initial and final likelihoods: -5.5424-1.5708i, > -133.8004-1.570796i. Location 144112: Algorithm did not converge. > Initial and final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i. > Location 144111: Algorithm did not converge. Initial and final > likelihoods: -16.8597-1.5708i, 0.74448. Aproximate percentage of fitted > locations: 100% > > So my two questions are: 1. Is this problematic? 2. Are there any fixes > to this issue? Thank you, Pablo > Date: Thu, 15 Oct 2015 13:38:22 +0000 > From: jbernal0...@yahoo.es > To: freesurfer@nmr.mgh.harvard.edu > CC: pablon...@hotmail.com > Subject: 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 sum(ni) and length(X) give the same value before > running the above command. > Cheers -Jorge > > > > De: pablo najt <pablon...@hotmail.com> > Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Enviado: Jueves 15 de octubre de 2015 7:18 > Asunto: Re: [Freesurfer] A mixed effect model approach in within > subject dataset {Disarmed} > > <!----> Thank you Martin. I am trying to run the following command > line and get the error below. Would you have a suggestion to overcome > this issue? Just in case I am also including a snapshot of my loaded > variables at the bottom. Many thanks, Pablo >> lhstats = > lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); > > > Warning: matlabpool will be removed in a future release. > > To query the size of an already started parallel pool, query the > 'NumWorkers' > > property of the pool. > > To check if a pool is already started use 'isempty(gcp('nocreate'))'.? > > Warning: matlabpool will be removed in a future release. > > To query the size of an already started parallel pool, query the > 'NumWorkers' > > property of the pool. > > To check if a pool is already started use 'isempty(gcp('nocreate'))'.? > > Warning: matlabpool will be removed in a future release. > > Use parpool instead.? > > Starting matlabpool using the 'local' profile ...? > > Error using matlabpool (line 148) > > Failed to start a parallel pool. (For information in addition to the > causing error, > > validate the profile 'local' in the Cluster Profile Manager.) > > > > > Error in lme_mass_fit (line 128) > > ? ? ? ? matlabpool(prs); > > > > > Error in lme_mass_fit_vw (line 73) > > [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); > > > > > Caused by: > > ? ? Error using parallel.internal.pool.InteractiveClient/start (line > 330) > > ? ? Failed to start pool. > > ? ? ? ? Error using parallel.Job/submit (line 304) > > ? ? ? ? You requested a minimum of 8 workers, but the cluster "local" > has the > > ? ? ? ? NumWorkers property set to allow a maximum of 4 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. > > ? ??? > > > To: freesurfer@nmr.mgh.harvard.edu > From: mreu...@nmr.mgh.harvard.edu > Date: Wed, 14 Oct 2015 10:54:41 -0400 > Subject: Re: [Freesurfer] A mixed effect model approach in within > subject dataset {Disarmed} > > Hi Pablo, > > you should run something like this to get the ni: > > [M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data) see > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > hope that helps, Martin > > > On 10/14/2015 10:43 AM, pablo najt wrote: > > <!----> Dear FS experts. I have query about a relating to a previous > email (below).?I am aiming to run a LME analysis on cross-sectional data > from different families and have variable 'family' (number of families) > as my NI vector.? My design has three groups and therefore I am not able > to use qdec. I am running the matlab commands below and finding some > difficulty would really appreciate if you could help out. Thanks Pablo > Start analysis as follows: > 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');? > > %---------------------I input the concatenated .mgh image from preproc > and > mris_surf2surf-----------------------------------------------------------------------% > > 3-Fit a vertex-wise lme model with random effects.: > lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); > > Here I am getting the following problems: %-------------------- If I use > number of families as my ni get the > following------------------------------------------------------------------------------------------------% > > > > lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex); > > > > Error using lme_mass_fit (line 108) > > > > The total number of measurements, indicated by sum(ni), mustbe the same > as the number of rows of the design > > > > matrix X > > > > > > > > > Error in lme_mass_fit_vw (line 73) > > > > [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); > > > > > My matrix is organised in "family", "group", Sex" and "age" columns". > ? ? > 4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix]; > F_lhstats = lme_mass_F(lhstats, CM); 5-Save results eg.:? > fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');?? > > Date: Thu, 10 Sep 2015 13:44:36 +0000 From: jbernal0...@yahoo.es To: > freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect > model approach in within subject dataset Hi Pablo I think you can use > LME to analyze your data by ordering the rows of your design matrix > appropriately. You can consider all subjects belonging to the same family > as if they were a single subject in a longitudinal analysis. You can put > in your design matrix all subjects belonging to family1 first, then all > subjects belonging to family 2 and so on. Then the 'ni' required by > lme_mass_fit_vw is a vector with the number of subjects in each family > as its entries (ordered according to your design matrix). So the length > of the 'ni' vector is equal to the number of different families in your > data. Now you can go further and additionally order the rows of your > design matrix within each family by age. This will allow you to test the > effect of age within family. When choosing the random effects for your > statistical model remember that a random effect can only be the intercept > term or any covariate that varies within family. For example you can > compare a model with a single random effect for the intercept term > against the same model but considering both the intercept term and age > as random effects. Hope that helps Cheers -Jorge > De: pablo najt <pablon...@hotmail.com> Para: " > freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: > Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect > model approach in within subject dataset <!----> Dear Freesurfer > users, I wanted to enquire if anyone had successfully been able to > implement Bernal's Linear Mixed Effects (LME) Models in cross-section > dataset *not longitudinal* (please see previous thread below). ?I am > willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 > covariates (sex, age, and family) with "family" variable been a > within-subject factor. LME?will allow?to control for the non-independence > of data contributed by patients and relatives from the same families. > Thanks in advance! Pablo From: michaelnot...@hotmail.com To: > freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 > Subject: [Freesurfer] Analysis of structural data acquired from multiple > sites by using a mixed effect model approach <!----> Hi everybody, I > want to compare the surface data of 3 groups (GroupA, GroupB and > Controlls) but have the problem that they were acquired from 4 different > scanner sites. As I can see it, there are three ways how I could tackle > this problem: 1. I could use mri_glmfit and create a qdec table / > fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And > then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 > -0.25] to compare GroupA to the Controlls. My Problem with this approach > is, that the sites don't contribute the same amount of subjects to the > analysis. I'm not sure if this could be handled by simply using a weighted > contrast. Meaning, if Site1 and Site2 had twice as many subjects than > Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 > 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account > for the variability between sites. In this case, I only need to specify > 3 classes (Class GroupA; Class Gro! > upB; Cla > ss Controlls) in my fsgd-file. And I use a design matrix that has 4 > dummy variables at the end, which specify to which site a subject belongs. > This approach might work, but I'm not confident that it is the right one. > 3. I could use a mixed effect model approach and specify site as a > random effect. If I understand it correctly, the mixed effect model > approach would be the best one, as it accounts for the variability within > sites. Is that correct or are there other issues/better approaches? I > tried to implement a mixed effect model by using Bernal's Linear Mixed > Effects (LME) Models ( > http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but > run into some problems. I'm not sure if LME can only be applied on > longitudinal data or if my implementation is wrong. I have a design > matrix X that specifies the characteristics of each subject per row as > follows: Intercept?? GroupA?? GroupB?? Controll?? Age?? IQ?? Site1?? > Site2?? Site3?? Site4 1? 1? 0? 0? 11.1? 99?? 0 0 1 0 1? 0? 1? 0? 11.1? 101? > 0 0 1 0 1? 1? 0? 0? 11.4? 95?? 1 0 0 0 1? 0? 0? 1? 12.4? 100? 1 0 0 0 ... > As I have no repeated measures, 'ni' is just a vector with length X > containing '1's. If I do now the vertex-wise linear mixed-effects > estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 > 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... > connected to 8 workers. ? Starting model fitting at each location ... ? > Location 24994: Index exceeds matrix dimensions. Location 24994: > Algorithm did not converge. Initial and final likelihoods: -10000000000, > -10000000000. Location 62484: Index exceeds matrix dimensions. Location > 62484: Algorithm did not converge. Initial and final likelihoods: > -10000000000, -10000000000. ... I've checked the matrix dimensions of X, > Y, ni and lhcortex and compared them to the LME mass_univariate example > stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. > Has anybody encountered similar problems? Is my approach of s! > pecifyin > g 'ni' as a vector of'1's even legitimate? Thanks, Michael > _______________________________________________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. > _______________________________________________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. > _______________________________________________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. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > _______________________________________________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. > _______________________________________________ > 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. > > > > > _______________________________________________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. > _______________________________________________ > 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. > > > > > _______________________________________________ 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > _______________________________________________ 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > _______________________________________________ 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > _______________________________________________Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps:// > mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in > this e-mail is intended only for the person to whom it isaddressed. If you > believe this e-mail was sent to you in error and the e-mailcontains patient > information, please contact the Partners Compliance HelpLine athttp:// > www.partners.org/complianceline . If the e-mail was sent to you in > errorbut does not contain patient information, please contact the sender > and properlydispose 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. > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/abe3af53/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ATT00002 > Type: image/jpeg > Size: 64802 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/abe3af53/attachment-0004.jpe > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ATT00003 > Type: image/jpeg > Size: 8031 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/abe3af53/attachment-0005.jpe > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ATT00004 > Type: image/jpeg > Size: 9926 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/abe3af53/attachment-0006.jpe > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: ATT00001 > Type: image/jpeg > Size: 13124 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/abe3af53/attachment-0007.jpe > > ------------------------------ > > Message: 4 > Date: Thu, 22 Oct 2015 10:58:55 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Sulcal depth units > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1510221058360.3...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Simon > > they are originally mm, but I believe we z-score normalize them so that > the sulc file is 0 mean and unit variance. > > cheers > Bruce > On Wed, 21 Oct 2015, Simon > Vandekar wrote: > > > Dear Freesurfer experts, > > > > I am reading the manuscript "Cortical Surface-Based Analysis II: > Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, > Sereno, and Dale (1999) where the estimation of sulcal depth is described > on page 199, however from the description I am still unsure of the exact > units of sulcal depth. > > Are the units for sulcal depth in mm or are they in arbitrary units? > > > > Thanks in advance, > > Simon > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > ------------------------------ > > Message: 5 > Date: Thu, 22 Oct 2015 11:05:06 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mris_expand - problem reading thickness > file? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1510221104450.3...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Alex > > if you upload the subject that is causing this problem I'll take a look. > What version are you running and what OS? > > cheers > Bruce > On Thu, 22 Oct 2015, Alex Puckett > wrote: > > > > > Hello! > > > > > > I'm having trouble with mris_expand using the -thickness flag.??If I > expand > > by a fixed distance instead of % thickness?then mris_expand works no > problem > > -??the program seems to be hanging up when?reading the thickness file. > Has > > anyone else?experienced?this? > > > > > > The command I'm running (from the surf folder)?is: > > > > mris_expand -thickness lh.white 0.5 lh.expandWhiteThick0p5 > > > > The output from this is: > > "?using distance as a % of thickness > > expanding surface lh.white by 50.0% of thickness and writing it to > > lh.expandWhiteThick0p5 > > reading thickness..." > > > > And then...nothing! Watching the CPU usage it appears that resources are > > used for about 10 -12 minutes and then drops to 0 and just sits there > for as > > long as I'll let it (>4 days)?- no error. > > > > Also, the thickness files do not appear to be corrupt. I can overlay the > > thickness data onto a surface no problem.? > > > > Any help would be appreciated. > > > > Cheers, > > > > Alex > > > > --------------------------------------------------------------------- > > > > FREESURFER_HOME: /usr/local/freesurfer > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > > > RedHat release: CentOS Linux release 7.1.1503 (Core)? > > > > Kernel info: Linux 3.10.0-229.1.2.el7.x86_64 x86_64 > > > > --------------------------------------------------------------------- > > > > > > > > > > > > > > > > > > > > ? > > ------------------------------ > > Message: 6 > Date: Thu, 22 Oct 2015 11:08:04 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] How to compute the measures on the average > brain? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1510221107490.3...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Mathieu > > I don't see any reason we wouldn't continue to support it > Bruce > On Thu, 22 Oct > 2015, Mathieu Dubois wrote: > > > Hi again, > > > > Another advantage of using qcache in my case is that the file names are > > automatically generated and therefore standard. > > > > Is there any risk (particularly for future compatibility) in using > > qcache? Did anyone had some problem with it? > > > > Thanks in advance, > > Mathieu > > > > Le 21/10/2015 18:07, Mathieu Dubois a ?crit : > >> Hi Doug, > >> > >> Thanks for your answer. > >> > >> If I understand correctly, the tutorial describes the use of > >> mris_preproc with a group description file. If the data has not been > >> cached, it will compute them and stack all the results in a big file > >> (will it write individual files?) . Of course if the data has been > >> cached, it will only stack them (this probably result in more disk usage > >> but that's OK). > >> > >> I don't plan to use FreeSurfer's linear model for group analysis (my > >> goal is to use those data in machine learning algorithms) but other > >> people at the institute I work for may be interested in that. I think > >> it's more convenient to have one file per subject (so I can group them > >> in a more flexible way). > >> > >> So I guess I can always run recon-all for each subject with -qcache (I > >> have read that is safe to do so) in order to generate the data for each > >> subject (this can easily be distributed across a cluster and compute > >> several measures). I can then load the data for each subject and people > >> interested into running FreeSurfer group analysis can also use them. Is > >> it correct? > >> > >> My only concern is: will -qcache be supported in future versions of > >> FreeSurfer? Couldn't some part of it (like the resampling on the average > >> subject but no the smoothing) be integrated into -all? > >> > >> Mathieu > >> > >> Le 21/10/2015 16:37, Douglas Greve a ?crit : > >>> Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, > >>> you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to > >>> do the group analysis, then mri_glmfit-sim to do the correction for > >>> multiple comparisons. > >>> doug > >>> > >>> On 10/21/15 10:15 AM, Mathieu Dubois wrote: > >>>> Hi, > >>>> > >>>> I'm a beginner with freesurfer so I apologize if it's a trivial > question. > >>>> > >>>> I recently run recon-all with the -all on many subjects. As far as I > can > >>>> say, all the steps worked. However, the measures on the average brain > >>>> (output of mris_preproc and friends) were not computed. > >>>> > >>>> A colleague told me that he usually re-run recon-all with the -qcache > >>>> flag to compute those. This seems to work but I don't understand if it > >>>> is the recommended way to run mris_preproc and why it is not included > >>>> with -all. Is it possible to get those measures in one call to > recon-all? > >>>> > >>>> I don't think that the issue comes from the data (e.g. that the > failing > >>>> of a step stops some branch of the pipeline) because it seems to run > >>>> correctly with -qcache. > >>>> > >>>> I haven't found any help on -qcache and the help of recon-all doesn't > >>>> mention mris_preproc or mri_surf2surf. > >>>> > >>>> Thanks in advance, > >>>> Mathieu > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>> _______________________________________________ > >>> 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. > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > Message: 7 > Date: Thu, 22 Oct 2015 11:39:22 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Talairach_afd error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1510221138530.19...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Anna > > are the talairach.xfm files generated by the two machines similar? > > Bruce > On Wed, > 21 Oct 2015, Anna I. Garcia Diaz wrote: > > > Dear all, > > I am having problems running the recon-all process. The error log is > attached to this e-mail.? > > > > This error appears only when I run recon-all in a machine able to > parallelize preprocesses, however, if I use the same > > reconstructed oriented image in a machine sent as a normal job directly > to the terminal, the preprocess runs without > > any errors and the output looks correct. I have tried to use the > -notal-check flag as the error log suggests, but it > > fails anyway.? > > > > Since our team is working in a longitudinal study, and the images from > the other time points have been preprocessed > > with the parallelizing machine, we are concerned that using the > non-parallelizing machine could add significant > > methodological variabilities to our studies, and we would rather be > consistent with the previous procedures.? > > > > Do you have any comments or further suggestions on how we might be able > to fix this error? > > > > Thanks in advance for your time and help > > Anna Garcia > > > > > > ------------------------------ > > Message: 8 > Date: Thu, 22 Oct 2015 11:42:07 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] How to compute the measures on the average > brain? > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <562903cf.6030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > No, we will continue to support it > > On 10/21/2015 11:13 PM, Mathieu Dubois wrote: > > Hi again, > > > > Another advantage of using qcache in my case is that the file names are > > automatically generated and therefore standard. > > > > Is there any risk (particularly for future compatibility) in using > > qcache? Did anyone had some problem with it? > > > > Thanks in advance, > > Mathieu > > > > Le 21/10/2015 18:07, Mathieu Dubois a ?crit : > >> Hi Doug, > >> > >> Thanks for your answer. > >> > >> If I understand correctly, the tutorial describes the use of > >> mris_preproc with a group description file. If the data has not been > >> cached, it will compute them and stack all the results in a big file > >> (will it write individual files?) . Of course if the data has been > >> cached, it will only stack them (this probably result in more disk usage > >> but that's OK). > >> > >> I don't plan to use FreeSurfer's linear model for group analysis (my > >> goal is to use those data in machine learning algorithms) but other > >> people at the institute I work for may be interested in that. I think > >> it's more convenient to have one file per subject (so I can group them > >> in a more flexible way). > >> > >> So I guess I can always run recon-all for each subject with -qcache (I > >> have read that is safe to do so) in order to generate the data for each > >> subject (this can easily be distributed across a cluster and compute > >> several measures). I can then load the data for each subject and people > >> interested into running FreeSurfer group analysis can also use them. Is > >> it correct? > >> > >> My only concern is: will -qcache be supported in future versions of > >> FreeSurfer? Couldn't some part of it (like the resampling on the average > >> subject but no the smoothing) be integrated into -all? > >> > >> Mathieu > >> > >> Le 21/10/2015 16:37, Douglas Greve a ?crit : > >>> Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, > >>> you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to > >>> do the group analysis, then mri_glmfit-sim to do the correction for > >>> multiple comparisons. > >>> doug > >>> > >>> On 10/21/15 10:15 AM, Mathieu Dubois wrote: > >>>> Hi, > >>>> > >>>> I'm a beginner with freesurfer so I apologize if it's a trivial > question. > >>>> > >>>> I recently run recon-all with the -all on many subjects. As far as I > can > >>>> say, all the steps worked. However, the measures on the average brain > >>>> (output of mris_preproc and friends) were not computed. > >>>> > >>>> A colleague told me that he usually re-run recon-all with the -qcache > >>>> flag to compute those. This seems to work but I don't understand if it > >>>> is the recommended way to run mris_preproc and why it is not included > >>>> with -all. Is it possible to get those measures in one call to > recon-all? > >>>> > >>>> I don't think that the issue comes from the data (e.g. that the > failing > >>>> of a step stops some branch of the pipeline) because it seems to run > >>>> correctly with -qcache. > >>>> > >>>> I haven't found any help on -qcache and the help of recon-all doesn't > >>>> mention mris_preproc or mri_surf2surf. > >>>> > >>>> Thanks in advance, > >>>> Mathieu > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>> _______________________________________________ > >>> 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. > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 9 > Date: Thu, 22 Oct 2015 11:48:26 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] normalization of hippocampal volume > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <5629054a.8090...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=euc-kr > > I'm not sure what you mean by either of those options. can you explain? > > On 10/22/2015 04:18 AM, geschwind2013 wrote: > > Hi, FS Experts, > > > > I?m using version 5.3 and have performed hippo-subfields analysis. > > > > To perform the statistics, shall I get the normalized volumes of each > hippo-subfields? > > or just to do correction for ICV is enough ? > > > > thanks.. > > > > Hyon > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 10 > Date: Thu, 22 Oct 2015 11:50:10 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] per analysis with covariates > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <562905b2.6070...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > what do you mean to control age and gender on both lGI and thickness? If > you have thickness = f(gender,age,lGI), then you control for gender, > age, and lGI on thickness. > > On 10/20/2015 06:20 AM, marica.pad...@libero.it wrote: > > > > Hi, > > > > I am running a vertex-wise correlation analysis between local > gyrification (-- > > y) and thickness (--pvr) using as covariates age and gender. > > I want to control for the effect of age and gender both the lGI and the > > thickness values. Does the command does this? Or the effect of the > covariates > > is only taken into account for the lGI? > > > > Here my command line: > > > > mri_glmfit --glmdir left --y lh.lGI.mgh --fsgd fsgd_control.txt --pvr lh. > > thickness.mgh --C contrast_control.txt --surface fsaverage lh > > > > And my contrast: > > > > 0 0 0 1 (first 0 for the class, second and third for the 2 covariates). > > > > Thanks, > > Marica > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 140, Issue 37 > ******************************************* >
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