Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Re: [Freesurfer] unit in 'search area' in the glmfit log
by Jeni Chen 03 Nov '15

03 Nov '15

Thank you Doug. I was actually referring to the following values (example of my log output below): $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/pathname cmdline mri_glmfit --y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C ./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C ./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask ./pathname/mask.mgh --sim mc-z 5000 1.3 ./pathname/csd/mc-z.abs.1.3.j001 --sim-sign abs --fwhm 13.034857 --fsgd ./pathname/y.fsgd dods --label /Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white sysname Darwin hostname computer.local machine x86_64 user jeni FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.034857 niters 125.000000 OneSampleGroupMean 0 y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh logyflag 0 usedti 0 FSGD ./pathname/y.fsgd labelmask /Volumes/pathname/lh_abcd_mask.label maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 14.1782 Matrix condition is 289425 Found 9260 points in label. Found 7440 voxels in mask Reshaping mriglm->mask... search space = 3795.353314 DOF = 37 thresh = 1.3, threshadj = 0.99897 I do see that it gives information on the number of voxels in the mask (which is 7440 in the above example). What I was referring to is the next number "search space = 3795.35..." Is that the search area? Also in your reply, I see the need to specify the mask.mgh. How do I specify it if my mask is a label file and not in mgh format? Thanks again. Jeni > On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote: > That number is in voxels or vertices. If you want surface area, then use > mri_segstats something like >> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh >> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat >> >> doug >> >> On 10/29/15 5:10 PM, Jeni Chen wrote: >> > Hello, >> > >> > When running the Clusterwise Correction for Multiple Comparisons, I used a >> > label as a mask to restrict search area. I want to find out the size of that >> > label, so I guess I can pull that information out from the "mri_glmfit.log", >> > specifically under 'searchspace'? Also I only see a numerical value there, I >> > assume it is in mm2? >> > >> > Thanks. >> > >> > Jeni

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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
by pablo najt 03 Nov '15

03 Nov '15

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.ThanksPablo 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 designmatrix 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: jbernal0019(a)yahoo.es To: freesurfer(a)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 <pablonajt(a)hotmail.com> Para: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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: michaelnotter(a)hotmail.com To: freesurfer(a)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 GroupB; Class 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 specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael _______________________________________________ Freesurfer mailing list Freesurfer(a)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(a)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(a)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.

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1.5T vs 3.0T longitudinal study...
by Gonzalo Rojas Costa 03 Nov '15

03 Nov '15

Hi: I have two timepoints of the same patient: the first is in 1.5T and the second in 3.0T... Is it possible to do the longitudinal study (subcortical volumes) using the Workflow Summary described in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ------------------------------------ Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clinica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim
by Douglas N Greve 03 Nov '15

03 Nov '15

The correct command line is --cache 4 neg --cache-label AC On 11/03/2015 03:36 PM, smcl(a)u.washington.edu wrote: > Hi Doug, > > > > So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot > find any documentation about what to put instead of --grf), as in > > mri_glmfit-sim --glmdir > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx > --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces > > I get back "ERROR: Flag 4 is unrecognized." > > If I try just --cache instead of --cache-label AC, I get back "ERROR: > cannot find > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh" > > Any thoughts? > > Many thanks, > Susan > > On Tue, 3 Nov 2015, Douglas N Greve wrote: > >> The fwhm.dat file was in the right place. You passed the wrong folder to >> mri_glmfit-sim. You should pass it >> >> cope7ACroi_rh.osgm.rfx >> >> doug >> >> >> On 11/03/2015 02:40 PM, smcl(a)u.washington.edu wrote: >>> It's: >>> >>> mri_glmfit --y >>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh >>> --osgm --glmdir >>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx >>> --surf fsaverage lh --label >>> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label >>> >>> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than >>> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also >>> happened for some other files needed and I moved them. Is the >>> problem something in my mri_glmfit command? >>> >>> Susan >>> >>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>> >>>> it cannot find this file >>>> >>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat >>>> >>>> >>>> which should have been created by mri_glmfit. What is your mri_glmfit >>>> command line? >>>> >>>> Also, don't use --grf, that is for volumes only >>>> >>>> >>>> On 11/03/2015 02:27 PM, smcl(a)u.washington.edu wrote: >>>>> Hi DOug, >>>>> >>>>> doug.log is attached >>>>> >>>>> the bash equivalent for |& is 2>&1 | >>>>> >>>>> thanks, >>>>> Susan >>>>> >>>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>>> >>>>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm >>>>>> not >>>>>> sure what the bash equivalent is. Maybe |2 instead of |& >>>>>> perhaps some bash experts can weigh in >>>>>> >>>>>> On 11/03/2015 01:41 PM, smcl(a)u.washington.edu wrote: >>>>>>> Hi Doug, >>>>>>> >>>>>>> Do you mean: >>>>>>> >>>>>>> mri_glmfit-sim --debug --glmdir >>>>>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm >>>>>>> >>>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee >>>>>>> doug.log? >>>>>>> >>>>>>> When I tried running the same code with |& tee doug.log at the end, >>>>>>> I kept getting: >>>>>>> >>>>>>> syntax error near unexpected token `&' >>>>>>> >>>>>>> Thanks, >>>>>>> Susan >>>>>>> >>>>>>> On Tue, 3 Nov 2015, Douglas N Greve wrote: >>>>>>> >>>>>>>> Can you run >>>>>>>> >>>>>>>> mri_glmfit-sim --debug --glmdir [my data >>>>>>>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg >>>>>>>> --cwpvalthresh 0.05 --2space |& tee doug.log >>>>>>>> >>>>>>>> and send me doug.log? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 11/02/2015 05:08 PM, smcl(a)u.washington.edu wrote: >>>>>>>>> Hi experts, >>>>>>>>> >>>>>>>>> I am having trouble performing a Monte Carlo correction using >>>>>>>>> mri_glmfit-sim. >>>>>>>>> >>>>>>>>> My data were sampled to fsaverage and smoothed at fwhm 5, using >>>>>>>>> mris_preproc. I then ran mri_glmfit on the data. >>>>>>>>> >>>>>>>>> I want to do my analysis/correction only in auditory cortex (AC) >>>>>>>>> so I did my own simulation in AC of each hemisphere using >>>>>>>>> mri_mcsim (as per >>>>>>>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo) >>>>>>>>> >>>>>>>>> So far, so good. >>>>>>>>> >>>>>>>>> But when I try to run: >>>>>>>>> >>>>>>>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm >>>>>>>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space >>>>>>>>> >>>>>>>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override >>>>>>>>> 5, but it didn't help. >>>>>>>>> >>>>>>>>> Any thoughts? Also, can you clarify which comparison neg vs pos >>>>>>>>> will give me? >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> >>>>>>>>> Susan McLaughlin, PhD >>>>>>>>> Research Scientist >>>>>>>>> Laboratory for Auditory Brain Sciences & Neuroengineering >>>>>>>>> Institute for Learning & Brain Sciences (I-LABS) >>>>>>>>> Portage Bay Bldg. Room 204 >>>>>>>>> University of Washington, Box 357988 >>>>>>>>> Seattle, WA 98195-7988 >>>>>>>>> >>>>>>>>> Ph: (206) 616-0102 Fx: (206) 221-6472 >>>>>>>>> Cell: 206-850-8638 >>>>>>>>> E-mail: smcl(a)uw.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> 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(a)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(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve(a)nmr.mgh.harvard.edu >>>>>> 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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> 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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> 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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu 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/

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Post-Doctoral position in brain imaging – University of Geneva {Disarmed}
by Narly Golestani 03 Nov '15

03 Nov '15

?Applications are invited for a Post-Doctoral position in the Brain and Language Lab (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org/>) at the University of Geneva. The position is for 2 years (or more), and will be at the new Biotech Campus (http://www.campusbiotech.ch/en/) Candidates should have a degree in Psychology and/or Cognitive Neuroscience, and should have a solid background in statistics and in the analysis of functional magnetic resonance imaging data. The projects will include brain imaging and behavioural studies on multilingualism and expertise, with a focus on executive skills, attention and statistical/language learning. The salary is competitive, starting salary at ~ 69, 000 CHF/year (~ 81, 000 CHF/year as of August 2016) depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. ?----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Department of Clinical Neuroscience Biotech Campus 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 http://www.brainandlanguagelab.org<https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…> ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Freesurfer 6.0
by Hoptman, Matthew 03 Nov '15

03 Nov '15

Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me. I also tried to ftp to your ftp site, and unfortunately, I got the message 421 Proxy is closed (unknown user location). Could you please tell me how I could get the new version of Freesurfer? Thanks, Matt IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Re: [Freesurfer] visualizing paths stats by voxel
by Janosch Linkersdörfer 03 Nov '15

03 Nov '15

Hi Anastasia and list, sorry, I just now got around to testing out the new build of dmri_paths you sent me. Sadly, the results look about the same: Here the path stats file for the left SLFt: What could be the problem?! I think I did what you suggested: - install the new version of dmri_paths (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it executable - rerun trac-all -path for the subjects with only one time point - rerun trac-all -stat for all subjects Also: Is that problem only a visualization problem, or does it also mean that the values I get for a participant at a specific part of a tract are not aligned and I cannot analyze the data in that way? Thanks for your help!! Best, Janosch > On 20 Aug 2015, at 21:35, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of dmri_paths tomorrow. You'll have to replace your copy of $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only for the subjects that have 1 time point. Then rerun "trac-all -stat" with all subjects together. And then tell us what other problem you find :) > > Best, > a.y > > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: > >> Hey Anastasia, >> >>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>> >>> >>> Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. >> >> OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it! >> >>> In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely. >> >> Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis... >> >>> >>> Thank you for trying things that nobody else has tried and finding these bugs! >> >> Somebody has to be the first, eh? :) >> >> Thank you very much, >> >> Janosch >> >>> >>> More soon, >>> a.y >>> >>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: >>> >>>> Hey Anastasia, >>>> >>>> thanks for looking into this. >>>> >>>>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> >>>>> Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects. >>>>> >>>>> I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well? >>>> >>>> Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. >>>> >>>> Thanks, >>>> >>>> Janosch >>>> >>>>> >>>>> Best, >>>>> a.y >>>>> >>>>> On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: >>>>> >>>>>> Hi Anastasia, >>>>>> >>>>>> yes, I am. But it looks similar in the distributed version :( >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Janosch >>>>>> >>>>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>>>> >>>>>>> >>>>>>> Hi Janosch - Are you by any chance using the dev version of freeview? >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: >>>>>>> >>>>>>>> Hi Anastasia and list, >>>>>>>> >>>>>>>> I'm trying to do analyses along the tract with the path_stats_byvoxel files. >>>>>>>> >>>>>>>> When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> this looks different to your slides: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Janosch >>>>>>> >>>>>>> >>>>>>> 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. >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >> >> >>

2 2

Adding more than 2 covariates in QDEC
by Deborrah Castillo 03 Nov '15

03 Nov '15

I wanted to ask if it is possible to run analysis in QDEC with more than 2 covariates for examples, instead of Age, I wanted to add depression scores or race? At the moment my qdec table has two groups, two covariates... Class Group1 Class Group2 Variables Age PainMeasure If it is not possible, what is other alternate method would you suggest I could use to run analysis to look at group differences in brain measures with covarying for Age and Race / Depression Score in FreeSurfer? Thank you. Aloha, Deborrah -- -- University of Hawaii John A. Burns School of Medicine Department of Medicine Neuroscience and Magnetic Resonance Research Program Queens Medical Center, 7th Floor UH Tower 1356 Lusitana Street Honolulu, HI 96813 Tel:+1-808-586-7488 Tel: +1808-586-7459 Fax:+1808-586-7465 Web: http://hawaii.edu/mri/home_v6.htm

2 1

cortical thickness - comparing two groups within a ROI
by Eryilmaz, H. Hamdi 03 Nov '15

03 Nov '15

Dear FS experts, I have a question about extracting average cortical thickness from a manually created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd file appears as the following: GroupDescriptorFile 1 Title PostPreFortification Class PostFort Class PreFort Input Subject1 PostFort Input Subject2 PostFort . . . The contrast that I use to compare these groups is [1 -1]. When I display the significance map for this contrast I get the following image on the left hemisphere: [X] My first question is, those blue clusters represent regions, where thickness is greater in the PreFort group, don't they? Assuming this is correct, I created a label for this region (which contains about 3000 vertices) and extracted the thickness value from this region for each subject using the following commands. These commands are part of scripts in which $subject and $label are defined. [X] to make a label for each subject (the original label was created on fsaverage): mri_label2label --srclabel $SUBJECTS_DIR/labels/${label}.label --srcsubject fsaverage --trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject --regmethod surface --hemi lh to create a stats file of this ROI containing several anatomical measures: mris_anatomical_stats -f $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh to compile thickness values from all subjects into one table: aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc NP_PostMINUSPre_IPS.label --meas thickness --tablefile $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt This table displays the average thickness value of my ROI for each subject. Based on this table I calculated the mean thickness for each group, which is as the following: PostFort: 3.043 PreFort: 2.842 My question is: If this cluster appears blue in the Post>Pre map, shouldn't the thickness have been greater in the PreFort group? Or am I missing a step? Many thanks in advance! Best, Hamdi

2 6

Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors UCSD
by Leyden, Kelly 03 Nov '15

03 Nov '15

Dear Freesurfers, I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral position with our lab at UC San Diego. Location: UCSD Multimodal Imaging Laboratory (MMIL) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: Flexible, but no later than January 2016 Seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and primary brain tumors. Our multimodal imaging team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming (i.e., MATLAB) and writing skills, experience in neuroimaging or a related field, and a strong interest in pursing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience working with neurological populations are encouraged to apply. Please send CV and cover letter to Dr. Carrie McDonald (camcdonald(a)ucsd.edu<mailto:camcdonald@ucsd.edu>). Thank you, Kelly Kelly Leyden, MRes Neuroimaging Research Associate Multimodal Imaging Laboratory University of California San Diego kleyden(a)ucsd.edu

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Freesurfer November 2015