Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Fwd: Question about Freesurfer LME analysis
by Bronwyn Overs 15 Jul '19

15 Jul '19

External Email - Use Caution Dear Freesurfer Mailing list, I have run a mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' and then applied an FDR correction across both hemispheres (syntax provided below). On completion I realised that m ost of the corrected p-values for my main and interaction effects were well above the alpha of 0.05. The corrected p-value thresholds in log base 10 format are included in the attached figure and summarised below. Summary of p-value thresholds in attached images: Figure Key Log10P P Figure 1 A1 -1.193 0.064 A2 -0.695 0.202 B1 -0.969 0.107 B2 -0.243 0.571 C1 -0.195 0.638 C2 -0.001 0.998 Figure 2 A -2.663 0.002 B -1.295 0.051 I have no idea why this has happened and would greatly appreciate any insight you can provide. I would also note that the same issue occurred in a model where we exclude all subjects with only a single time-point. However, it did not occur when we included only Caucasians in our analysis and excluded the two dummy coded ethnicity covariates. This leads me to think its something to do with the complexity of the model, but I cannot understand why the error is only occurring when we correct for multiple comparisons. I have provided the details of sample and methods below. Sample Our sample includes 112 controls subjects, and 106 at-risk subjects (individuals with a first degree relative of BD but not personal history of BD). All subjects are aged between 12 and 30 years. 153 or these subjects have 2 time-points (77 control, 76 at-risk), while the remaining 65 individuals have only 1 MRI time-point. We also have mixed ethnicites - 165 Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians). Analysis Design The QDEC file contains the following 6 variables: 1. Y (years between scans) 2. A (baseline age) 3. G (group, 1=case, 0=control) 4. S (sex, 1=female, 0=male) 5. E1 (Ethnicity 1, 1=asian, 0=other) 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other) Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)] i.e. main effects for each of the qdec variables + an interaction term for years X group DVs: Cortical thickness, area and volume Model: Mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' CODE: % Read in surface files [Y,mri] = fs_read_Y(mgh); % Read in qdec file Qdec = fReadQdec(qdec); % Remove fsid from qdec Qdec = rmQdecCol(Qdec,1); % Store col 1 (fsid-base) in sID variable sID = Qdec(2:end,1); % Remove col 1 (fsid-base) from Qdec array Qdec = rmQdecCol(Qdec,1); % Convert Qdec to numeric matrix M M = Qdec2num(Qdec); % Sort data and evaluate design matrix [M,Y,ni] = sortData(M,1,Y,sID); X = eval([ones(length(M),1) M M(:,1).*M(:,3)]) % Compute vertex-wise temporal covariance estimates. [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3); %Segmentation and model fitting. [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y, ni); %Check surfaces. surfcomp(Th0, RgMeans, sphere, fig1, fig2) Correction for multiple comparisons: FDR across both hemispheres CODE: P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth); thrlh(r,2) = {pcor}; thrrh(r,2) = {pcor}; [~,dc] = size(detvtx); dvtx(r,2) = {dc}; Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Re: [Freesurfer] freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Did you try, $ ldd /usr/local/freesurfer/bin/freeview | grep not ? - R. On Jul 12, 2019, at 08:42, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeviewBut when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd freeview | grep notldd: ./freeview: No such file or directory.Thank you for your help,JC.---------- Forwarded message ---------De: Juan Rivas <jcrn12(a)gmail.com>Date: vie., 12 jul. 2019 a las 6:57Subject: freeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>That is what happened:$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directoryJC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: lun., 15 jul. 2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>Hello JC,Try this to see what libs are missing,$ ldd /usr/local/bin/freeview | grep not- R._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Fwd: Freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview. If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which freeview” will likely tell you where the binary is.  You should have already set FREESURFER_HOME to point to the freesurfer  installation and then did the source of the shell init file (SetUpFreeSurfer.sh for bash or sh, SetUpFreeSurfer.csh for csh).  See the wiki page here under setup and configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndIn… That should have put freeview in your PATH so that “which freeview” works. What you want to do is to cd into the directory where the freeview binary lives and run ldd on it.  If “which freeview” returned /usr/local/bin/freeview then you could “cd /usr/local/bin” and from there directly run “ldd freeview | grep not”. - R.  On Jul 12, 2019, at 07:32, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        That is what happened:$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or directoryJC.---------- Forwarded message ---------De: fsbuild <fsbuild@contbay.com>Date: lun., 15 jul. 2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <jcrn12(a)gmail.com>Hello JC,Try this to see what libs are missing,$ ldd /usr/local/bin/freeview | grep not- R.On Jul 12, 2019, at 06:19, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18This is the message I get:$ freeviewsh: 8: freeview: not found$  which freeview                  $ /usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry `ldd --help' for more information.Thank you very much,JC.El lun., 15 jul. 2019 a las 12:50, fsbuild (<fsbuild(a)contbay.com>) escribió:Hello Juan,For CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ sudo yum install libgfortran.x86_64For Ubuntu,$sudo apt-get install gfortranOne thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which freeview/usr/local/bin/freeview- then check you have the ldd command, $ which ldd/usr/bin/lddIf the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing.  Prior to doing the install of libgfortran above, it should list libgfortran is missing.$ ldd `which freeview` | grep notAlso it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.- R.On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        ---------- Forwarded message ---------De: Juan Rivas <jcrn12(a)gmail.com>Date: vie., 12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild <fsbuild(a)contbay.com>Hi, thank you for your answer.I did what you recommended to me, and I get this message:freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) escribió:Hello JC,Your machine could be missing the qt5 libraries/files.On Ubuntu linux you can try installing them with,$ sudo apt-get install qt5-default qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory.How can I fix it?Thanks a lot,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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optseq2 parameters setup
by Tugce Duran 15 Jul '19

15 Jul '19

External Email - Use Caution Hi Dr. Greve, I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI task for our study. There are 80 face-name pairs that we will use and the duration can be between 3.5 and 4.75 secs. I have used the following command: optseq2 --ntp 200 --tr 2 --psdwin 0 32 2 --ev facename 4 80 --nkeep 3 --o trial2 --tnullmin 0 --tnullmax 6 --nsearch 10000 Total scan time appx 6-7 mins. Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we change the variety amount of the jitters? Are more jitters good or bad (instead of just having 2 secs and 4 secs, let's say we get 0.25, 1, 2, 3 and 4 secs) ? Q2: For the event design I am interested in above, what would be the "best" parameters used? Trial2-001.par: 0.0000 1 4.000 1.0000 facename 4.0000 1 4.000 1.0000 facename 8.0000 1 4.000 1.0000 facename 12.0000 0 2.000 1.0000 NULL 14.0000 1 4.000 1.0000 facename 18.0000 1 4.000 1.0000 facename 22.0000 1 4.000 1.0000 facename 26.0000 1 4.000 1.0000 facename 30.0000 1 4.000 1.0000 facename 34.0000 1 4.000 1.0000 facename 38.0000 1 4.000 1.0000 facename 42.0000 0 4.000 1.0000 NULL 46.0000 1 4.000 1.0000 facename 50.0000 1 4.000 1.0000 facename 54.0000 1 4.000 1.0000 facename 58.0000 1 4.000 1.0000 facename 62.0000 1 4.000 1.0000 facename 66.0000 1 4.000 1.0000 facename 70.0000 1 4.000 1.0000 facename 74.0000 0 2.000 1.0000 NULL 76.0000 1 4.000 1.0000 facename 80.0000 0 2.000 1.0000 NULL 82.0000 1 4.000 1.0000 facename . . . . 372.0000 0 4.000 1.0000 NULL 376.0000 1 4.000 1.0000 facename 380.0000 1 4.000 1.0000 facename 384.0000 1 4.000 1.0000 facename 388.0000 1 4.000 1.0000 facename 392.0000 1 4.000 1.0000 facename 396.0000 1 4.000 1.0000 facename Thank you in advance! Tugce Tugce Duran Graduate Student, Biomedical Sciences MS Program Neuroscience Concentration | Section on Gerontology & Geriatric Medicine, WFSM [2color] Graduate Programs in Biomedical Sciences 525 Vine Street, Suite 150, Winston-Salem, NC 27101 * 317-893-9100 | * tduran(a)wakehealth.edu<mailto:tduran@wakehealth.edu> | |[Image result for linked in]linkedin.com/in/tugceduran/<http://linkedin.com/in/janesmith/> The information contained in this message is privileged and confidential information intended for the sole use of the addressee. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, please notify the person listed above immediately by e-mail, and delete the original message and attachments.

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Re: [Freesurfer] Freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. On Jul 12, 2019, at 06:19, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18This is the message I get:$ freeviewsh: 8: freeview: not found$  which freeview                  $ /usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry `ldd --help' for more information.Thank you very much,JC.El lun., 15 jul. 2019 a las 12:50, fsbuild (<fsbuild(a)contbay.com>) escribió:Hello Juan,For CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ sudo yum install libgfortran.x86_64For Ubuntu,$sudo apt-get install gfortranOne thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing....This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which freeview/usr/local/bin/freeview- then check you have the ldd command, $ which ldd/usr/bin/lddIf the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing.  Prior to doing the install of libgfortran above, it should list libgfortran is missing.$ ldd `which freeview` | grep notAlso it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.- R.On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        ---------- Forwarded message ---------De: Juan Rivas <jcrn12(a)gmail.com>Date: vie., 12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild <fsbuild(a)contbay.com>Hi, thank you for your answer.I did what you recommended to me, and I get this message:freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) escribió:Hello JC,Your machine could be missing the qt5 libraries/files.On Ubuntu linux you can try installing them with,$ sudo apt-get install qt5-default qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory.How can I fix it?Thanks a lot,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] general installation and configuration questions (new user!)
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Hello Robin, I believe folks use the freesurfer binary archive expanded/installed on file servers that are remotely mounted, e.g., thru NFS, so everyone can share a common installation.  IT/dev-ops can implement that in different ways, e.g., maybe the freesurfer installation actually lives on a fast RAID/redundant file system over NFS, etc.  But you ultimately need to set FREESURFER_HOME in your shell environment point to wherever freesurfer is installed which could be a remote mount point on your local computers file system.  Hopefully a remote mount point to the freesurfer installation (via NFS) is standardized to be the same path for everyone on their local machines. Fast disks and fast filesystems can always help with speeding up read/writes of data.  SSD storage hanging off the latest PCIe buss designs should outperform hard drives. Users often have a local disk in their machine to process data (preferably not the same disk as the boot partition is on).  Or maybe IT has some available storage over NFS for users to process their data, though read/writes over NFS are going to be slower than working off a local disk (with or w/o -openmp).   You could use soft links to point to different parts of the data if you wanted to physically re-locate pieces of it, but any paths thru soft links should make it look like there is a single tree with the data. - R. On Jul 15, 2019, at 05:06, Robin Warne <R.Warne(a)kent.ac.uk> wrote:        External Email - Use Caution        Hi folks, I am new to the Freesurfer world and I have a couple of questions about installing the application, specifically around the 10Gb “footprint” of data, after unpacking the archive file. So I have run through the installation and configuration steps outlined on the Wiki page, which is great, by the way!  Running through the steps first time around went without a hitch but the conversion of the sample data took many hours.  If I have to run that conversion again, I will try the recon-all with “ -openmp { some appropriate value } “ to try and speed it up. I’m guessing that the sample data is occupying a large part of the 10Gb disk space “footprint” so is it appropriate to remove it, without breaking anything?  If we wanted to install Freesurfer on to a server, for multiple users to access, is that possible?  Somewhere like ‘/usr/local’, as described in the Wiki? Thanks in advance, for any guidance anyone can offer. Robin Warne,University of Kent (U.K.) _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Research Specialist position on the Midlife in the US Neuroscience Project
by CHM Recruiting 15 Jul '19

15 Jul '19

External Email - Use Caution The Center for Healthy Minds is hiring a Research Specialist! The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening, and scheduling for research at the University of Wisconsin-Madison's Center for Healthy Minds. This individual may work on several research projects examining the import of individual differences in the time course of emotional responses for varied domains including cognition, health, and well-being, while elucidating the critical functional and structural brain substrates underlying these relationships. Please view the attached position description for more information and instructions on how to apply.

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Freeview
by Juan Rivas 15 Jul '19

15 Jul '19

External Email - Use Caution ---------- Forwarded message --------- De: Juan Rivas <jcrn12(a)gmail.com> Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild <fsbuild(a)contbay.com> Hi, thank you for your answer. I did what you recommended to me, and I get this message: freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory. What could be the next step? JC. El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) escribió: > Hello JC, > > Your machine could be missing the qt5 libraries/files. > > On Ubuntu linux you can try installing them with, > $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev > > On CentOS linux, > $ sudo yum install qt-create qt-config.x86_64 > $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64 > > - R. > > On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote: > > External Email - Use Caution > > Hello, I am trying to use freeview, but everytime I try I get this message: > freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot > open shared object file: No such file or directory. > How can I fix it? > Thanks a lot, > JC. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] Freeview
by fsbuild 15 Jul '19

15 Jul '19

External Email - Use Caution Hello JC, Your machine could be missing the qt5 libraries/files. On Ubuntu linux you can try installing them with,$ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev On CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64 - R.. On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory.How can I fix it?Thanks a lot,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MRI Technologist Job Posting at The Ohio State University
by Prakash Lab 15 Jul '19

15 Jul '19

External Email - Use Caution Hello, The Center for Cognitive and Behavioral Brain Imaging (CCBBI) at The Ohio State University is seeking to hire a Magnetic Resonance Imaging (MRI) Technologist. Please see attached document for full description. Best Regards, The Clinical Neuroscience Laboratory [image: The Ohio State University] The Clinical Neuroscience Laboratory Department of Psychology 74 Psychology Building, 1835 Neil Avenue, Columbus, OH 43210 614-292-9568 Office ra(a)clinicalneurosciencelab.com www.clinicalneurolab.org Confidentiality Notice: This email transmission (including any documents, files or attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, you are hereby notified that any disclosure, copying or distribution, or any use of the enclosed or attached information is strictly prohibited. If you have received this transmission in error, please notify me immediately by return email and delete all materials without reading, copying, saving or printing them.

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Freesurfer July 2019