Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

qdec
by Richter, Julia 15 Jun '12

15 Jun '12

Dear all, after comparing two groups in qdec and hitting the question "Does the average thickness differ between group 1 and group 2?", do yellow areas mean that group 1 has a thicker cortex in that area than group 2? Thanks, Julia

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1 Group (2 Levels) 2 Covariates
by Jeff Sadino 15 Jun '12

15 Jun '12

Hello, I want to do an analysis with 1 Group (Control and HIV) with two covariates (Age and ICV). Qdec only lets me choose one covariate. So instead I choose two nuisance variables. No matter how many different permutations I run on this, I can not get it to duplicate my SAS results, and the Qdec results look suspiciously wrong. Also, when I do it manually with the mri_glmfit command, I still can not duplicate the SAS results. I have tried both demeaning and not demeaning. This should be pretty straight forward? Am I missing something obvious? How would one do a 1 Group (2 levels) 2 Covariate analysis in QDEC? Thank you, Jeff

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Scripting with fs 5.1 vs 5.0
by Nicole Senecal 14 Jun '12

14 Jun '12

Hi all, I'm having trouble getting anything through on 5.1 using scripts, although I can run recon-all at the commandline. I'm running freesurfer on a remote cluster, not locally. Specifics of the cluster itself aside, with 5, I could run: *vbbatch -c * *"PATH=$PATH:/usr/local/freesurfer_64bit_5; export PATH; * *FREESURFER_HOME=/usr/local/freesurfer_64bit_5; export FREESURFER_HOME; * *SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects; export SUBJECTS_DIR;** * *recon-all -i SW419_Day1.mgz -subject SW419Day1_fullrecon -all" -d1 -r* With 5.1, I have to specify MINC_BIN_DIR within this command (get an error if I don't, saying that it's not defined) and I still get stuck in the talairach transform, with: mritotal -verbose -debug -clobber -modeldir /../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22637/src.mnc transforms/talairach.auto.xfm mritotal: Command not found. Clearly mritotal is working if recon-all at the commandline works. Do I need to specify more environmental variables somewhere for 5.1? I've tried specifying MINC_BIN_DIR, MINC_LIB_DIR, and MNI_DIR in the command as well, with no luck. My bash profile includes: PATH=$PATH:/usr/local/freesurfer5-1/bin FREESURFER_HOME=/usr/local/freesurfer5-1 SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects MINC_BIN_DIR=/usr/local/freesurfer5-1/mni/bin MINC_LIB_DIR=/usr/local/freesurfer5-1/mni/lib PERL5LIB=/usr/local/freesurfer5-1/mni/lib/perl5/5.8.5 MNI_DIR=/usr/local/freesurfer5-1/mni FSFAST_HOME=/usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT=nii And on startup I see: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer5-1 FSFAST_HOME /usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /jet/kable/CorticalThickness/Subjects MNI_DIR /usr/local/freesurfer5-1/mni FSL_DIR /usr/local/fsl thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

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task-related functional connectivity analyses freesurfer 5.1.0
by Maya Rosen 14 Jun '12

14 Jun '12

Dear Freesurfers, I'm really glad to see the (relatively) new functional connectivity commands. It seems to be working really well. Has anyone tried to do task-related functional connectivity? I would like to compare functional connectivity with the hippocampus during two different conditions of my task, but I haven't found any documentation on how to do this or even if it is possible with the current commands. I'm thinking of trying to use a tpexclude file and excluding all time points except Condition A and running functional connectivity on just those time points. And then making a separate tpexclude file that excludes all of the time points except those in Condition B and running functional connectivity on that (both with hippocampal seeds). This would give me maps for each condition. Is there a standard statistical test to compare one map to another? This seems to be a work-around, so I'm curious if anyone has a better solution to do task-related functional connectivity in Freesurfer 5. Please let me know if you've done this or know how to! Thanks! Maya

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correction for multiple comparisons
by Marie Schneider 14 Jun '12

14 Jun '12

Dear FreeSurfer experts, I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups. I do the comparison with the sample of two groups in qdec. Correcting for multiple comparisons, I get a significant result using FDR, but no significant result using Monte Carlo simulation. How can that be? I analyze the sample with the three groups by mri_glmfit. In your tutorial, I only found how to correct for multiple comparisons with the Monte Carlo simulation using the command line, but not how to correct with FDR using the command line. Is there a possibility to do this? If not, how many iterations are usual to use within the Monte Carlo simulation? Any help is appreciated. Thank you very much, Marie

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Re: [Freesurfer] matrix error
by Douglas N Greve 14 Jun '12

14 Jun '12

In matlab Xsss = sqrt(sum(X.^2)); Xn = X ./ repmat(Xsss,[ntptot 1]); Then look at the condition of Xn On 06/12/2012 06:12 PM, mdkruepke(a)uwalumni.com wrote: > due to their similarity is it not possible to run this analysis? also > how did you adjust for the scale presented here? > > On Tue, Jun 12, 2012 at 5:06 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > When I adjusted for the scale, the matrix is still ill-conditioned. It > looks like some of the columns are very similar to each other. > doug > > On 06/12/2012 05:15 PM, mdkruepke(a)uwalumni.com > <mailto:mdkruepke@uwalumni.com> wrote: > > Hello- > > > > I am trying to analyze the cortical thickness between two groups of > > subjects Cl1 and CL2. When i run the GLM i receive the error: > > > > matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > I am under the impression the error could be due to the > > non-uniformity in the range/scale of the regressors. > > > > here is my information: > > > > contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > > > > > 1) mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd > PvNPeverything.fsgd > > dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir > > lh.PvNPeverything.glmdir > > > > 2) (sample of my fsgd) - there are no columns with all 0's in them > > GroupDescriptorFile 1 > > Title Methedone Comparison > > Class Cl1 > > Class Cl2 > > Variables > WAISIQtrait_anxietyalcohol_yearheroin_yearcocaine_yearcannabis_yearmeth_yearamphetamines_yearmeth_amphet_yearhallucinogens_year > > > > > inhalants_yearmethodne_yearopiates_yearpills_yearopitates_pills_yearother_year > > total_years > > InputM87160505Cl18633103911011180066049 > > InputM87161888Cl11095900722000000000032 > > InputM87107477Cl1893412091309961001910057 > > InputM87199897Cl11174402301000000915015360 > > InputM87146570Cl1944226038000000000637 > > InputM87189755Cl111159110.52150331.500000036 > > InputM87169696Cl18622201114000000000025 > > InputM87187366Cl11065128027002020000000075 > > InputM87178857Cl211748044805570400.080.08042.08 > > InputM87165923Cl21034052015000000011023 > > InputM87110556Cl21346040115000000000020 > > InputM87183811Cl2974315083000000000026 > > > > 3) design matrix > > > > 1 0 86 0 33 0 10 0 3 > 0 9 0 11 0 0 0 1 > 0 1 0 > > 1 0 8 0 0 0 0 0 6 > 0 6 0 0 0 49 0 > > 1 0 109 0 59 0 0 0 0 > 0 7 0 22 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 32 0 > > 1 0 89 0 34 0 12 0 0 > 0 9 0 13 0 0 0 9 > 0 9 0 > > 6 0 10 0 0 0 1 0 9 > 0 10 0 0 0 57 0 > > 1 0 89 0 40 0 15 0 5 > 0 2 0 30 0 10 0 0 > 0 > > 10 0 2 0 0 0 0 0 0 > 0 0 0 0 0 0 0 59 > 0 > > 1 0 77 0 44 0 0 0 0 > 0 3 0 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 3 0 > > 1 0 91 0 22 0 6 0 0 > 0 3 0 0 0 0 0 0 > 0 0 0 > > 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> > 0 1 0 91 0 37 0 0 0 > 0 0 0 0 8 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 12 > > 0 1 0 91 0 48 0 0 0 > 0 0 0 0 1 0 0 0 > 0 0 0 0 > > 0.25 0 0 0 0 0 0 0 0 > 0 0 0 0 0 4.25 > > 0 1 0 94 0 58 0 1 0 > 0 0 0.67 0 4 0 5 0 > 0 0 > > 5 0 0 0 3 0 0 0 0 > 0 0 0 0 0 0 0 13.67 > > 0 1 0 114 0 48 0 17 0 > 0 0 6 0 17 0 0 0 > 7 0 > > 7 0 5 0 0 0 0 0 0 > 0 2 0 2 0 0 0 50 > > 0 1 0 106 0 54 0 15 0 > 0 0 7 0 15 0 0 0 > 15 0 > > 15 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 44 > > 0 1 0 74 0 46 0 0 0 > 0 0 0 0 5 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 5 > > 0 1 0 91 0 43 0 0 0 > 0 0 0 0 0 0 0 0 > 0.33 0 > > 0.33 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0.33 > > 0 1 0 80 0 27 0 3 0 > 30 0 0 0 30 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 60 > > 0 1 0 97 0 33 0 0.5 0 > 0 0 0.25 0 2 0 2 0 > 0 0 > > 2 0 0 0 0.17 0 0 0 0 > 0 0 0 0 0 0 0 4.92 > > 0 1 0 100 0 31 0 6 0 > 0 0 0 0 5 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 9 > > 0 1 0 109 0 29 0 0 0 > 0 0 0 0 13 0 0 0 > 10 0 > > 10 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 24 > > 0 1 0 80 0 37 0 0 0 > 0 0 8 0 8 0 0.5 0 > 0 0 > > 0.5 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 16.5 > > 0 1 0 72 0 55 0 10 0 > 0 0 0 0 10 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 20 > > 0 1 0 103 0 40 0 0 0 > 0.5 0 1 0 8 0 0.67 0 > 0 0 > > 0.67 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 10.17 > > 0 1 0 77 0 32 0 0 0 > 0.5 0 0 0 12 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 12.5 > > 0 1 0 120 0 28 0 0 0 > 0 0 4 0 12 0 0 0 > 7 0 7 > > 0 4 0 0 0 0 0 0 0 > 0 0 0 0 7 0 34 > > 0 1 0 86 0 32 0 11 0 > 0 0 8 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 19 > > 0 1 0 91 0 44 0 2 0 > 0 0 1 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 3 > > 0 1 0 94 0 50 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 > > 0 1 0 100 0 29 0 5 0 > 0 0 0 0 16 0 17 0 > 0 0 > > 17 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 38 > > 0 1 0 94 0 25 0 4 0 > 0 0 0.5 0 10 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 12.5 > > 0 1 0 74 0 51 0 10 0 > 0 0 0 0 20 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 30 > > 0 1 0 97 0 36 0 30 0 > 0 0 20 0 33 0 5 0 > 6 0 > > 11 0 6 0 0 0 0 0 0 > 0 0 0 0 0 0 0 90 > > 0 1 0 117 0 35 0 0 0 > 0 0 0 0 3 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 5 > > 0 1 0 80 0 51 0 7 0 > 4 0 0 0 8 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 19 > > 0 1 0 103 0 28 0 9 0 > 0 0 1 0 1 0 0 0 > 8 0 > > 8 0 8 0 0 0 0 0 0 > 0 0 0 0 0 0 0 27 > > 0 1 0 103 0 74 0 6 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 6 > > 0 1 0 89 0 57 0 10 0 > 0 0 0 0 0 0 15 0 > 0 0 > > 15 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 18 > > 0 1 0 109 0 33 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > > 0 1 0 109 0 28 0 3 0 > 0 0 2 0 2 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 5 > > 0 1 0 91 0 27 0 20 0 > 0 0 15 0 0 0 3 0 > 0 0 3 > > 0 0 0 0 0 0 0 17 0 > 0 0 17 0 0 0 55 > > 0 1 0 89 0 48 0 9 0 > 0 0 0.25 0 10 0 20 0 > 0 0 > > 20 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 39.25 > > 0 1 0 97 0 28 0 10 0 > 0 0 4 0 10 0 5 0 > 0 0 5 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 29 > > 0 1 0 100 0 40 0 3 0 > 0 0 0 0 0.17 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 3.17 > > 0 1 0 89 0 21 0 20 0 > 8 0 25 0 25 0 10 0 > 0 0 > > 10 0 0 0 2 0 0 0 0 > 0 0 0 0 0 0 0 90 > > 0 1 0 103 0 54 0 10 0 > 0 0 2 0 0 0 0 0 > 2 0 2 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 12 > > 0 1 0 77 0 49 0 0 0 > 0 0 10 0 12 0 0 0 > 4 0 4 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 2 0 42 > > 0 1 0 89 0 42 0 0 0 > 0 0 4 0 10 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 14 > > 0 1 0 117 0 34 0 25 0 > 0 0 2 0 25 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 52 > > 0 1 0 83 0 56 0 12 0 > 0 0 0 0 15 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 15 > > 0 1 0 91 0 33 0 0 0 > 0 0 0 0 2 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 2 > > 0 1 0 106 0 36 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > > 0 1 0 120 0 50 0 1 0 > 0 0 0 0 2 0 1 0 > 0 0 > > 1 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 6 > > > > > > -- > > Michael D. Kruepke > > PhD - University of Illinois at Urbana-Champaign > > BA - Psych - University of Wisconsin-Madison > > mdkruepke(a)gmail.com <mailto:mdkruepke@gmail.com> > <mailto:mdkruepke@gmail.com <mailto:mdkruepke@gmail.com>> > > (262)-483-7449 <tel:%28262%29-483-7449> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Michael D. Kruepke > PhD - University of Illinois at Urbana-Champaign > BA - Psych - University of Wisconsin-Madison > mdkruepke(a)gmail.com <mailto:mdkruepke@gmail.com> > (262)-483-7449 <tel:%28262%29-483-7449> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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QDEC Analysis of only one group
by Dhinakaran Chinappen 14 Jun '12

14 Jun '12

Dear Freesurfer Experts, For one of our studies, I have used QDEC to analyze the relationship between cortical thickness and a series of variables. I wanted to double check to see if it is okie to have a qdec table which only includes the diseased population and the covariates (such as FSIQ). After multiple comparison correction, a few clusters were obtained, where the correlation between thickness and the covariate differs from zero. Please let me know if QDEC should only be used for comparison between groups or if it okie to study only one cohort and subsequently analyze the trend of a variable with cortical thickness. Best, Dhinakaran.

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Building FreeSurfer with OpenMP enabled
by Akio Yamamoto 14 Jun '12

14 Jun '12

Hi all, I'm attempting to build FreeSurfer with OpenMP enabled. After checking out a copy of the main dev trunk from the CVS repository, I did the configuration with "--enable-openmp" option and run 'make'. Compilation successfully finished and all of 'make check' tests passed. Now I have two questions. (1) Although 'recon-all' finished without error, the results are slightly different from those obtained by the binary distribution (stable v5.1.0). I also find that the message format in a log file (recon-all.log) is not the same as that of the stable version, so I wonder if the source code in the main dev trunk is modified/updated from the stable version... Is it okay to ignore the slight difference of the results? (2) Despite the openmp option being enabled, it looks like the program runs as a single-thread mode. I actually find the message "NUMBER OF OPENMP THREADS = 1" in a log file. Do I need to specify some option when running 'recon-all' script? Any suggestion and/or help would be appreciated. Best, Akio Yamamoto

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suggestions for bandpass filters?
by Caspar M. Schwiedrzik 14 Jun '12

14 Jun '12

Dear all, I would like to apply a bandpass filter both to my fMRI data as well as to regressors in my GLM. I was wondering whether anyone has suggestions for particular filter types and filter orders? I find this seldomly reported in fMRI papers. I was thinking in using Matlab's filtfilt. Any suggestions would be appreciated. Thanks, Caspar

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Mris_anatomical_stats: smoothing does not work with surface area maps
by Jürgen Hänggi 14 Jun '12

14 Jun '12

Dear FS experts I have done group comparisons wrt thickness and surface area. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted. When using mris_anatomical_stats, values are different for thickness maps depending whether I used the --nsmooth 15 option or not. So good so far. However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth option. It seems that the --nsmooth option in mris_anatomical_stats does not affect (smooth) the surface area maps. Is there any solution to also smooth surface area maps with mris_anatomical_stats? I use the Mac FS 5.1.0 version Thanks in advance Best regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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