Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

precoloring - adjusted errors
by Caspar M. Schwiedrzik 15 Jun '12

15 Jun '12

Hi! I am processing a resting state data set, which I would like to low pass filter to get rid of some artifacts. The sample will be very small, so I won't run a RFX GLM, but an FFX GLM and/or single subject analyses. Since the low pass filter introduces high autocorrelations, it does not make sense to whiten the data before the GLM. However, in order not to violate the assumptions of the OLS, I would like to use the precoloring approach described in Worsley & Friston 1995. Is that by any chance implemented in FSFAST, and if not, where would be the right place to add it? Thanks in advance, Caspar

2 5

recon error- too many arguments?
by Borzello, Mia 15 Jun '12

15 Jun '12

Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject XXXX_SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M

4 4

TRACULA dpath problem
by XJ Kang 15 Jun '12

15 Jun '12

Hi, I am trying to run the last step of TRACULA. I used the command line: % trac-all -path -c mytracula.conf Here is all the info I got on the screen: INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012 I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are? I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine. Thanks. XJ Kang

2 1

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

2 1

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

1 0

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

1 0

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

1 0

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

2 5

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 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 8 0 > > 1 0 103 0 29 0 20 0 3 > 0 11 0 27 0 0 0 11 > 0 > > 11 0 5 0 0 0 0 0 0 > 0 1 0 1 0 0 0 78 > 0 > > 1 0 117 0 44 0 0 0 23 > 0 0 0 10 0 0 0 0 > 0 0 > > 0 0 0 0 0 9 0 15 0 > 0 0 15 0 3 0 60 0 > > 1 0 94 0 42 0 26 0 0 > 0 3 0 8 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 6 0 37 0 > > 1 0 91 0 38 0 20 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 20 0 > > 1 0 86 0 45 0 3 0 1 > 0 2 0 7 0 0 0 0 > 0 0 0 > > 1 0 0 0 0 0 1 0 0 > 0 1 0 1 0 14 0 > > 1 0 114 0 50 0 5 0 1 > 0 3 0 10 0 0 0 0.08 > 0 > > 0.08 0 0 0 0 0 0.33 0 1 > 0 0 0 1 0 0 0 > 20.42 0 > > 1 0 109 0 27 0 5 0 5 > 0 4 0 14 0 0 0 0 > 0 0 0 > > 5 0 0 0 0 0 1 0 4 > 0 5 0 0 0 38 0 > > 1 0 97 0 29 0 23 0 1 > 0 22 0 24 0 0 0 15 > 0 15 > > 0 12 0 0 0 0 0 14 0 > 0 0 14 0 0 0 111 0 > > 1 0 106 0 23 0 7 0 0 > 0 4 0 6 0 0 0 2 > 0 2 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 19 0 > > 1 0 131 0 25 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 74 0 54 0 12 0 0 > 0 0 0 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23 0 4.5 0 > 0 0 3 0 20 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 27.5 > > 0 1 0 72 0 48 0 3 0 > 0 0 0 0 9 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 94 0 47 0 3.5 0 > 0 0 4 0 15.5 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 23 > > 0 1 0 100 0 45 0 0 0 > 0 0 0 0 2 0 0 0 > 0.5 0 > > 0.5 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 6.5 > > 0 1 0 100 0 36 0 15 0 > 0 0 0 0 10 0 0 0 > 0 0 > > 0 0 3 0 0 0 0 0 0 > 0 0 0 0 0 0 0 28 > > 0 1 0 94 0 45 0 0 0 > 15 0 0 0 20 0 0 0 > 0 0 0 > > 0 0 0 0.5 0 0 0 0 0 > 0 0 0 0 5 0 50.5 > > 0 1 0 103 0 58 0 11 0 > 2 0 6 0 6 0 0 0 > 0 0 0 > > 0 18 0 0 0 0 0 0 0 > 0 0 0 0 0 0 35 > > 0 1 0 83 0 31 0 22 0 > 0 0 0 0 15 0 0 0 > 0 0 0 > > 0 0 0 0.5 0 0 0 0 0 > 0 0 0 0 0 0 35.5 > > 0 1 0 91 0 54 0 10 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 25 > > 0 1 0 97 0 38 0 5 0 > 0 0 1 0 7 0 0 0 > 0 0 0 > > 0 1 0 0 0 0 0 0 0 > 0 0 0 0 0 0 14 > > 0 1 0 72 0 34 0 9 0 > 0 0 0 0 9 0 3 0 > 0 0 3 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 12 > > 0 1 0 80 0 44 0 1 0 > 0 0 1 0 4 0 0 0 > 2 0 2 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 7 > > 0 1 0 114 0 54 0 14 0 > 0 0 0 0 14 0 0 0 > 14 0 > > 14 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 38 > > 0 1 0 89 0 33 0 9 0 > 17 0 17 0 9 0 0 0 > 0 0 0 > > 0 5 0 0 0 0 0 0 0 > 0 0 0 0 0 0 49 > > 0 1 0 89 0 60 0 0 0 > 0 0 10 0 16 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 26 > > 0 1 0 72 0 42 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 89 0 34 0 1 0 > 0 0 0 0 5 0 0 0 > 1 0 1 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 8 > > 0 1 0 94 0 53 0 5 0 > 0 0 5 0 5 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 25 0 15 0 > 0 0 23 0 31 0 3 0 > 0 0 > > 3 0 5 0 5 0 0 0 0 > 0 0 0 0 0 0 0 82 > > 0 1 0 91 0 36 0 8 0 > 0 0 0 0 19 0 0 0 > 0 0 > > 0 0 6 0 0 0 0 0 0 > 0 0 0 0 0 0 0 33 > > 0 1 0 100 0 53 0 20 0 > 0 0 1 0 3 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 42 0 20 0 > 0 0 15 0 15 0 5 0 > 0 0 > > 5 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 45 > > 0 1 0 91 0 52 0 8 0 > 0 0 0 0 10 0 0 0 > 4 0 > > 4 0 2 0 0 0 0 0 1 > 0 0 0 1 0 0 0 18 > > 0 1 0 74 0 36 0 0 0 > 0 0 1 0 2 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 43 0 2 0 > 0 0 0 0 11 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 13 > > 0 1 0 91 0 24 0 1 0 > 0 0 1 0 14 0 0 0 > 12 0 > > 12 0 0 0 0 0 0 0 0 > 0 0 0 0 0 1 0 29 > > 0 1 0 109 0 24 0 13 0 > 0 0 3 0 3 0 0 0 > 0 0 0 > > 0 10 0 0 0 0 0 0 0 > 0 0 0 0 0 0 27 > > 0 1 0 117 0 39 0 21 0 > 0 0 1 0 1 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 3 0 6 > > 0 1 0 126 0 40 0 15 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 77 0 50 0 5 0 > 0.17 0 0 0 6 0 0 0 > 0 0 0 0 > > 0.25 0 0 0 0 0 0 0 0 > 0 0 0 0 0 11.42 > > 0 1 0 86 0 37 0 7 0 > 3 0 1 0 7 0 0 0 > 5 0 5 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 23 > > 0 1 0 91 0 40 0 12 0 > 0 0 0 0 12 0 8 0 > 0 0 8 > > 0 0 0 0 0 0 0 0.5 0 > 0 0 0.5 0 0 0 32.5 > > 0 1 0 97 0 42 0 1.5 0 > 0 0 2 0 6 0 4 0 > 0 0 4 > > 0 0.5 0 0 0 0 0 0 0 > 0 0 0 0 0 0 14 > > 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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