Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Testing installation, recon-all problem
by Tetiana Dadakova 19 Jan '11

19 Jan '11

Dear Freesurfer users, I installed Freesurfer and now I am trying to test the installation. When I type <recon-all -s bert -all>, I get an error <ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert> But actually I do have write permission to this folder. Do you have any idea what can be wrong? Or what else should I check regarding installation to understand where this problem comes from? Thank you for your time, Tetiana.

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How to make a surface overlay? - repost
by Ed Gronenschild 19 Jan '11

19 Jan '11

Hi, I've done some statistics on thickness and volume of the default cortical regions (segIDs 1000 - 1035 and 2000 - 2035) for a number of subjects. How can I show for instance the p values (expressed as -log(p)) as an overlay on the pial surface of fsaverage? Ed

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qdec
by 汪贵宏 19 Jan '11

19 Jan '11

Hi everybody, > > I tried to run the qdec-tool, but experienced some problems . I got different thickness in one area. In detail: 1. When I open the qdec.table.dat ,the thickness is different from the thickness got from the display in Find Clusters and Goto Max,I really do not know why? 2. Can qdec contrast 34 areas in the same time, I mean that I set 34 Continuous Variables in qdec.table.dat to run qdec, is it right? 3.Why did the results I got from two differentqdec.table.dat had no difference,one qdec.table.dat has 34 Continuous Variables but the other had only one Continuous Variable,such as insula? Thanks for your answer! wang

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Segmentation Fault Question
by Allie Rosen 18 Jan '11

18 Jan '11

Hi, I am accessing my subject directory on a network attached drive. When I run mri glmfit it segfaults. However, it works if the subject directory is on my own computer. Do you have any way to do this with the subject directory on the network drive? Below is a sample output. Thanks, Allie Caduceus:~/ammonis/fsSubjects/subjects_archive> mri_glmfit --y lh.smoothed.thickness.6.mgz --fsgd GDF1.txt doss --glmdir lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C ContrastAge.txt gdfReadHeader: reading GDF1.txt INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.0625 1 PCS 9.875 2 Neuro 17.8125 3 Extro 30 4 Open 28.875 5 Agree 32.4375 6 Consc 34.625 Class Means of each Continuous Variable 1 Control 40.0625 9.8750 17.8125 30.0000 28.8750 32.4375 34.6250 INFO: gd2mtx_method is doss Reading source surface /media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /media/AMMONIS/fsSubjects/subjects_archive cmdline mri_glmfit --y lh.smoothed.thickness.6.mgz --fsgd GDF1.txt doss --glmdir lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C ContrastAge.txt sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/subjects_archive/lh.smoothed.thickness.6.mgz logyflag 0 usedti 0 FSGD GDF1.txt glmdir lh.smoothed.thickness.6.glmdir IllCondOK 0 DoFFx 0 Creating output directory lh.smoothed.thickness.6.glmdir Segmentation fault

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New Random Field Theory tool specifically for Freesurfer-based data analyses
by jorge luis 18 Jan '11

18 Jan '11

Dear freesurfers I have uploaded to the NITRC neuroimage database a new tool called RFT_FDR. This tool implements Random Field Theory and Hierarchical multiple comparison corrections specifically for Freesurfer's surface data. The tool depends on Worsley´s SurfStat toolbox which is already included as a tool’s subdirectory. You need also to have the Freesurfer’s freesurfer/matlab directory added to your Matlab’s search path. That’s all. Directions on how to use this tool are in the usage.txt file. I think it is a pretty easy way to perform RFT correction in Freesurfer. It can save you a lot of time, when compared with the Freesurfer’s simulation, and is usually more sensitive and flexible (eg. there are some restrictions for the design matrix that may prevent the use of Freesurfer’s permutation testing). The tool also implements a method for optimizing the amount of smoothing in cortical thickness analyses which is based on a hierarchical RFT-FDR multiple comparison correction (Neuroimage 52, 158-171). Cheers Jorge Luis Bernal Rusiel

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contrast matrix for 2 discrete factors and 3 continuous variables
by Jose Luis Cantero Lorente 18 Jan '11

18 Jan '11

-  Dear Freesurfers, My experimental design includes 2 discrete factors and 3 continuous variables: Discrete factors: - Diagnosis with three levels (A, B, C) - Gender with two levels (Males, Females) Continuous variables: - Mean cortical thickness in the left hemisphere (CTLH) - Age - Performance in a memory test (TASK) The FSGD file would be as follows: GroupDescriptorFile 1 Title Thickness-subj Class AMale Class AFemale Class BMale Class BFemale Class CMale Class CFemale variables ZCTLH ZAGE Input control_01 AMale -1.04398 0.24789 Input control_02 AMale 1.22853 -0.72343 Input control_03 AFemale .13773 -1.37097 Input control_04 AFemale .41043 0.24789 Input mci_01 BMale -.77128 0.24789 Input mci_02 BMale -2.40749 0.73354 Input mci_03 BFemale -.86218 -1.0472 Input mci_04 BFemale .50133 0.23777 Input ad_01 CMale -.75678 0.22789 Input ad_02 CMale -2.88749 0.63047 Input ad_03 CFemale -.96015 -1.4452 Input ad_04 CFemale .80712 -0.37567 … We are assuming different offsets and different slopes (DDOS). The following contrast would test the null hypothesis whether there is a difference between B and C (T-test) regressing out the effect of the remaining variables. 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Could you help me to build the contrast for testing interactions in the above experimental design? In the FSwiki examples, you add one column when you have two factors with two levels each, and one continuous variable. I am not sure how many columns should I add in our particular case and why. Null hypothesis: is there an interaction between diagnosis (B > C) and gender regressing out the two remaining variables? Assuming that you add one column per variable that is regressed out, the contrast would be as follows: 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Is this correct? Any help will be very appreciated. Many thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Converting nii to label....
by Joseph Andreano 18 Jan '11

18 Jan '11

Hi, I have a volume in .nii format which I would like to use as an ROI to extract signal from, using func2roi-sess. However, func2roi requires a label. How would I convert a .nii volume to a label? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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mkanalysis-sess -gui
by Iris.steinmann 18 Jan '11

18 Jan '11

Hi Freesurfers, I have a little problem: I use a linux mashine with ubuntu 10.10 and installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz.. Most commands are working well (like tkmedit, tksurfer …), but I have a problem to get an analyse gui with (mkanalysis-sess -gui). I just get a long error report from matlab. I created a startup.m file for matlab like the following: %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% addpath('~/freesurfer/matlab/'); Does anyone has an idea what could be wrong? I would be so thankfull! Iris

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two issues with the processing stream
by Ilana Hairston 17 Jan '11

17 Jan '11

Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted. thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** What might have been is an abstraction Remaining a perpetual possibility Only in a world of speculation T.S. Eliot

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How to make a surface overlay?
by Ed Gronenschild 17 Jan '11

17 Jan '11

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