Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

variables and glmfit...
by Cameron Ellis 02 Apr '08

02 Apr '08

Hi all, I have two questions regarding glmfit and testing for effects of different variables. I have four groups. When testing for effects of age across all of the groups, will there be a difference when assigning each group a class in my fsgd file, with age as a variable, like so: Class PH Class PL Class VH Class VL Variables age Input NEAA004 PH 30 Input NEAA006 PH 21 Input NEAA007 PL 42 Input NEAA020 PL 27 Input NEAA024 VH 26 Input NEAA025 VH 24 Input NEAA039 VL 24 Input NEAA052 VL 33 . . etc... and setting up a contrast matrix: 0 0 0 1; and alternatively setting up my fsgd file with a single group, like so: Class subj Variables age Input NEAA004 subj 30 Input NEAA006 subj 21 Input NEAA007 subj 42 Input NEAA020 subj 27 Input NEAA024 subj 26 Input NEAA025 subj 24 Input NEAA039 subj 24 Input NEAA052 subj 33 . . etc... and setting up a contrast matrix: 0 1? Is the first options controlling for effects of group? Would I want to do this? My second question is in regards to controling for a discrete variable like gender. Should male and female be coded as dummy variables 0 and 1 in the fsgd file? I have tried this and my results seem to make more sense than when I run the same analysis in qdec where I did not code the variables in this way. Should I be doing so in qdec as well? Thanks! Cameron

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FreeSurfer for Redhat 7.3
by Woo-Suk, Tae 02 Apr '08

02 Apr '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Hi!I would like to know the version of Freesurfer for Redhat 7.3.Best regards.Woo-Suk, TaeChucheon, Korea

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mri_surfcluster CWP values
by James N Porter 01 Apr '08

01 Apr '08

Hello- When I look at the CWP results of mri_surfcluster in the sig.cluster.sum versus the resultant sig.cluster.mgh, the results are different. Specifically, all clusters negatively correlated with my independent variable display a value in tksurfer of -1+CWP, and clusters that are positively correlated display a value of 1-CWP. Which values should I believe as my actual p-values, the .sum's CWP or the .mgh's added/subtracted values? Thanks for your help, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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recon-all exits with error
by Goradia, Dhruman D 01 Apr '08

01 Apr '08

Hello All, I have a library problem when I run recon-all. Recon-all exits with ERROR during the cortribbon step. I am using FC8 x86_64 OS on an Intel Xeon 64 bit machine. I have installed CentOS4-x86_64-v4.0.2 version of freesurfer. The library in question "libexpat.so.0" has been installed and is located in /usr/lib however, the problem persists. The command and error is: recon-all -s 24560 -cortribbon INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r-- 1 giang users 698777 Apr 1 11:29 /usr/local/freesurfer/subjects/24560/scripts/recon-all.log Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer #-------------------------------------------- #@# Cortical ribbon mask Tue Apr 1 14:24:12 EDT 2008 /usr/local/freesurfer/subjects/24560/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 24560 mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Apr 1 14:24:12 EDT 2008 Any help is greatly appreciated. Thank you, Dhruman PS: Sorry if you received the email twice.

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qdec regression coeffs
by James N Porter 01 Apr '08

01 Apr '08

Hello All- When viewing the scalar overlays in qdec, how do I tell which coefficient is being displayed when I select "Regression Coefficients" from the menu? Having more than one regressor, I would expect more than one overlay of coefficients. Am I missing something very elementary? -- --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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structures list
by Lindsay Casmaer 01 Apr '08

01 Apr '08

Does the website contain a list of structures labeled in both version 3 and version 4? I am looking for both cortical and subcortical segmentation labels. Thanks, Lindsay

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recon-all exits with errors
by Goradia, Dhruman D 01 Apr '08

01 Apr '08

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glm_fit question...
by Cameron Ellis 01 Apr '08

01 Apr '08

Hi all, Is it necessary to include a value in your contrast matrix for every class and variable in your fsgd file? It seems that this is the case. My understanding is that if you weight a variable 0 then it is automatically controlled for. So if am required to weight a variabe in the contrast matrix that do not want to control for, then to not control for it I have to make a different fsgd file without that variable? Thanks, Cameron

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unable to load flat.asc in MATLAB
by SHRIKANTH KULASHEKHAR 01 Apr '08

01 Apr '08

Hi, I have been trying to plot flattened cortex surfaces using MATLAB but have been unsuccessful so far. After flattening the cortex in freesurfer, I convert in into an ascii file by using: mris_convert -p label1.flat label1.flat.asc But then fail to read the *.asc file as a patch in MATLAB using the read_asc.m from the Freesurfer MATLAB toolbox. Are there any other MATLAB codes to read and plot the *.flat.asc files ? Thank you. Shriks Share files, take polls, and discuss your passions - all under one roof. Go to http://in.promos.yahoo.com/groups

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Cannot download new Leopard release
by Juergen Haenggi 01 Apr '08

01 Apr '08

Dear FS experts I tried to download freesurfer-Darwin-tiger-i686-stable-pub-v4.0.3-full.dmg but when I klicked on the link on your website the following error occurred. 550: Failed to change directory This did not occurred when I downloaded the CENTOS release Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Freesurfer April 2008