Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

scatterplots in tkmedit
by Victoria Williams 25 Feb '09

25 Feb '09

Hello, I ran a GLM using a 4d skeletonized Fractional Anisotropy volume as my input into mri_glmfit with one variable. As this analysis is not surface based, I must open the results (sig.mgh) using tkmedit as an overlay. My goal is to open a scatterplot similar to that in tksurfer which shows the voxel value vs. variable score for each individual subject at a particular location. When I try to load the GDF file (the y.fsgd output in glmdir right?), it also asks for a registration file. I don't think there is a register.dat file as an output in the glmdir.... so, I was wondering what registration file it is looking for? Thanks for the help! Tori

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GLM Contrast
by Jeff Sadino 25 Feb '09

25 Feb '09

Hello, I am running the mri_glmfit and would like to doublecheck my contrast file. This is my fsgd file: MeasurementName thickness Class ctrl Class cd Class nc Variables age ed Input 040002_S04 nc 42.62 18 Input 040005_HG01 nc 45.26 15 Input 040008_S01 nc 26.92 16 Input 050015_S01 nc 46.65 12 .. .. .. with values for cd and ctrl as well. I want to see if there are differences in thickness between my control group and my cognitive deficit group after taking into account for age and education. This is my matrix file: 1 -1 0 0 0 0 0 0 0 for ctrl, cd, nc, ctrl age, cd age, nc age, ctrl ed, cd ed, nc ed Will this matrix file work for my hypothesis? It seems like if the last 6 are zeros, then it will not be taking age and education into account? And then also, since I have 90 subjects in all, will I need to correct for multiple comparisons? Thank you in advance, Jeff Sadino _________________________________________________________________ Access your email online and on the go with Windows Live Hotmail. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_AE_Access_022009

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question about spmregister-sess
by Srihasam, Krishna 25 Feb '09

25 Feb '09

Hi, I am trying to register my functional images with a high resolution anatomical image. I am getting a really bad registration. The anatomical image has the following stats: Dimension : 126x165x103 Voxel size : 1 x 1 x 1 Fov : 165 nFrames : 1 Orientation: RPI Primary Slice Direction : axial The functional image has : Dimension : 84 x 96 x 33 x158 Voxel size : 1.4583 x 1.4583 x 1.5 Fov : 84 nFrames : 158 Orientation: RPI Primary Slice Direction : axial I am using the following command to do the registration: "Spmregister-sess -sf sessid -df sesspar " It looks like something to do with the scaling factor. But, I have no idea how to change it. Any help will be welcome.. -Krishna

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Freesurfer Problem
by Naveen Kumar Yadav, Mr 25 Feb '09

25 Feb '09

Hi, I used Linux Red Hat 5 to install the freesurfer from your website. I followed the downloading and Installing steps as mentioned in your website. But when I tried to Test the Freesurfer Instalation it gave me the following message [inverse@localhost subjects]# tkmedit bert orig.mgz tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory. So I am wondering does it make difference if we download the latest Freesurfer software on Redhat 5 or Redhat 9. Is the error is due to linux version or is there is anyother problem. We used this Unix command to download the sofware on Redhat 5 ...freesurfer-Linux-rh9-stable-pub-v4.2.0.... Please let me know the solution. I will be thankful to you. Thanks Regards Naveen K. Yadav MSc Research Assistant Dept. of Ophthalmology McGill Vision Research McGill University Montreal, Quebec, Canada

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Freesurfer Problem
by Naveen Kumar Yadav, Mr 25 Feb '09

25 Feb '09

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error reading curvature file
by Barnali Basu 24 Feb '09

24 Feb '09

Hi I have completed autorecon1 and autorecon2 successfully. When I try to overlay lh.curv on lh.sphere in tksurfer, it gives the following output/error. Any suggestions anybody? tksurfer bert lh sphere surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131870, faces=263736 mrisReadTriangleFile(/usr/local/freesurfer/subjects/bert/surf/lh.orig): surface doesn't match /usr/local/freesurfer/subjects/bert/surf/lh.sphere mrisReadTriangleFile failed. MRISreadOriginalProperties: could not read surface file /usr/local/freesurfer/subjects/bert/surf/lh.orig Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/usr/local/freesurfer/subjects/bert/surf/lh.white): surface doesn't match /usr/local/freesurfer/subjects/bert/surf/lh.sphere mrisReadTriangleFile failed. % ERROR: number of vertices in /usr/local/freesurfer/subjects/bert/surf/lh.curv does not match surface (146926,131870)surfer: error reading curvature file Thanks -- Barnali Basu

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help in process order
by asaf achiron 24 Feb '09

24 Feb '09

Dear group after finishing Recon-all for 100 patients... i did not really understand what is my next step: a. to use Qdec b. to use asegstats2table/aparcstats2table and then thank you asaf

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The 4th International Summer School in Biomedical Engineering - Brain connectivity and information transfer
by Ting-Shuo Yo 24 Feb '09

24 Feb '09

The 4th International Summer School in Biomedical Engineering, "Brain connectivity and information transfer", will be held Aug. 13-27, 2009 on Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig. In recent years, the phenomenon of connectivity has been recognized as a major determinant of brain function. The objective of the International Summer School is to provide in depth education and practical exercises on techniques of computing and analyzing connectivity in the brain, covering both theoretical foundations and practical applications. The International Summer School provides contact with leading experts in the fields and is expected to facilitate the exchange of ideas on latest developments. [Topics] Anatomical connectivity Functional connectivity between electrophysiological, peripheral and metabolic signals Effective connectivity in the signal and source space of EEG/MEG as well as fMRI Neural mass models and neural field models Applications Validation techniques For more information, please see: http://www.tu-ilmenau.de/fakia/Summerschool-2009.summerschool-2009.0.html?&…

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qdec thickness and repeatability
by bell0368＠umn.edu 23 Feb '09

23 Feb '09

All, I am going to run an analysis of cortical thickness reproducibility; there are at least two methods that seem obvious. I could run qdec analysis with time1 and time2 as different groups or I could run the methods below. Are the commands below the same ones used in the qdec GUI? As far as I can tell, they will both give me cortical thickness differences on a vertex by vertex basis. There are probably some subtle differences in the way they are coded, but any major changes? Thanks. http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility

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Announcing the 2009 FSL & FreeSurfer Course : 12-16 June, San Francisco
by Steve Smith 23 Feb '09

23 Feb '09

http://www.fmrib.ox.ac.uk/fslcourse/sanfrancisco2009.html We are pleased to announce the 2009 FSL & FreeSurfer course in San Francisco, USA. It will run immediately before the Human Brain Mapping conference, in the same venue - the San Francisco Marriott. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to fully analyse their own FMRI and MRI data sets. Numbers of attendees are strictly limited and are available on a first- come-first-served basis. For more details and to register for the course, see the course web page at: http://www.fmrib.ox.ac.uk/fslcourse/sanfrancisco2009.html See you there! Regards, course organisers.

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Freesurfer