Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

About the area of the vertices in the surfaces
by jorge luis 30 Jun '08

30 Jun '08

Hello all I have some questions: I would like to know how freesurfer computes the vertex’s wise areas? eg. thouse in lh.area. It should be expected that the sum of the areas of all the vertices across a surface equals the total surface area? To be much specific: Can I compute the area of an 'activated' cortical ROI in the average subject by simply adding the area of all its vertices? In adavance thank you Jorge Phd Student ¿No te gusta tu dirección de correo? Consigue una que te guste de verdad - millones de direcciones de correo disponibles en Yahoo! http://es.docs.yahoo.com/mail/nueva_direccion.html

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about thalamus segmentation
by abel cruz vadell 30 Jun '08

30 Jun '08

Hello I have read in some emails about the improvement of the subcortical segmentation in the last FreeSurfer versions. I have 40 subjects processed with the 4.01 version and my attention is focused in the thalamus. Has been improvement the segmentation of this structure in the later FreeSurfer versions? In positive case, is possible to use my 4.01 segmentation in the newer versions or I need to do the overall processing again? Thanks in advance Abel ______________________________________________ Enviado desde Correo Yahoo! La bandeja de entrada más inteligente.

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Massive recon-all.log files
by Sky Raptentsetsang 27 Jun '08

27 Jun '08

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FreeSurfer Stop run autorecon-all at mri_fix_topology Stop run autorecon-all at mri_fix_topology Stop run autorecon-all at mri_fix_topology FreeSurfer stop running at mri_fix_topology with no error message
by Yuan Xu 27 Jun '08

27 Jun '08

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research position in San Francisco, CA
by Brian Roach 27 Jun '08

27 Jun '08

FreeSurfer users, We are looking for new and experienced brain imagers wanting to work in our UCSF-affiliated research lab. Please apply at the following link if interested: http://www.ncire.org/positions.php?id=145 thank you, Brian

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Sulcal CSF in aseg
by Juergen Haenggi 27 Jun '08

27 Jun '08

Dear FS experts In the aseg file there are several CSF labels. Does the term "csf" mean sulcal CSF of both cerebral hemispheres, and does the term "restCSF" mean CSF in cisterns? 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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Deflate compression support
by Jan Kalkus 27 Jun '08

27 Jun '08

Hi, I'm using mris_make_template to create a template with some monkey data. At the very end I get this message: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error I've recompiled libtiff with the #define COMPRESSION_SUPPORT option in the tifconf.h file, but I keep getting the same message. Does anyone have any suggestions? - Jan Kalkus

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make_average_subjects & FS v4.0.5
by antonio cerasa 27 Jun '08

27 Jun '08

Dear Freesurfers I am trying to build an average subject (dataset with 38 subjects) under FS v4.0.5 (freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz). It seems to work fine. But, when I click the Analyze button of Qdec, the error show as below: Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh reading group avg surface area 828 cm^2 from file Reading in average area /usr/local/freesurfer/subjects/fsaverage/surf/rh.white.avg.area.mgh reading group avg surface area 990 cm^2 from file Reading in average area /usr/local/freesurfer/subjects/fsaverage/surf/rh.pial.avg.area.mgh reading group avg surface area 828 cm^2 from file Couldn't find file /usr/local/freesurfer/subjects/fsaverage/surf/rh.curv I don't know how to deal with this problem. Could you tell me how to resolve this? Thanks in advance. Antonio -------------------------------------------------------------------------- Antonio Cerasa PhD Part-time lecturer: University of Calabria UNICAL & University "Magna Graecia" UNICZ. Laboratory of Neuroimaging Institute of Neurological Sciences National Research Council (CNR) C/Da Burga 44, 87050 Cosenza, Italy. Phone: +39 0984.9801270 Fax: +39 0984.969306 Phone mob: +39 333/9633511 http://www.isn.cnr.it/public/pagine_ita/settori_neuroimg.asp

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qdec
by Judith Segall 26 Jun '08

26 Jun '08

Hi. I am running qdec on freesurfer v 4.0.5. I am getting the following error messages: WARNING: Marker for class Main was invalid. WARNING: Color for class Main was invalid. My two two classes (male and female) are not being configured. I know from reading the freesurfer support lists that this was a problem in earlier versions of qdec, so is there a patch that I can install to remedy this? Thanks. Judith S.

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What's wrong in fmc.nii data?
by Zhen Zonglei 26 Jun '08

26 Jun '08

Hi all: When I run selxavg3-sess on a analysis with 'fmc' as 'funcstem', the program report the following error, but when I did the same analysis on the same data with 'fmcsm6' as 'funcstem', the program could run successfully. our data was preprocessed with the command 'preproc-sess -sf cm_sess -df sesspar' and our freesurfer version is stable 4.0.1. We hope our analysis can do on the data with no smoothing to keep the resolution of the data. What's wrong in fmc.nii data? Thanks very much. ERROR: cannot find slice 000 for /nfs/h2/r5/data2/cm1/bold/407/fmc ??? Error using ==> fmri_bfiledim Could not find any slices with stem /nfs/h2/r5/data2/cm1/bold/407/fmc Error in ==> MRIread at 126 [nrows ncols ntp fs ns endian bext] = fmri_bfiledim(fstem); Error in ==> flac_customize at 65 mri = MRIread(fstem,1); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Best regards Zonglei Zhen

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Freesurfer June 2008