Freesurfer September 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
96 discussions

How to display a large set of peaks on inflated brain?
by Keith Duncan 12 Sep '08

12 Sep '08

Hi FS experts, I am trying to display a large set of peaks on an inflated brain to illustrate the spread of the peaks over a gyrus & sulcus, similar to what might be done in a meta-analysis. Is there an easy way to do this? I tried generating a binary mask in 3D (in MNI space) and then converting that to a .w file using mri_vol2surf but some of the peaks seem to be lost and the peaks that do appear, are splodges rather than a neat circle/ellipse/whatever, which makes it look like an activation map. Thanks in advance! Keith

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freesurfer
by Hwee Ling Lee 12 Sep '08

12 Sep '08

Hi All, I was looking for methods to create a superior temporal sulcus mask (upper and lower boundary). >From my understanding, Freesurfer does a pretty good job in labeling the sulcus, hence I was wondering if there are possible ways to write the particular ROI as a mask image for each individual subject, and preferably to be in the MNI space or if not, at least in the native space. Thank you. Best wishes, HweeLing ----------------------------------------------------------------------- Hwee Ling, Lee Max-Planck Institute for Biological Cybernetics Cognitive Neuroimaging Spemannstrasse 41 72076 Tuebingen Germany Tel: +49-70701-601-1785 Fax: +49-7071-601-616 hwee-ling.lee(a)tuebingen.mpg.de hweeling.lee(a)gmail.com http://www.kyb.mpg.de/~hweeling -----------------------------------------------------------------------

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Are the average subjects generated by different version of Freesurfer differ greatly?
by Zhangyuanchao 12 Sep '08

12 Sep '08

Are the average subjects generated by different version of Freesurfer differ greatly? I obtained the cortical thickness,lGI using Freesurfer 4.0.3, However, average subject can not be generated using Freesurfer 4.0.3 because of error.Can I use the average subject generated using Freesurfer of another version? Thanks! --------------------------------- 雅虎邮箱，您的终生邮箱！

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Brodmann's area 46
by antonio cerasa 12 Sep '08

12 Sep '08

Dear List, Apologies if this is a simple question, but how can I define the BA 46 within ROI: middle frontal gyrus plus middle (or superior) frontal sulcus?-------------------------------------------------------------------------- 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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dicom image viewer
by dahlia＠nmr.mgh.harvard.edu 11 Sep '08

11 Sep '08

Hi, What do people usually use to view dicom images, and how do I invoke this viewer? Thanks! Dahlia.

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Segfault in mris_fwhm?
by Mark J. Pearrow 11 Sep '08

11 Sep '08

Hi all, I've run into a snag whilst running mris_fwhm: $ mris_fwhm --i <snip>/all.nii --s <SUBJID> --hemi rh --sum <snip>/ fwhm.sum <SUBJID> rh white Number of vertices 136129 Number of faces 272254 Total area 88745.070312 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.651919 AvgVtxDist 0.883205 StdVtxDist 0.255280 Polynomial detrending, order = 0 Computing spatial AR1 ERROR: MRISar1: Surf/Src dimension mismatch. Segmentation fault All of the unpacking, reconstruction, and preprocessing up till that point have all been done using a pretty typical FS stream (with the exception of not smoothing in the volume) using FS 4.0.5. The segfault happens with both the mris_fwhm binary that comes with FS 4.0.5 and with the one I built from last night's CVS tree. I haven't run it under a debugger yet but was wondering if this has been seen before, etc. mjp

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segmentation fault (core dumped), when making average subject
by Zhangyuanchao 11 Sep '08

11 Sep '08

Dear Mr or Ms, My computer was installed with Freesurfer v4.0.3,centos4, To make an average surface,I launch "make_average_subject" command, I come across an error : Processing subject 25/52 sh45 ... Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg Segmentation fault (core dumped). Could you help me? How can I solve the problem? Thanks! yczhang --------------------------------- 雅虎邮箱，您的终生邮箱！

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segmentation fault (core dumped)
by Zhangyuanchao 11 Sep '08

11 Sep '08

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exporting label/segmented regions in diffusion space
by vin 11 Sep '08

11 Sep '08

Hello Freesurfers ! I have very basic question. I suceesfully completed autorecon first time and now I want to extract the segmentated brain regions/ labels, as a ROI, so that I can use them in diffusion(b0) space. can any one suggest me related wiki page, where I could start for this and understand registeration( diffusion to freesurfer image) and than take the segmented regions and convert them in NIFTI format for example for FSL probtrack. Thank you, vin

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(no subject)
by Al-Radaideh Ali 11 Sep '08

11 Sep '08

Dear FreeSufer Experts, I was running the recon-all autorecon-all -s bert step and I have got the error message below. this is the first time I see this message although I have analysed more than 7 MPRAGEs. Any suggestions please? Note: I usually call my subject as bert. Thanks Ali #@# Talairach Failure Detection Tue Sep 9 16:02:41 BST 2008 /data_local/ali/freesurfer/subjects/MPRAGE/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0090, pval=0.0000 < threshold=0.0050) Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Sep 9 16:02:41 BST 2008 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer September 2008