Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

eTIV bug
by Sasha Wolosin 01 Jun '06

01 Jun '06

Dear all, I have processed all my data using Stable v3.0.1. Does the eTIV bug effect any other volume measures? If I want to compute eTIV for my data, should I install the lates version and re-run mri_label_volume -eTIV ? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Recon error
by Frederick Powell 01 Jun '06

01 Jun '06

gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz: No such file or directory mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz, -1): read error I went into my subjects directory and to the subject that I ran with the error and received the above. -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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directional cosine error?
by Nguyen, Thang Q 01 Jun '06

01 Jun '06

Hello all, I get a directional cosine error when I try to register data or extract values from them so I tried mri_info and get this message: mri_info subj1.img matfile: only read 256 bytes of name (810698068 specified) MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile subj1.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find subj1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in subj1.mat file ----------------------------------------------------------------- Volume information for subj1.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 79.0000 0.0000 2.0000 0.0000 -95.0000 0.0000 0.0000 2.0000 -68.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 -0.0000 -0.0000 39.5000 0.0000 0.5000 0.0000 47.5000 0.0000 0.0000 0.5000 34.0000 0.0000 0.0000 0.0000 1.0000 Here is the mat file: Subj1 2.000000 2.000000 200.000000 1.054861e+00 -2.348376e-02 -1.086195e-01 7.747378e-01 9.350572e-02 -3.302234e-01 1.067427e+00 -3.124532e+01 -4.640190e-02 -9.299399e-01 -3.056859e-01 -7.546637e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round What does the matlab error mean? Why can't it read the directional cosine? -Thang

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error in 'create surface'
by Joongnam Yang 01 Jun '06

01 Jun '06

Hi all, I posted a question, but for some reason, I didn't get any response. Please help me on this. Here is the question. I ran 'process volume' and 'create surface' on csurf. The created surface (left inflated) has brain stem attached to it. So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. No change took place. I tried commandline 'recon-all -stage1 -subjid ID', with no luck. Would someone suggest any comment on this? Nam.

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Problems with Auto Reconall
by Frederick Powell 01 Jun '06

01 Jun '06

using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.117 0.005 0.077 -0.516; -0.015 1.062 0.148 -22.126; -0.084 -0.173 1.230 -34.192; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... Segmentation fault Linux killiany 2.6.9-34.ELsmp #1 SMP Wed Mar 8 00:27:03 CST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Wed May 31 16:54:11 EDT 2006 Above are the errors that I have recieved while trying to run the latest version of auto recon. Please help I am continuously getting teh Segmentation Fault error. I am running 3t MPRAGE images. Thanks -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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Using cortical segmentation in an anatomy project
by Ivan Blagoev Topolsky 01 Jun '06

01 Jun '06

Hello ! I work for the department of Anatomy (http://www.medecine.unige.ch/GRAC/) in the Centre Médical Universitaire of the Université de Genève (http://www.unige.ch/) We're planning to use the FreeSurfer software suite (or more precisely, the surface-based stream ) in a project that aims to synthesize brain models for teaching through rapid-prototyping (like 3D-printing) out of brain MRI, thus by-passing and giving an alternative to using dead human bodies for teaching. I have 2 questions relative to this project : - Does anyone here have recommendations (or references) about MRI sequence parameters to obtain best contrast for optimal segmentation ? Our preliminary test data wasn't top quality indeed, and we're planning to obtain new datasets. Does anyone has some tips to give us ? - The download page mentions that the source code will be soon released (https://surfer.nmr.mgh.harvard.edu/fswiki/Download?action=highlight&value=s…) but that we'll have to wait until all non-releasable modules are replaced with open-source-able ones. How far has the OS'ing effort gone until now ? Most specifically, which modules are already OS'able ? And how much effort remain to be done ? When will we see an OS'ed version ? Under what license are those sources going to be released ? (GPL, BSD, other ?) Thank you and have a nice day. - Ivan Topolsky -

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Cortical thickness difference measurement
by Joao Pereira 01 Jun '06

01 Jun '06

Hello again! Firstly, let me thank you for your precious previous advices, which pointed me in the right direction. I have another question for you: I have read your article on Reliability of MRI cortical thickness measurements and its relation with scanner and field, and I would like to know what function did you use to subtract the subjects' average cortical thickness files in order to have a cortical thickness difference layer. I don't know if this is a very basic question, but I can't seem to find how to do it with FS. Thank you! Joao Pereira

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Freesurfer June 2006