Freesurfer July 2004

freesurfer@nmr.mgh.harvard.edu

16 participants
23 discussions

Making own template for registration
by Hämäläinen Janne 05 Jul '04

05 Jul '04

Hi, I asked about these things earlier (see http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2004-June/000134.html) but we're still having troubles. We're trying to create our own template for the registration procedure. The idea was to make the template by first registering all the other template surfaces to one single surface and proceed from there. We've tried the method 'mris_make_template', which we've interpreted to be the one intended for the procedure. However, we're getting an error when, for example, attempting to create a template from the Freesurfer example data 'bert': > mris_make_template rh sphere bert template_test <OUTPUT> creating new parameterization... processing subject bert reading spherical surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sphere... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.inflated... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sulc... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.smoothwm... writing updated template to template_test... HIPS unsupported </OUTPUT> So, are we doing something wrong, or could there perhaps be something wrong with our installation? Any help would be appreciated. Thanks in advance, -Janne Hämäläinen -- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne dot hamalainen at hus dot fi

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parcellation file format
by Darren Weber 03 Jul '04

03 Jul '04

Dear Bruce, can we read the parcellation annotation file into matlab? Essentially, how can we obtain a list of all the vertex indices and their classification? Best, Darren -- Darren L. Weber, Visiting Postdoctoral Fellow, China Basin Landing, Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94143-0946 Address for express mail/deliveries: 185 Berry Street, Suite 350, San Francisco, CA 94107 voice:(1) 415 353-9444 fax: (1) 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "People travel to wonder at the height of the mountains, at the huge waves of the seas, at the long courses of the rivers, at the vast compass of the ocean, at the circular motion of the stars; and they pass by themselves without wondering." --St. Augustine (b. 354, d. 430) "A good traveler has no fixed plan and is not intent on arriving." --Lao Tzu

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inflation<-> area
by L.Scheef＠uni-bonn.de 01 Jul '04

01 Jul '04

Dear list members, I wonder if during the inflation process "areas" are preserved. Or does inflation induces local deformations? Best wishes, Lukas Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef(a)uni-bonn.de

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Freesurfer July 2004