Hi Bruce and Florent, Your comments re: isoptropic voxels raised a question for me. How is mgz different to cor format? Does mri_convert not interpolate to 1mm3 for mgz? The imaging parameters are: IR prep time, 500 ms; TE minimum, 2.8 ms; TR 13.9 ms; bandwidth, 15.63 kHz; 1 NEX; 20° flip angle; 2 mm contiguous slices; FOV 24 cm; up to 128 volumes for full brain coverage; 512 (frequency, SI) by 256 (phase) matrix, zipped to 512 in phase direction with extended dynamic range.
-----Original Message----- From: florent segonne [mailto:fsegonne@csail.mit.edu] Sent: Wed 14/09/2005 6:29 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] large radius
Hi Alex, I think that mri_watershed is 'incorrectly' assuming 1*1*1mmm isotropic voxels. We'll update the code so that it won't stop there. Florent ------------------------------------- Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne ------------------------------------- On Tue, 13 Sep 2005, Bruce Fischl wrote: > Hi Alex, > > the 2mm slice thickness could be trouble. Usually we don't recommend trying > to recon cortical models with any dimension greater than 1.5mm. Why do > anisotropic? Can you describe the rest of the acquisition parameters? > > Bruce > > > On Tue, 13 Sep 2005, Fornito, Alexander wrote: > >> HI, >> I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I >> seem to be able to convert them to .mgz ok, but when I run mri_watershed I >> get an error saying "main radius too high" (output below). Any ideas as to >> what's happening? >> Thanks, >> Alex >> >> >> mri_watershed 1001670.mgz 1001670_brain.mgz >> >> >> ************************************************************ >> The input file is 1001670.mgz >> The output file is 1001670_brain.mgz >> If this is incorrect, please exit quickly the program (Ctl-C) >> >> >> *************************WATERSHED************************** >> preflooding height equal to 25 percent >> Sorting... >> first estimation of the COG coord: x=253 y=50 z=235 r=135 >> first estimation of the main basin volume: 10415397 voxels >> Error >> main radius too high >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >