[Freesurfer] large radius
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
Re: [Freesurfer] large radius
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
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] large radius
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:[EMAIL PROTECTED] 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
