Hi David, usually this means the topology fixing has encountered a very large defect, typically caused by the cerebellum or skull being attached to one of the cortical hemispheres. Try looking at the orig.nofix in tksurfer or the filled.mgz in tkmedit and do a sanity check on them.
cheers, Bruce On Tue, 15 Dec 2009, David Qixiang Chen wrote: > Hi, > We are having one scan going through recon-all that is taking way > longer than ordinary. Other scans took about 20-30 hours to calculate, > while this particular scan is taking 3+ days and has still not being > completed. > Just wondering how often something like this happens, and if there's > any known problems with this sort of thing. Here's the mri_info > output: > > Starting DICOMRead2() > dcmfile = /media/HIPPO/scans/normals/C11/T1/C11_0.dcm > dcmdir = /media/HIPPO/scans/normals/C11/T1 > Ref Series No = 3 > Found 162 files, checking for dicoms > Found 160 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 1 > Vs: 0 0 1 > Second Sorting > Counting frames > nframes = 1 > nslices = 160 > ndcmfiles = 160 > PE Dir = ROW (dicom read) > Volume information for C11_0.dcm > type: dicom > dimensions: 256 x 256 x 160 > voxel sizes: 0.9375, 0.9375, 1.0000 > type: SHORT (4) > fov: 240.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -80.0, zend: 80.0 > TR: 11.96 msec, TE: 5.05 msec, TI: 300.00 msec, flip > angle: 20.00 degrees > nframes: 1 > ras xform not present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = > 5.3850 > : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = > 30.3850 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > 27.4266 > Orientation : ??? > Primary Slice Direction: unknown > > voxel to ras transform: > -0.9375 0.0000 -0.0000 125.3850 > 0.0000 -0.9375 -0.0000 150.3850 > 0.0000 0.0000 1.0000 -52.5734 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 0.878906 > > ras to voxel transform: > -1.0667 0.0000 0.0000 133.7440 > 0.0000 -1.0667 0.0000 160.4107 > -0.0000 -0.0000 1.0000 52.5734 > 0.0000 0.0000 0.0000 1.0000 > _______________________________________________ > 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
