where is it getting stuck? that is, look at the recon-all.log (and recon-all.cmd file). often times recon-all gets stuck in the topology fixer, because of some horrible wm.mgz file, which itself could be due to other problems. also, i assume the first thing performed before starting recon-all was to open the dicom in tkmedit (tkmedit -f name-of-first-slice.dcm) and check if it 'looks good' (that is, looks like all the other good images that you have processed).
n. On Tue, 2009-12-15 at 17:15 -0500, 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
