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