how do the surfaces look? On Sun, 29 Jan 2006, Daniel Goldenholz wrote:
Hi Freesurfers,
It has been a long time since I had the pleasure of recon-all'ing anything. Many things have changed.
I ran recon-all today (based on the dev installation) and I got all sorts of interesting warnings. Should I care? If so, what should I do?
Below are a few selected lines from the huge pile of output from autorecon1...
... $Id: fsl_rigid_register,v 1.13 2006/01/24 19:51:34 greve Exp $ Sun Jan 29 12:44:41 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting
/autofs/space/megraid_043/seder/freesurfer/nmr00036 calling eval flirt -in /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-2.hdr -out /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/cor-1.hdr -omat /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/tmp-mri_motion_correct.fsl-2184/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image ... mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2831/nu0.mnc Can't find the talairach xform '/autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm does not exist ... ... trying /autofs/space/megraid_043/seder/freesurfer/nmr00036/mri/transforms/talairach.xfm ...which does not exist
.... Iteration 1 Sun Jan 29 12:53:19 EST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.2831/nu0.mnc ./tmp.mri_nu_correct.mni.2831/nu1.mnc Not implemented yet in cache_volume_range_has_changed()
Mode: atlas analysis ****VALIDATION*** THE SEGMENTATION IS PROBABLY NOT CORRECT ....