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
....
--
Daniel Goldenholz
-----------------------------------------------------
Cell: 617-935-9421 http://people.bu.edu/danielg/
"Mavet v'chaim b'yad halashon"
"Life and death are in the hands of language"
- Proverbs 18:21
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