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Hi,
we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz?
endorphin.32> ls -l ucsf_disc01/mri/orig/ total 5784 - -rw-rw-rw- 1 dweber dnl 5907576 May 3 13:52 orig.mgz
endorphin.31> recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer - -rw-rw---- 1 dweber dnl 56553 May 3 13:55 /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version #-------------------------------------------- #@# MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006
Thanks, Darren
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Darren L. Weber, Ph.D. Postdoctoral Scholar
Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA.
Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)