I don't think that recon-all deletes the label dir (or any other dir). One thing you can do is to run it with -debug and capture the output (both stdout and stderr). The output will be everything it is doing (so it will be huge), but it can then be searched for an rm cmd.
doug
Juergen Haenggi wrote:
Dear Freesurfer users
we are running Freesurfer 3.0.4. (64bit) on a grid computer. If we run recon-all -all with the -dontrun flag, everything is fine. But if we then run the analysis, it run until it tried to write the /label/lh.aparc.annot file. The Freesurfer said there is no directory called "label". But this directory was there and I guess that Freesurfer itself has deleted the label directory.
Does anyone had a similar problem or any idea where the problem is?
Thanks a lot in advance Best regards
Juergen
Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi@bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website)
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