Dear Freesurfer users
we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then created the "label" folder in advance, but after running the analysis, this folder is no longer available. The first recon-all command generated only the following five folders: mri, scripts, stats, surf, touch. When running locally on my workstation, everthing works fine.
Any idea what is wrong.
The owners of the supercomputer asked me whether there is a possibility to test the Freesurfer software in a shorter time, i.e. not to run the whole pipe with a brain because it takes about 30 hours to complet. Therefore my question: Is it possible to do a shorter test of the whole pipe or to run a evaluation tool?
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) ----------------------------------------------
Hi Juergen,
you can use -noaseg and only do one hemisphere (-hemi lh) which should make it quite a bit faster, but of course it won't work as well without the aseg. Did you check the recon-all.log to see if it had errors making directories? Although it should have aborted then.
cheers, Bruce
On Fri, 12 Jan 2007, Juergen Haenggi wrote:
Dear Freesurfer users
we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then created the "label" folder in advance, but after running the analysis, this folder is no longer available. The first recon-all command generated only the following five folders: mri, scripts, stats, surf, touch. When running locally on my workstation, everthing works fine.
Any idea what is wrong.
The owners of the supercomputer asked me whether there is a possibility to test the Freesurfer software in a shorter time, i.e. not to run the whole pipe with a brain because it takes about 30 hours to complet. Therefore my question: Is it possible to do a shorter test of the whole pipe or to run a evaluation tool?
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can try executing it with the -dontrun option
doug
Juergen Haenggi wrote:
Dear Freesurfer users
we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then created the "label" folder in advance, but after running the analysis, this folder is no longer available. The first recon-all command generated only the following five folders: mri, scripts, stats, surf, touch. When running locally on my workstation, everthing works fine.
Any idea what is wrong.
The owners of the supercomputer asked me whether there is a possibility to test the Freesurfer software in a shorter time, i.e. not to run the whole pipe with a brain because it takes about 30 hours to complet. Therefore my question: Is it possible to do a shorter test of the whole pipe or to run a evaluation tool?
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Juergen Haenggi