Can you run /mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log and send me dng.log ?
doug On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote: > du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is > the “not found” error telling me that a binary is not found, or that > some expected output file is not found? I was looking for /bin/imtest > and /bin/remove_ext, and those binaries indeed do not exist, but we’ve > run Freesurfer on another dataset (but on another workstation, but > neither were those two binaries to be found on that workstation). >> Is your /tmp space full? >> >> On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: >> >//>/I was hoping the developers might be able to help with a problem I'm >> >/>/having with a sub-step of preproc-sess./ >> >/I executed the following: />//>/preproc-sess -s FS_T1_501 -surface >> self lhrh -fwhm 6 -per-run -fsd bold />//>/In the relevant output, I >> see mktemplate-sess completed, followed by a />/call to >> mkbrainmask-sess, which eventually reported: />//>/# ---------- Using >> FSL's BET to Extract Brain------------------ # >> />//home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold />/bet.fsl >> /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 >> />//usr/local/freesurfer/bin/bet.fsl: 1: >> />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found >> />//usr/local/freesurfer/bin/bet.fsl: 1: >> />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found >> />//usr/local/freesurfer/bin/bet.fsl: 1: >> />//usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found >> />//usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator >> />//usr/local/freesurfer/bin/bet.fsl: 231: >> />//usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found/ > > > /********************************************** > * Chris McNorgan > * Assistant Professor > * Department of Psychology > * University at Buffalo, > * The State University of New York > * http://ccnlab.buffalo.edu/ > * Office: 716.645.0236 > * Lab: 716.645.0222 > **********************************************/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
