Can you delete them again and re-run? So far, I have not seen anything that recon-all is doing wrong, and I can't debug it until I do! doug
Chindhuri Selvadurai wrote: > Yes, I ran it with the -i first, and I got this error: > > ERROR: You are trying to re-run an existing subject with (possibly) > new input data (-i). If this is truly new input data, you should delete > the subject folder and re-run, or specify a different subject name. > If you are just continuing an analysis of an existing subject, then > omit all -i flags. > > > I deleted all the files, and re-ran, and it still didn't work, so I then > deleted the -i flag and tried again. > > > >> In the log file, it says that you did not run it with the -i. Check your >> command line. >> doug >> >> Chindhuri Selvadurai wrote: >> >>> Hello, >>> >>> I am having trouble doing a recon-all of my data. >>> >>> pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i >>> /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-000015-000001.dcm >>> -mail chin...@nmr.mgh.harvard.edu' >>> >>> Here is the error: >>> ERROR: no run data found in >>> /autofs/cluster/manoach/dod/subjects/DODASD001/mri. Make sure to have a >>> volume called 001.mgz in >>> /autofs/cluster/manoach/dod/subjects/DODASD001/mri/orig. If you have a >>> second run of data call it 002.mgz, etc. >>> >>> I usually do the recon all through launchpad first before any other >>> preprocessing, and hadn't had a problem before? Not sure why this is the >>> case this time. What step should be done before this to get the data in >>> the mri? >>> >>> My subjects_dir is /cluster/manoach/dod/subjects >>> >>> Thanks so much! >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > > Best, > > Chindhuri Selvadurai > > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
