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 _______________________________________________ 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.
