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 chinsel@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!
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 chinsel@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
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 chinsel@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 greve@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
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 chinsel@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 greve@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@nmr.mgh.harvard.edu
-
Chindhuri Selvadurai -
Douglas N Greve