What is the model of the scanner? I think there is an error in there because it can' find the parameters it needs. You can also try something like
mri_convert 160 11147SACC000.MR.RESEARCH_NEURO. test.mgh this might print something more informative to the terminal. You can also try mri_probedicom --i 11147SACC000.MR.RESEARCH_NEURO. doug On 05/23/2014 10:18 AM, Caroline Lewis wrote: > That doesn't sound good. Does tag 28, 30 mean the voxel size is > missing, why would this be? It is a Siemens dicom from a 3T scanner - > not sure which model but I can find out. > > Do you have any idea why I am getting errors for some runs in the > scan. info file as such?: > > 7 t1_mprage_tra_p2_iso_1.0 err 0 0 0 160 > 11147SACC000.MR.RESEARCH_NEURO. > > Thanks Doug, > > Caroline > > > On Thu, May 22, 2014 at 6:52 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > hmmm, if it does not have tag 28 30, then something is really wrong. > This is a Siemens dicom, right? What scanner? > doug > > > On 05/22/2014 06:05 PM, Caroline Lewis wrote: > > Thanks Douglas. Now I am running into other errors. I ran the > command: > > > > unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ > > ? -run 8 bold nii 001.nii > > > > ERROR: reading > > > > 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm > > tag 28 30 > > > > Also, some of the runs in the "scan.info <http://scan.info> > <http://scan.info>" file say > > "err" where it should say "ok" > > > > Do you have any idea why I'm getting these errors? > > > > Thanks, > > > > Caroline > > > > > > On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > Remove the \<<NIFTI>> > > > > On 05/22/2014 03:45 PM, Caroline Lewis wrote: > > > Hi, > > > > > > I am trying to unpack dicom files and convert them to > nifti, but am > > > running into an error. I ran the following command with no > issue: > > > unpacksdcmdir -src dicomdir -targ targetdir -scanonly > > targetdir/scan.info <http://scan.info> <http://scan.info> > <http://scan.info> > > > > > > > > > however, when I try to run the next command to actually unpack > > the data: > > > > > > unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ > > > ? -run 7 3danat mgz 001.mgz \<<NIFTI>> > > > > > > I get the following error message: Missing name for redirect. > > > Thanks, > > > > > > Caroline > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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
