Doug, Thanks for responding. It looks like we were feeding it obliqued data. When we used our deobliqued data, it ran just fine.
Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstill...@laureateinstitute.org | ashley-still...@utulsa.edu On 11/19/14, 10:47 AM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >Was the dicom anonymized? Also, mosaics are usually fMRI or DTI. Are you >sure this is a high-res anatomical that will be suitable for recon-all? >doug > >On 11/19/2014 11:41 AM, Ashley Stillman wrote: >> Hi Freesurfer team, >> >> Any ideas for the below issue we are having? >> >> We are having issues running recon-all on our dicom files, as they are >> saved as a mosaic. When we open the original dicom file (attached) it >> lists out the rows, columns and slices. However, when we run >> mriparsesdcmdir, it just posts 0¹s for the rows and columns (screen >> shot attached). >> >> We are able to recreate the output file necessary to run recon-all >> (basically fill in the missing 0¹s). Is there a way to tell recon-all >> to call on this file to retrieve the missing data manually? >> >> Thank you, >> Ashley >> /Ashley N. Stillman/ >> Clinical Psychology Graduate Research Assistant >> University of Tulsa, T.R.A.P.T. Lab >> Laureate Institute for Brain Research >> email: anstill...@laureateinstitute.org >> <mailto:anstill...@laureateinstitute.org> | ashley-still...@utulsa.edu >> <mailto:ashley-still...@utulsa.edu> >> >> >> >> _______________________________________________ >> 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
