Dear FS users, No I can't run it without anonymization. Anyway, I do not know if this can be of any help but here attached you can see the error that stopped the reconstruction when I tried to run the nifti version of the "mosaic' dicom; I transformed the dmc2nii with MRIcron.
Thanks, Marianna -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 6, 2016 2:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz Not sure. This one did not look like a mosaic (it had 256x256 voxels). Can you run it without anonymization? On 12/06/2016 01:40 PM, Marianna Riello wrote: > Yeah they do not come directly from the scanner. They are anonymized. > The same were the enhanced version of the dicom (with 170 files per dicom) > but these in particular didn't show any error with mri_convert. > So why should these mosaic ones show the error? > > Thanks, > Marianna > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Tuesday, December 6, 2016 12:59 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz > > This file is missing critical information. Did this come directly from your > scanner or was it changed in some way (eg, anonymized)? > > > On 12/06/2016 10:32 AM, Marianna Riello wrote: >> Yes I did it, I used your mail but it gives me an error. >> Check attachment. >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> Greve >> Sent: Tuesday, December 6, 2016 10:23 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz >> >> I did not. You should have had an opportunity to enter an email >> address of the recipient. You can use my email >> >> >> On 12/5/16 6:35 PM, Marianna Riello wrote: >>> I uploaded the dicom mosaic on Martinos Center. >>> I am wondering whether you received it.... >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Monday, December 5, 2016 12:13 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz >>> >>> Can you upload the dicoms to >>> https://gate.nmr.mgh.harvard.edu/filedrop2 >>> >>> >>> On 12/05/2016 12:09 PM, Marianna Riello wrote: >>>> Dear all, >>>> >>>> Thank you. I tried but still is showing the same error (check >>>> 2Error >>>> attachment) Do you have any other suggestions? >>>> >>>> Thanks in advance, >>>> Marianna >>>> >>>> -----Original Message----- >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of >>>> Douglas N Greve >>>> Sent: Monday, December 5, 2016 12:00 PM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz >>>> >>>> Try not including the "-it dicom" arg and see if that works >>>> >>>> >>>> On 12/05/2016 10:01 AM, Marianna Riello wrote: >>>>> Dear all again, >>>>> >>>>> Thanks for your reply. >>>>> Please check the error attached when trying to convert the DICOM Mosaic >>>>> in .mgz file when using mri_convert. >>>>> >>>>> Thanks in advance, >>>>> Marianna >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of >>>>> Douglas N Greve >>>>> Sent: Friday, December 2, 2016 12:17 PM >>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz >>>>> >>>>> It will handle mosaics (as the mosaics that fMRI data will come in). >>>>> Hard to say what is going on without more specifics (command line, >>>>> terminal output) >>>>> >>>>> >>>>> On 12/02/2016 10:26 AM, Marianna Riello wrote: >>>>>> Dear all, >>>>>> >>>>>> I am wondering whether mri_convert can compute .mgz files for the >>>>>> reconstructions with the 'Mosaic Format SIEMENS DICOM files'. >>>>>> >>>>>> I have been computing .mgz with the enhanced format .dcm so far, >>>>>> and it always worked. >>>>>> >>>>>> I have used mri_convert to compute .mgz from .nii (I previously >>>>>> transformed the mosaic .dcm format in nifti with mricron but the >>>>>> reconstruction failed) >>>>>> >>>>>> Thanks in advance, >>>>>> >>>>>> Marianna >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> 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 >>>> >>>> >>>> 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 >>> -- >>> 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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 >> >> >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
