If MRIcro gets the orientation right, then that will be stored in the nifti file and be inherited by the mgz.
doug
Gabriel Go.Es. wrote:
Thanks Doug,
The answer is yes, I can convert to NIfTY with using MRIcro (DCM2nii) and then use mri_convert to convert to mgz but, how can I be sure that this will not change the handedness???'
Bests, Gabriel
Date: Tue, 1 Feb 2011 10:59:56 -0500 From: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
There is a tag in this file that our DICOM reader does not recognize:
280092 DCM Unrecognized VR code (??) in readVRLength
Unfortunately, we're using a 3rd party dicom reader that is quite brittle, and I don't know a way around it. Can you convert to nifti using MRIcro and then use mri_convert to convert to mgz?
doug
Gabriel Go.Es. wrote:
Dear FS users
I'm using FS v5 to convert some dicom images to mgz running the
comand:
mri_convert -it dicom -ot mgz 000001.DCM 001.mgz
And get the error:
ERROR: /root/trabajo/freesurfer/subjects/sujeto1/mri/orig/MPRAGE1/000001.DCM is not a dicom file
But when I try to open the file in MRIcro it is a dicom (philips)
file
(see attached file), can any one help me with this?
Regards, Gabriel
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