Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data

It should be in the same space. How do you know it is not? Make sure that you just pass one dicom file to recon-call (I noticed that you have a wildcard character in there).

doug

yzhangd@artsci.wustl.edu wrote:

I have run the following command to create a 001.mgz file from raw *.dcm data:

recon-all -s <subjid> -i <path to *.dcm data>

The output 001.mgz file is not in the same native space as the original *.dcm data. Could anyone tell me what space the 001.mgz file is in? Does the above command change the orientation (i.e does it rotate/translate) besides simply converting from .dcm to 001.mgz

thanks a lot

yuning

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