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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