Use mri_vol2vol, something like:
mri_vol2vol --mov ribbon.mgz --targ rawavg.mgz --regheader --o
ribbon-in-rawavg.nii --interp nearest
doug
Arthur Mikhno wrote:
Hi,
I am trying to convert the ribbon (amongst other mgz files) from a
freesurfer run to the native space ANALYZE file I initially imported
into freesurfer. I need to do this to create a cortical ribbon mask as
a pre-processing step for normalization (with another package).
However, every mgz file in the mri/ folder, after conversion, has a
slightly different spatial distribution after conversion. Although,
when I convert 001.mgz and rawavg.mgz the resultant image matches the
image I imported exactly. By spatial distribution I mean, minor
cortical fold shifts (up down, left right) and individual minor
rotations in the cortical folds, some minor internal translations.
I think I tracked the problem down to the conform step, when
rawavg.mgz gets conformed (mri_convert --conform) to 1x1x1mm and saved
as orig.mgz.
I need to ensure a spatially correct cortical ribbon in the native
space data. Is there any way to un-conform ? or some way to say,
convert orig.mgz BACK to rawavg.mgz?
For reference, this is the command I am using to convert .mgz to
ANALYZE (.hdr, .img):
mri_convert --out_orientation LSP -rl native_mri.img orig.mgz
converted_native_mri.img
I would really appreciate any help as this is my LAST roadblock!
Thanks in advance,
-Arthur
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