Hi Jenifer
sometime scanners will upsample by zero-padding on the scanner. This
doesn't actually create any information, but some clinicians like it. That
is, your underlying data may actually be close to 1mm iso, even though the
in plane is apparently 0.48mm. You can probably tell this visually (if it
is not terribly noisy). In that case highres is not worth it. I guess you
can try it both ways and see
Bruce
On
Sun, 10 Jun 2018, Juranek, Jenifer wrote:
External Email - Use Caution
I offered to help a colleague with some Freesurfer analyses, but when I looked
at the data they were
processing, I found:
1) highly anisotropic voxdims
2) sub-mm in-plane resolution
Data were acquired on a 3T Siemens Tim Trio. I don’t think they were trying to
deviate from the
recommended 1x1x1mm specs, but somehow it looks like they did since the 001.mgz
file does not
conform to the FS standard.
Output for mri_info on their 001.mgz file is listed below. They did not keep
the file converted by
mri_convert (nii or dicom) in their FS_sub directory, so I’m limited to the
001.mgz.
I’m running FSv6 in my lab, is the hires flag appropriate in this situation?
Any suggestions?
Many Thanks,
Jenifer
[orig]$ mri_info 001.mgz
Volume information for 001.mgz
type: MGH
dimensions: 448 x 512 x 192
voxel sizes: 0.478516, 0.478516, 1.000000
type: SHORT (4)
fov: 245.000
dof: 0
xstart: -107.2, xend: 107.2
ystart: -122.5, yend: 122.5
zstart: -96.0, zend: 96.0
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