Hi Anneliis
freeview tries to guess the right window levels to display a volume, but
sometimes fails. Try changing the min/max or window/level with the T1.mgz
highlighted and see if it looks better. Alternatively, load the norm.mgz,
which will probably look better with freeview's default algorithm
cheers
Bruce
On Wed, 21
Nov 2018, Anneliis Sartin-tarm wrote:
External Email - Use Caution
Hello all,
I have been running into a curious problem with a couple brains (8 out of 150
seem to have this
problem) running through the recon-all pipeline. Upon loading brainmask.mgz,
T1.mgz, and
corresponding white matter and pial surfaces in Freeview, my colleague and I
received an error that
T1.mgz failed to load. Segmentation and parcellation seemed to run smoothly and
accurately, however,
the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow
(our server through
which we run recon-all and store our data has tons of available memory), we
reran the
brains affected. Upon loading up the same re-run surfaces, T1.mgz loaded into
the GUI as white,
washed out voxels, displaying no brain at all. The size of this file is large,
as well as all other
surface and volume files. Curiously, the brainmask file seems
normalized/stripped fine and surfaces
displayed over the T1 look accurately segmented. I attached a screenshot
displaying the T1.mgz file
and surfaces that I'm referring to.
I have a few concerns and questions. Because T1.mgz doesn't seem to be
necessary for downstream
manual editing and processing, can we proceed as normal, only displaying and
using the brainmask
file to make edits? Will our surface and volume metrics export properly without
a usable T1 file?
Lastly, any clues to how this might have occurred are welcomed. It seems like
the mri_normalize step
is the culprit, although the nu.mgz files corresponding to these brains seem
normally sized.
Best,
Anneliis Sartin-Tarm
Associate Research Specialist
Neurocircuitry of Trauma and PTSD Study
UW-Madison Dept. Psychiatry
608-262-6375
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