PVC will increase signal in some regions and will decrease it in others.
Eg, for FDG it will increase it in GM and decrease it in WM. The reason
you are seeing such a wide range is that the MG correction subtracts the
WM then divides by the GM partial volume fraction (PVF, a number
between 0 and 1). This requires a mask of some sort because there will
be some voxels where the GM PVF is 0 (and you can't divide by 0). When
you ran mri_gtmpvc with the --mgx option, you had to supply a threshold
(eg, .01). This is the minimum allowed PVF before the voxel is masked
out. If you used .01, then the multiplier could be as large as 1/.10 =
100, which agrees with the range you are seeing. Because of this
problem, you must do the MG voxel-wise analysis on the surface where the
GM PVF will be high. For subcortical analysis, you must use a mask of
subcortical GM structures. The mask must be used when smoothing because
you must only smooth within the mask (not such a problem on the
surface). Note that there are many paper that use MG in a volume-based
voxel-wise analysis; in my opinion, these studies are invalid.
On 8/18/17 11:47 AM, John Anderson wrote:
Hi Dr Greve, Thank you very much for the great answers.
Kindly, I have one last question.
The range of the signal intensity within the voxels in the original
SUV maps is min=0.00 and max=3.017629
For the mgx images it is min=-43.74384 and max=88.468712
The difference in the range of signal intensity in the mgx images is
largely wide. It seems that PVC increases the signal intensity. Is
this correct?
Am I doing something wrong. I plan to include these images in
voxel-wise analysis so I am curious about this difference between the
images.
Thanks for any clarification!
On 8/18/17 10:20 AM, John Anderson wrote:
Hi Dr Greve,
I followed the steps in WIKI to do SUV-surface based analyses + PVC. I
have the following questions and I highly appreciate your input:
1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and
mgx.ctx.subgm) is not like the original SUV image that has been fed
to the pipeline. i.e. I start with image-dimensions 128X128X128 :
2X2X2 and end up with 79X113X102 : 2X2X2
Also FOV is different as well between the original SUV image /256/
and the output mgx images /158/. How this happen? I am I doing
something wrong?
I set up mri_gtmpvc to reduce the field of view to a bounding box
around the head to reduce memory and computational loads. You can turn
this off with --no-reduce-fov
2. Some voxels in the mgx images has negative signal intensity. is
this normal?
Yes. MG works by estimating the contribution of non-GM to GM and
subtracting it out. If the estimate is too high, then it can cause
negative values.
Thank you for any clarification.
John
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
