Dear Dr Greve,
Thank you so much for the detailed explanation. I have additional question and
I highly appreciate any clarification.
By reviewing the log file "mri_gtmpvc.log" I see that this program apply
smoothing FWHM=6 mm on the input SUVR maps and the output mgx images are
smoothed according to this default feature.
1. What is the importance of smoothing in this case?
2. Can I turn this feature off?
3. I want to do PVC without smoothing, is this possible?
Thanks
John
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.
> -------- Original Message --------
> Subject: Re: pet surfer
> Local Time: August 18, 2017 11:47 AM
> UTC Time: August 18, 2017 3:47 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> 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
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