It is not clear in the manual where can I find it. In pet surfer page "--psf
FWHM is the full-width/half-max of the the point-spread function of the scanner
as measured in image space. Eg, an HR+ is typically about 6mm."
Is it in the DICOMs? Is there an y formula to calculate it? Any reference that
mri_gtmpvc rely on it to measure it?
Thank you for any clarification!
John
read the petsurfer page for how to select the psf
On 08/21/2017 04:52 PM, John Anderson wrote:
\
> -------- Original Message --------
> Subject: Re: smoothing
> Local Time: August 21, 2017 4:52 PM
> UTC Time: August 21, 2017 8:52 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> Perfect!
>
> Please how can I choose the correct value for PSF
> in the manual psf is the scanner psf FWHM in mm were can I find this value?
>
> It does not apply any smoothing. It attempts to remove smoothing, but you
> have to tell it how much smoothing to remove. You probably told it 6mm
>
> On 08/21/2017 12:15 PM, John Anderson wrote:
>
>>
>
>> 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
>
> Sent with [ProtonMail](https://protonmail.com) Secure Email.
>
>> -------- Original Message --------
>> Subject: Re: smoothing
>> Local Time: August 21, 2017 12:15 PM
>> UTC Time: August 21, 2017 4:15 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>
>> 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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