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.anderso@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:
- 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
- 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
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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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:
- 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
- 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
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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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:
- 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
- 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
read the petsurfer page for how to select the psf
On 08/21/2017 04:52 PM, John Anderson wrote:
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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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:
- 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
- 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
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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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:
- 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
- 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
The PSF is not necessarily a known value. Usually people get the value from a phantom study done on the type of scanner they are using. You can look through the lit to see if someone using your scanner (and pet recon) has done this.
On 08/21/2017 05:05 PM, John Anderson wrote:
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 ofthe scanner as measured in image space. Eg, an HR+ is typically about6mm."
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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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.
- What is the importance of smoothing in this case?
- Can I turn this feature off?
- 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.anderso@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:
- 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
- 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@nmr.mgh.harvard.edu
-
Douglas N Greve -
John Anderson