Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float
I want to smooth two different modality-images using the cortical thickness smoothing method.
Thank you for any advice! John
Hi John
I don't think fslmaths takes a surface topology so they won't be the same (mri_surf2surf smooths within the surface and fslmaths smooths in the volume I believe)
cheers Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float
I want to smooth two different modality-images using the cortical thickness smoothing method.
Thank you for any advice! John
Dear Dr Bruce, I highly appreciate the response. I want to smooth PET volumetric images, when I use "fslmaths", it shifts the signal from the cortex to the underlying structures. I think (depending on wiki) that Freesurfer handles this issue by smoothing on sphere. Which is the recommendded stream in PETsurfer.
I am wondering if there are any commands within Freesurfer that can be used to smooth volumtric PET images without taking the average signal of the neighboring voxels (like in Gaussian smoothing).
Also, I have question about mri_fwhm: what is the difference between the flags (--smooth-only; --fwhm). I am aware that "mri_fwhm" is very well explained in FS wiki, but I was unable to exactly understand the difference. For instance when I use the flag --smooth-only the output image is somehow similar to the input image. Is Gaussian in this cases ~1
Thanks in advance! J
-------- Original Message -------- Subject: Re: [Freesurfer] cortical thickness smoothing Local Time: December 12, 2017 10:38 AM UTC Time: December 12, 2017 3:38 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
I don't think fslmaths takes a surface topology so they won't be the same (mri_surf2surf smooths within the surface and fslmaths smooths in the volume I believe)
cheers Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths": fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float I want to smooth two different modality-images using the cortical thickness smoothing method. Thank you for any advice! John
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.
You have to sample the volumetric PET data onto the surface (mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote:
Dear Dr Bruce, I highly appreciate the response. I want to smooth PET volumetric images, when I use "fslmaths", it shifts the signal from the cortex to the underlying structures. I think (depending on wiki) that Freesurfer handles this issue by smoothing on sphere. Which is the recommendded stream in PETsurfer.
I am wondering if there are any commands within Freesurfer that can be used to smooth volumtric PET images without taking the average signal of the neighboring voxels (like in Gaussian smoothing).
Also, I have question about mri_fwhm: what is the difference between the flags (--smooth-only; --fwhm). I am aware that "mri_fwhm" is very well explained in FS wiki, but I was unable to exactly understand the difference. For instance when I use the flag --smooth-only the output image is somehow similar to the input image. Is Gaussian in this cases ~1
mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM but I extended it to be able to apply smoothing (--fwhm) as well as measure the smoothness. The --smooth-only says to not do the FWHM estimate (just smooth it).
Thanks in advance! J
-------- Original Message -------- Subject: Re: [Freesurfer] cortical thickness smoothing Local Time: December 12, 2017 10:38 AM UTC Time: December 12, 2017 3:38 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
I don't think fslmaths takes a surface topology so they won't be the same (mri_surf2surf smooths within the surface and fslmaths smooths in the volume I believe)
cheers Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths": fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float I want to smooth two different modality-images using the cortical thickness smoothing method. Thank you for any advice! JohnThe 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Dr Greve thank you so much for the advice.
Kindly, I have one addition question and I highly appreciate your feedback! Smoothing on surface is very interesting and it is really more accurate than applying the Gaussian smoothing directly on volumetric images. I don't see any aggressive shifts in the signal when I smooth on surface! In this context, I want to know if the following procedure is legitimate:
To smooth PET volumetric images. I am thinking of using "mri_vol2surf" to sample and smooth the PET images on surface. Can I then use "mri_surf2vol" to move the smoothed images on surface to volume. How about the subcortical regions- is the smoothing on surface applicable for the whole brain, or just for the regions between pial/white?
You have to sample the volumetric PET data onto the surface
(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote:
Dear Dr Bruce, I highly appreciate the response.
I want to smooth PET volumetric images, when I use "fslmaths", it
shifts the signal from the cortex to the underlying structures. I
think (depending on wiki) that Freesurfer handles this issue by
smoothing on sphere. Which is the recommendded stream in PETsurfer.
I am wondering if there are any commands within Freesurfer that can be
used to smooth volumtric PET images without taking the average signal
of the neighboring voxels (like in Gaussian smoothing).
Also, I have question about mri_fwhm:
what is the difference between the flags (--smooth-only; --fwhm). I am
aware that "mri_fwhm" is very well explained in FS wiki, but I was
unable to exactly understand the difference. For instance when I use
the flag --smooth-only the output image is somehow similar to the
input image. Is Gaussian in this cases ~1
mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM
but I extended it to be able to apply smoothing (--fwhm) as well as
measure the smoothness. The --smooth-only says to not do the FWHM
estimate (just smooth it).
Thanks in advance!
J
-------- Original Message --------
Subject: Re: [Freesurfer] cortical thickness smoothing
Local Time: December 12, 2017 10:38 AM
UTC Time: December 12, 2017 3:38 PM
From: fischl@nmr.mgh.harvard.edu
To: John Anderson John.anderso@protonmail.com, Freesurfer support
Hi John
I don't think fslmaths takes a surface topology so they won't be the same
(mri_surf2surf smooths within the surface and fslmaths smooths in the
volume I believe)
cheers
Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts,
I ran recon-all with the flag -qcache to generate smoothed
cortical thickness maps.
In order to check how the flag "-qcache" is smoothing the
cortical thickness data. I looked into the
file $subj_dir/scripts/recon-all.log" which showed that the
following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval
lh.sulc.fsaverage.mgh --tval
lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar
smoothing method to the smoothing
output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean
<output_image.nii> -odt float
I want to smooth two different modality-images using the cortical
thickness smoothing method.
Thank you for any advice!
John
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.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 12/13/17 8:03 AM, John Anderson wrote:
Dear Dr Greve thank you so much for the advice.
Kindly, I have one addition question and I highly appreciate your feedback! Smoothing on surface is very interesting and it is really more accurate than applying the Gaussian smoothing directly on volumetric images. I don't see any aggressive shifts in the signal when I smooth on surface! In this context, I want to know if the following procedure is legitimate:
To smooth PET volumetric images. I am thinking of using "mri_vol2surf" to sample and smooth the PET images on surface. Can I then use "mri_surf2vol" to move the smoothed images on surface to volume. How about the subcortical regions- is the smoothing on surface applicable for the whole brain, or just for the regions between pial/white?
You can, but this is usually only done for display purposes (eg, you want to show the surface data in the volume along with the subcortical data). Usually, we do three separate analyses: left hemi, right hemi, and subcortical, smoothing each one in the appropriate way.
You have to sample the volumetric PET data onto the surface
(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote:
Dear Dr Bruce, I highly appreciate the response.
I want to smooth PET volumetric images, when I use "fslmaths", it
shifts the signal from the cortex to the underlying structures. I
think (depending on wiki) that Freesurfer handles this issue by
smoothing on sphere. Which is the recommendded stream in PETsurfer.
I am wondering if there are any commands within Freesurfer that can be
used to smooth volumtric PET images without taking the average signal
of the neighboring voxels (like in Gaussian smoothing).
Also, I have question about mri_fwhm:
what is the difference between the flags (--smooth-only; --fwhm). I am
aware that "mri_fwhm" is very well explained in FS wiki, but I was
unable to exactly understand the difference. For instance when I use
the flag --smooth-only the output image is somehow similar to the
input image. Is Gaussian in this cases ~1
mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM
but I extended it to be able to apply smoothing (--fwhm) as well as
measure the smoothness. The --smooth-only says to not do the FWHM
estimate (just smooth it).
Thanks in advance!
J
-------- Original Message --------
Subject: Re: [Freesurfer] cortical thickness smoothing
Local Time: December 12, 2017 10:38 AM
UTC Time: December 12, 2017 3:38 PM
From: fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu
To: John Anderson <John.anderso@protonmail.com
mailto:John.anderso@protonmail.com>, Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
Hi John
I don't think fslmaths takes a surface topology so they won't be
the same
(mri_surf2surf smooths within the surface and fslmaths smooths in the
volume I believe)
cheers
Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts,
I ran recon-all with the flag -qcache to generate smoothed
cortical thickness maps.
In order to check how the flag "-qcache" is smoothing the
cortical thickness data. I looked into the
file $subj_dir/scripts/recon-all.log" which showed that the
following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval
lh.sulc.fsaverage.mgh --tval
lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar
smoothing method to the smoothing
output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean
<output_image.nii> -odt float
I want to smooth two different modality-images using the cortical
thickness smoothing method.
Thank you for any advice!
John
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.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu mailto: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
To reinforce what bruce is saying, mri_surf2surf does surface-based smoothing (ie, along the cortical surface), whereas fslmaths does volume-based smoothing which does not take into account the anatomy
On 12/12/2017 10:38 AM, Bruce Fischl wrote:
Hi John
I don't think fslmaths takes a surface topology so they won't be the same (mri_surf2surf smooths within the surface and fslmaths smooths in the volume I believe)
cheers Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float
I want to smooth two different modality-images using the cortical thickness smoothing method.
Thank you for any advice! John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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John Anderson