Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer.
Thank you.
You can use the wmparc, which includes ROIs of the WM underlying each cortical area, right below the grey-white boundary surface. These are the relevant tutorials:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 2:03 AM To: Freesurfer Support List Subject: [Freesurfer] Mean diffusivity on cortex?
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Thanks Dr Yendiki. I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer.
Thank you.
What effect are you trying to measure with MD on the cortex?
________________________________ From: Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 3:12 AM To: Freesurfer Support List; Yendiki, Anastasia Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see whether cortical MD increases can be detected relative to non-carriers, and if so, is the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
#yiv9314780658 P {margin-top:0;margin-bottom:0;}What effect are you trying to measure with MD on the cortex?
From: Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 3:12 AM To: Freesurfer Support List; Yendiki, Anastasia Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki. I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer.
Thank you. _______________________________________________ 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.
Sorry, my question wasn't very clear. I meant to ask what sort of biological effect you're hoping to measure using MD.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 6:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] Mean diffusivity on cortex?
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see whether cortical MD increases can be detected relative to non-carriers, and if so, is the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
What effect are you trying to measure with MD on the cortex?
________________________________ From: Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 3:12 AM To: Freesurfer Support List; Yendiki, Anastasia Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the
MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal
cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting
the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
Thank you both. How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea. Best Wishes,Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting
the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'll let Doug chime in on that tool.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofield@yahoo.com] Sent: Saturday, August 12, 2017 6:54 AM To: Freesurfer support list Subject: Re: [Freesurfer] Mean diffusivity on cortex?
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting
the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.commailto:shane.schofield@yahoo.com> wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are looking for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting
the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me
to smooth the data after spatial normalisation? I have also used the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is yes, are there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
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
Hi Dr Greve, Thank you very much! I will use the MGX CTX volume for the surface sampling. Best Wishes,Shane.
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
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
Hi Dr Greve, Are the settings correct to do partial volume correction of my MD images? mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shane
you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
shane.schofield@yahoo.com wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
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.
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
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.partners.org/complianceline%20. 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
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 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 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
Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.partners.org/complianceline%20. 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
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 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 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
Hi Dr Greve, On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data. Thanks for your help again.
On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me
to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
<shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on
smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.partners.org/complianceline%20. 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
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 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 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
SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly.
On 08/16/2017 02:50 PM, Shane Schofield wrote:
Hi Dr Greve,
On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data.
Thanks for your help again.
On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hello Dr Greve,
I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision?
Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD
images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can
be a
marker of neurodegeneration. The idea is that during the early stages
of a
disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
> Thanks Dr Yendiki. > > I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me > to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial. > > > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield <shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>>
wrote:
> > > Hi DTI Experts, > > Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on > smoothing ? > > DT_RECON has been completed in Freesurfer. > > Thank you. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu
mailto: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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
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-- 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 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/
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Okay I understand.
So I ideally would like to do the PetSurfer before actually working on the BPND but I already got them in the BPND format as well as the raw dynamic images. I tried to obtain the BPND data out from PetSurfer myself, but then I realise I don't any time.dat with me.mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gzIs there a way to extract the time.dat in the DICOM? Can you show me an example of what it is the correct time.dat so I can ask my colleagues if they have it somewhere? Thanks a lot!! On Wednesday, August 16, 2017, 10:46:09 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly.
On 08/16/2017 02:50 PM, Shane Schofield wrote:
Hi Dr Greve,
On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data.
Thanks for your help again.
On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield shane.schofield@yahoo.com wrote:
Hello Dr Greve,
I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision?
Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD
images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can
be a
marker of neurodegeneration. The idea is that during the early stages
of a
disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
> Thanks Dr Yendiki. > > I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me > to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial. > > > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield <shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>>
wrote:
> > > Hi DTI Experts, > > Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on > smoothing ? > > DT_RECON has been completed in Freesurfer. > > Thank you. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.partners.org/complianceline%20
http://www.partners.org/complianceline%20. 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 <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>
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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
<mailto: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 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/
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-- 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 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/
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Sorry, I don't know if that info is in PET dicom files
On 08/16/2017 07:14 PM, Shane Schofield wrote:
Okay I understand.
So I ideally would like to do the PetSurfer before actually working on the BPND but I already got them in the BPND format as well as the raw dynamic images. I tried to obtain the BPND data out from PetSurfer myself, but then I realise I don't any time.dat with me. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat*time.dat* --o mrtm1 --no-est-fwhm --nii.gz Is there a way to extract the time.dat in the DICOM? Can you show me an example of what it is the correct time.dat so I can ask my colleagues if they have it somewhere?
Thanks a lot!!
On Wednesday, August 16, 2017, 10:46:09 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly.
On 08/16/2017 02:50 PM, Shane Schofield wrote:
Hi Dr Greve,
On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data.
Thanks for your help again.
On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield <shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com> wrote:
Hello Dr Greve,
I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision?
Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD
images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:
The mri_gtmpvc command will remove volume fraction effects. Look
at the
PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably
regress
thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be
possible
to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>>>
wrote:
Agreed, especially so with MD. Keep in mind that you¹re
upsampling MD
from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? > > Dr Yendiki, I am trying to investigate whether cortical MD can
be a
>marker > of neurodegeneration. The idea is that during the early stages
of a
>disease, > cellular microstructure may breakdown before cortical thinning
occurs.
>This > results in "less" barriers against diffusion resulting in an
increase of
> MD. > > > On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>>>
wrote:
> > > Hi Shane > > you probably don't need cvs as it is more to extend the
surface-based
> registration to the entire volume. Here you just need the
surface-based
> registration I believe. Use mri_vol2surf to sample the FA
onto the
>surface. > After that it is identical to a thickness study > > cheers > Bruce > > > > On Fri, 11 Aug 2017, Shane Schofield > wrote: > > > Thanks Dr Yendiki. > > > > I am more interested to compare MD in grey matter regions by
putting
>the > MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
> Would you recommend me > > to smooth the data after spatial normalisation? I have
also used
the
> mri_cvs_register as described on the tutorial. > > > > > > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield > <shane.schofield@yahoo.com
mailto:shane.schofield@yahoo.com <mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>>>
wrote:
> > > > > > Hi DTI Experts, > > > > Is it sensible to do comparisons of MD on the cortex surface
like a
>normal > cortical thickness comparisons between group? If the answer is
yes, are
> there recommended on > > smoothing ? > > > > DT_RECON has been completed in Freesurfer. > > > > Thank you. > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu
mailto: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
http://www.partners.org/complianceline%20
http://www.partners.org/complianceline%20
http://www.partners.org/complianceline%20. 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. >
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The data in gtm.nii.gz is in floating point. If you want to change the gtm.stats file, you'll have to rescale the input, eg, fscalc input.nii.gz mul 1000 -o input-time-1000.nii.gz
On 08/15/2017 04:09 AM, Shane Schofield wrote:
Hello Dr Greve,
I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision?
Thank you.
On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line
On 08/14/2017 04:12 PM, Shane Schofield wrote:
Hi Dr Greve,
Are the settings correct to do partial volume correction of my MD
images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale
Thank you!
On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter
On 08/12/2017 10:55 AM, Bruce Fischl wrote:
Hi Shane
we do have some tools to deal with it like mri_compute_volume_fractions and mri_compute_volume_intensities, or maybe Doug's PET stuff. At the very least you should probably regress thickness out.
cheers Bruce
On Sat, 12 Aug 2017, Shane Schofield wrote:
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a
silly
idea.
Best Wishes, Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu
<mailto:AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@mgh.harvard.edu>> wrote:
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD
varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> wrote:
Hi Shane
not really - it totally depends on the size of the effect you are
looking
for. I would be *very* careful about partial volume effects though
cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can
be a
marker of neurodegeneration. The idea is that during the early stages
of a
disease, cellular microstructure may breakdown before cortical thinning
occurs.
This results in "less" barriers against diffusion resulting in an
increase of
MD.
On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
wrote:
Hi Shane
you probably don't need cvs as it is more to extend the
surface-based
registration to the entire volume. Here you just need the
surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study
cheers Bruce
On Fri, 11 Aug 2017, Shane Schofield wrote:
> Thanks Dr Yendiki. > > I am more interested to compare MD in grey matter regions by
putting
the MD on the surface, and then do a glmfit type of comparisons. Is
that OK?
Would you recommend me > to smooth the data after spatial normalisation? I have also used
the
mri_cvs_register as described on the tutorial. > > > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield <shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com
<mailto:shane.schofield@yahoo.com mailto:shane.schofield@yahoo.com>>
wrote:
> > > Hi DTI Experts, > > Is it sensible to do comparisons of MD on the cortex surface
like a
normal cortical thickness comparisons between group? If the answer is
yes, are
there recommended on > smoothing ? > > DT_RECON has been completed in Freesurfer. > > Thank you. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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