[Freesurfer] Question about global mean cortical thickness

[Zhiliang Long]

Dear FS experts:
 I am writting to ask for help about the computation of global mean 
thickness. On the FAQ page, one suggestion is that the global mean thickness is 
equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / 
(lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and ?h.surfarea 
are calculated. 
Any suggestions are appreciated.
Thanks for your time.


Best
Zhiliang Long___
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.

Re: [Freesurfer] Custom intensities in aparc+aseg

[Bruce Fischl]

you mean instead of colors? I guess it would be easy enough to do in 
matlab. Read in the aseg, use find to find the indices of all the voxels 
with a particular label, then replace the label with whatever intensity 
you want.

cheers
Bruce
On Sat, 12 Aug 2017, Martin Kavec wrote:

> Dear all,
> 
> I ran my subjects through recon-all successfully. I am in a need to have
> custom intensities for segmentation and parcellation in aparc+aseg. Say, 10
> - ventricles, 20 - amygdala, 30 - putamen, ...
> 
> I would appreciate advice on how I could achieve that.
> 
> Thanks in advance,
> 
> Martin
> 
>
___
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] Custom intensities in aparc+aseg

[Martin Kavec]

Dear all,

I ran my subjects through recon-all successfully. I am in a need to have
custom intensities for segmentation and parcellation in aparc+aseg. Say, 10
- ventricles, 20 - amygdala, 30 - putamen, ...

I would appreciate advice on how I could achieve that.

Thanks in advance,

Martin
___
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.

Re: [Freesurfer] Mean diffusivity on cortex?

[Bruce Fischl]

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
 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"  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
>>  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
>>  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


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.

Re: [Freesurfer] Mean diffusivity on cortex?

[Yendiki, Anastasia]

I'll let Doug chime in on that tool.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield 
[shane.schofi...@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 
 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" 
> 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
>> > 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
>> > 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


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.

Re: [Freesurfer] TRACULA trac-all speed

[Yendiki, Anastasia]

Hi Mina - The part that takes long is running bedpost. If you run trac-all with 
the -jobs flag, it'll write out a text file with command lines that can be run 
in parallel.
https://surfer.nmr.mgh.harvard.edu/fswiki//trac-all#Parallelprocessing

I do have long-term plans for not using bedpost, but that's not going to be 
until the next version release.

Hope this helps,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Mina Fakhry 
[dr.minafak...@live.com]
Sent: Saturday, August 12, 2017 6:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA trac-all speed

I am currently using the last stable version freesurfer 6.0

I gave TRACULA a try on one subject and it took more that 2.5 days to finish 
the steps, with PC specs:

- Processor core i7 4 GHz

- VGA Nvidia GTX 980 with 1500 CUDA cores

- 16 GB RAM


I tried to speed it up (trac-all command) using openmp or use-gpu, but non of 
them worked.


Is there any way to speed the TRACULA processing??
___
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.

Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

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 
 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"  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
>>  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
>>  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


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] TRACULA trac-all speed

[Mina Fakhry]

I am currently using the last stable version freesurfer 6.0

I gave TRACULA a try on one subject and it took more that 2.5 days to finish 
the steps, with PC specs:

- Processor core i7 4 GHz

- VGA Nvidia GTX 980 with 1500 CUDA cores

- 16 GB RAM


I tried to speed it up (trac-all command) using openmp or use-gpu, but non of 
them worked.


Is there any way to speed the TRACULA processing??
___
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.