Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Alright, thanks a lot for your help Bruce.

Best,

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France

2016-12-12 17:33 GMT+01:00 Bruce Fischl :

> because filling in the T1 may cause artifacts
>
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> Would you please give me the reasons why the former would be better ?
>> Ismail
>>
>> PhD candidate
>> Neurocentre Magendie, INSERM
>> Bordeaux, France
>>
>>
>> 2016-12-12 15:47 GMT+01:00 Bruce Fischl :
>>   the former I think, but it's an empirical question
>>   Bruce
>>   On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>>
>>   > Hi Bruce,
>>   > Thanks for your answer.
>>   > What do you think would be better, run recon-all on the original
>> data (with
>>   > lesions) then edit the aseg for the juxtacortical lesions or use
>> a lesion
>>   > filling on the T1 and then run recon-all on it.
>>   > Thanks again.
>>   >
>>   > Cheers,
>>   >
>>   > Ismail
>>   >
>>   > PhD candidate
>>   > Neurocentre Magendie, INSERM
>>   > Bordeaux, France
>>   >
>>   > 2016-12-09 22:58 GMT+01:00 Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>:
>>   >   I Ismail
>>   >
>>   >   yes, if you have juxtacortical lesions you should label
>> them as
>>   >   such in
>>   >   the aseg, then I think it should work
>>   >
>>   >   cheers
>>   >   Bruce
>>   >   On Fri, 9 Dec 2016, Ismail Koubiyr
>>   >   wrote:
>>   >
>>   >   > Dear Freesurfer experts,
>>   >   > We are facing a problem in our study and would need your
>>   >   advice on it.
>>   >   > We want to get an accurate measurement for the cortical
>>   >   thickness from our
>>   >   > MS patients data. For that we are using 3D T1 and FLAIR
>>   >   (recon-all will be
>>   >   > used with the FLAIR option so that we can a more accurate
>> pial
>>   >   surface).
>>   >   > However, we were wondering if running recon-all on the raw
>>   >   data would lead
>>   >   > to some errors specially because of the juxtacortical
>> lesions
>>   >   or not. Or, is
>>   >   > it better to first apply a lesion filling using our lesion
>>   >   mask ?
>>   >   > I should specify that we will use the longitudinal
>> pipeline if
>>   >   it is of any
>>   >   > use.
>>   >   >
>>   >   > Thank you all.
>>   >   >
>>   >   > Ismail
>>   >   >
>>   >   > PhD candidate
>>   >   > Neurocentre Magendie, INSERM
>>   >   > Bordeaux, France
>>   >   >
>>   >   >
>>   > ___
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>>   > 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.
>>   >
>>   >
>>   >
>>   >
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Bruce Fischl]

because filling in the T1 may cause artifacts
On Mon, 12 Dec 2016, Ismail 
Koubiyr wrote:



Would you please give me the reasons why the former would be better ?
Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France


2016-12-12 15:47 GMT+01:00 Bruce Fischl :
  the former I think, but it's an empirical question
  Bruce
  On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

  > Hi Bruce,
  > Thanks for your answer.
  > What do you think would be better, run recon-all on the original data 
(with
  > lesions) then edit the aseg for the juxtacortical lesions or use a 
lesion
  > filling on the T1 and then run recon-all on it.
  > Thanks again.
  >
  > Cheers,
  >
  > Ismail
  >
  > PhD candidate
  > Neurocentre Magendie, INSERM
  > Bordeaux, France
  >
  > 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
  >       I Ismail
  >
  >       yes, if you have juxtacortical lesions you should label them as
  >       such in
  >       the aseg, then I think it should work
  >
  >       cheers
  >       Bruce
  >       On Fri, 9 Dec 2016, Ismail Koubiyr
  >       wrote:
  >
  >       > Dear Freesurfer experts,
  >       > We are facing a problem in our study and would need your
  >       advice on it.
  >       > We want to get an accurate measurement for the cortical
  >       thickness from our
  >       > MS patients data. For that we are using 3D T1 and FLAIR
  >       (recon-all will be
  >       > used with the FLAIR option so that we can a more accurate pial
  >       surface).
  >       > However, we were wondering if running recon-all on the raw
  >       data would lead
  >       > to some errors specially because of the juxtacortical lesions
  >       or not. Or, is
  >       > it better to first apply a lesion filling using our lesion
  >       mask ?
  >       > I should specify that we will use the longitudinal pipeline if
  >       it is of any
  >       > use.
  >       >
  >       > Thank you all.
  >       >
  >       > Ismail
  >       >
  >       > PhD candidate
  >       > Neurocentre Magendie, INSERM
  >       > Bordeaux, France
  >       >
  >       >
  > ___
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  > 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.
  >
  >
  >
  >
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Would you please give me the reasons why the former would be better ?

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France


2016-12-12 15:47 GMT+01:00 Bruce Fischl :

> the former I think, but it's an empirical question
> Bruce
> On Mon, 12 Dec 2016, Ismail Koubiyr wrote:
>
> > Hi Bruce,
> > Thanks for your answer.
> > What do you think would be better, run recon-all on the original data
> (with
> > lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> > filling on the T1 and then run recon-all on it.
> > Thanks again.
> >
> > Cheers,
> >
> > Ismail
> >
> > PhD candidate
> > Neurocentre Magendie, INSERM
> > Bordeaux, France
> >
> > 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
> >   I Ismail
> >
> >   yes, if you have juxtacortical lesions you should label them as
> >   such in
> >   the aseg, then I think it should work
> >
> >   cheers
> >   Bruce
> >   On Fri, 9 Dec 2016, Ismail Koubiyr
> >   wrote:
> >
> >   > Dear Freesurfer experts,
> >   > We are facing a problem in our study and would need your
> >   advice on it.
> >   > We want to get an accurate measurement for the cortical
> >   thickness from our
> >   > MS patients data. For that we are using 3D T1 and FLAIR
> >   (recon-all will be
> >   > used with the FLAIR option so that we can a more accurate pial
> >   surface).
> >   > However, we were wondering if running recon-all on the raw
> >   data would lead
> >   > to some errors specially because of the juxtacortical lesions
> >   or not. Or, is
> >   > it better to first apply a lesion filling using our lesion
> >   mask ?
> >   > I should specify that we will use the longitudinal pipeline if
> >   it is of any
> >   > use.
> >   >
> >   > Thank you all.
> >   >
> >   > Ismail
> >   >
> >   > PhD candidate
> >   > Neurocentre Magendie, INSERM
> >   > Bordeaux, France
> >   >
> >   >
> > ___
> > 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.
> >
> >
> >
> >
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Bruce Fischl]

the former I think, but it's an empirical question
Bruce
On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

> Hi Bruce,
> Thanks for your answer.
> What do you think would be better, run recon-all on the original data (with
> lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> filling on the T1 and then run recon-all on it.
> Thanks again.
> 
> Cheers,
> 
> Ismail
> 
> PhD candidate
> Neurocentre Magendie, INSERM
> Bordeaux, France
> 
> 2016-12-09 22:58 GMT+01:00 Bruce Fischl :
>   I Ismail
>
>   yes, if you have juxtacortical lesions you should label them as
>   such in
>   the aseg, then I think it should work
>
>   cheers
>   Bruce
>   On Fri, 9 Dec 2016, Ismail Koubiyr
>   wrote:
>
>   > Dear Freesurfer experts,
>   > We are facing a problem in our study and would need your
>   advice on it.
>   > We want to get an accurate measurement for the cortical
>   thickness from our
>   > MS patients data. For that we are using 3D T1 and FLAIR
>   (recon-all will be
>   > used with the FLAIR option so that we can a more accurate pial
>   surface).
>   > However, we were wondering if running recon-all on the raw
>   data would lead
>   > to some errors specially because of the juxtacortical lesions
>   or not. Or, is
>   > it better to first apply a lesion filling using our lesion
>   mask ?
>   > I should specify that we will use the longitudinal pipeline if
>   it is of any
>   > use.
>   >
>   > Thank you all.
>   >
>   > Ismail
>   >
>   > PhD candidate
>   > Neurocentre Magendie, INSERM
>   > Bordeaux, France
>   >
>   >
> ___
> 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.
> 
> 
> 
>
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Hi Bruce,

Thanks for your answer.
What do you think would be better, run recon-all on the original data (with
lesions) then edit the aseg for the juxtacortical lesions or use a lesion
filling on the T1 and then run recon-all on it.
Thanks again.

Cheers,

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France

2016-12-09 22:58 GMT+01:00 Bruce Fischl :

> I Ismail
>
> yes, if you have juxtacortical lesions you should label them as such in
> the aseg, then I think it should work
>
> cheers
> Bruce
> On Fri, 9 Dec 2016, Ismail Koubiyr
> wrote:
>
> > Dear Freesurfer experts,
> > We are facing a problem in our study and would need your advice on it.
> > We want to get an accurate measurement for the cortical thickness from
> our
> > MS patients data. For that we are using 3D T1 and FLAIR (recon-all will
> be
> > used with the FLAIR option so that we can a more accurate pial surface).
> > However, we were wondering if running recon-all on the raw data would
> lead
> > to some errors specially because of the juxtacortical lesions or not.
> Or, is
> > it better to first apply a lesion filling using our lesion mask ?
> > I should specify that we will use the longitudinal pipeline if it is of
> any
> > use.
> >
> > Thank you all.
> >
> > Ismail
> >
> > PhD candidate
> > Neurocentre Magendie, INSERM
> > Bordeaux, France
> >
> >
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Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Bruce Fischl]

I Ismail

yes, if you have juxtacortical lesions you should label them as such in 
the aseg, then I think it should work

cheers
Bruce
On Fri, 9 Dec 2016, Ismail Koubiyr 
wrote:

> Dear Freesurfer experts,
> We are facing a problem in our study and would need your advice on it.
> We want to get an accurate measurement for the cortical thickness from our
> MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be
> used with the FLAIR option so that we can a more accurate pial surface).
> However, we were wondering if running recon-all on the raw data would lead
> to some errors specially because of the juxtacortical lesions or not. Or, is
> it better to first apply a lesion filling using our lesion mask ?
> I should specify that we will use the longitudinal pipeline if it is of any
> use.
> 
> Thank you all.
> 
> Ismail
> 
> PhD candidate
> Neurocentre Magendie, INSERM
> Bordeaux, France
> 
>
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[Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

[Ismail Koubiyr]

Dear Freesurfer experts,

We are facing a problem in our study and would need your advice on it.
We want to get an accurate measurement for the cortical thickness from our
MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be
used with the FLAIR option so that we can a more accurate pial surface).
However, we were wondering if running recon-all on the raw data would lead
to some errors specially because of the juxtacortical lesions or not. Or,
is it better to first apply a lesion filling using our lesion mask ?
I should specify that we will use the longitudinal pipeline if it is of any
use.

Thank you all.

Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France
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