Re: [Freesurfer] FoV in additional scan

2016-09-19 Thread Iglesias Gonzalez, Eugenio 
It does perform a registration, but this requires a decent initial alignment.


Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 19 Sep 2016, at 14:43, pierre deman 
> wrote:

Does it perform a coregistration automatically when specified two images or is 
it better to perform it before running the recon-all ?

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio 
> wrote:
Hi Renate,
as long as the additional scan is more or less aligned with the T1 in physical 
coordinates (i.e., they appear decently aligned when you open them in 
Freeview), you should be fine and not need to do anything.
Cheers,
/E

Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata 
> wrote:

Dear Eugenio,

We have another question about the Hippo Sf Segmentation with an additional 
scan.

Some of our additional scans (FLAIRs or T2s) have a bigger field of view as 
compared to the T1 (ex.: they cover more of the neck almost up to the shoulders 
of the subjects, while the T1 has the "normal" FoV).

Should the additional scan be cropped or  preprocessed in any way (ex.: bias 
field correction)?  And if so, should we process the T1 in the same way or is 
it generally recommended to just use the raw images?

Thank you!

Renata


___
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.




--
DEMAN Pierre
Mobile : +33 7 82 57 80 94
___
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 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] FoV in additional scan

2016-09-19 Thread Vaz pandolfo, Renata 
Okay, thanks!

Best,

Renata

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi Renate,
> as long as the additional scan is more or less aligned with the T1 in
> physical coordinates (i.e., they appear decently aligned when you open them
> in Freeview), you should be fine and not need to do anything.
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata  wrote:
>
> Dear Eugenio,
>
> We have another question about the Hippo Sf Segmentation with an
> additional scan.
>
> Some of our additional scans (FLAIRs or T2s) have a bigger field of view
> as compared to the T1 (ex.: they cover more of the neck almost up to the
> shoulders of the subjects, while the T1 has the "normal" FoV).
>
> Should the additional scan be cropped or  preprocessed in any way (ex.:
> bias field correction)?  And if so, should we process the T1 in the same
> way or is it generally recommended to just use the raw images?
>
> Thank you!
>
> Renata
>
>
>
___
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] FoV in additional scan

2016-09-19 Thread Iglesias Gonzalez, Eugenio 
Hi Renate,
as long as the additional scan is more or less aligned with the T1 in physical 
coordinates (i.e., they appear decently aligned when you open them in 
Freeview), you should be fine and not need to do anything.
Cheers,
/E

Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata 
> wrote:

Dear Eugenio,

We have another question about the Hippo Sf Segmentation with an additional 
scan.

Some of our additional scans (FLAIRs or T2s) have a bigger field of view as 
compared to the T1 (ex.: they cover more of the neck almost up to the shoulders 
of the subjects, while the T1 has the "normal" FoV).

Should the additional scan be cropped or  preprocessed in any way (ex.: bias 
field correction)?  And if so, should we process the T1 in the same way or is 
it generally recommended to just use the raw images?

Thank you!

Renata

___
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] FoV in additional scan

2016-09-19 Thread pierre deman 
Does it perform a coregistration automatically when specified two images or
is it better to perform it before running the recon-all ?

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi Renate,
> as long as the additional scan is more or less aligned with the T1 in
> physical coordinates (i.e., they appear decently aligned when you open them
> in Freeview), you should be fine and not need to do anything.
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata  wrote:
>
> Dear Eugenio,
>
> We have another question about the Hippo Sf Segmentation with an
> additional scan.
>
> Some of our additional scans (FLAIRs or T2s) have a bigger field of view
> as compared to the T1 (ex.: they cover more of the neck almost up to the
> shoulders of the subjects, while the T1 has the "normal" FoV).
>
> Should the additional scan be cropped or  preprocessed in any way (ex.:
> bias field correction)?  And if so, should we process the T1 in the same
> way or is it generally recommended to just use the raw images?
>
> Thank you!
>
> Renata
>
>
>
> ___
> 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.
>
>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
___
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.