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
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 <rvp8@njit.edumailto:rvp8@njit.edu> 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
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.iglesias@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 rvp8@njit.edu 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
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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 <deman.pierre@gmail.commailto:deman.pierre@gmail.com> 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 <e.iglesias@ucl.ac.ukmailto:e.iglesias@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.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/
On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata <rvp8@njit.edumailto:rvp8@njit.edu> 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.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.
-- DEMAN Pierre Mobile : +33 7 82 57 80 94 _______________________________________________ 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.
Okay, thanks!
Best,
Renata
On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio < e.iglesias@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 rvp8@njit.edu 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@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Eugenio -
pierre deman -
Vaz pandolfo, Renata