Dear Freesurfer expert,
I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2.
Below are the details about the 2 images.
T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).
The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly.
Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation?
Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output?
Any suggestion will help.
Sincerely thanks, Xiaowei.
[Cleveland Clinic logo]
Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Hi Xiaowei
you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz
The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well
cheers Bruce
On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote:
Dear Freesurfer expert,
I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2.
Below are the details about the 2 images.
T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8)
T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).
The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly.
Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation?
Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output?
Any suggestion will help.
Sincerely thanks,
Xiaowei.
Cleveland Clinic logo
Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health
Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi Xiaowei, this was my mistake when I wrote the article in the wiki. The images do not need to be in the same orientation (I already changed this in the wiki). They need to be coarsely registered in physical coordinates (i.e., the need to look approximately registered when you open them in FreeView). If you manually rotate / translate the T2, make sure that you check the "do not resample" box when you save the rotated scan in order not to lose information. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Xiaowei Zhuang" ZHUANGX@ccf.org Cc: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 16, 2016 11:16:48 PM Subject: Re: [Freesurfer] Hippocampal subfield segmentation with T1&T2
Hi Xiaowei
you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz
The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well
cheers Bruce
On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote:
Dear Freesurfer expert,
I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2.
Below are the details about the 2 images.
T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8)
T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).
The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly.
Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation?
Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output?
Any suggestion will help.
Sincerely thanks,
Xiaowei.
Cleveland Clinic logo
Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health
Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Eugenio Iglesias -
Zhuang, Xiaowei