Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using the bbregister tool and registered B0 image to my orig.mgz. I then used this dat to align my aseg to my diffusion space image and it worked well. The issue is when I try to use it to transform my hippocampal subfield volumes to diffusion space. They just don't line up. Is this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using the bbregister tool and registered B0 image to my orig.mgz. I then used this dat to align my aseg to my diffusion space image and it worked well. The issue is when I try to use it to transform my hippocampal subfield volumes to diffusion space. They just don't line up. Is this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If that is the situation, then you can use the --int flag to bbregister
On 04/02/2014 12:19 PM, Bruce Fischl wrote:
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampal subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat file automatically so created this using the bbregister tool and registered B0 image to my orig.mgz. I then used this dat to align my aseg to my diffusion space image and it worked well. The issue is when I try to use it to transform my hippocampal subfield volumes to diffusion space. They just don't line up. Is this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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
freesurfer@nmr.mgh.harvard.edu
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Erik O'Hanlon