Apologies.
forwarded it on now
Thanks a million
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 ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
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 hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
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 us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
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
[IMAGE]
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
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