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: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fis...@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: erikohan...@rcsi.ie W: www.rcsi.ie > > RCSI DEVELOPING HEALTHCARE LEADERS > WHO MAKE A DIFFERENCE WORLDWIDE > > > > 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
