>>should I now rerun the bbregsiter and create a new dat file for the subfield >> volume to orig.mgz image?
I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
