First run this tkregister2 --mov hipposubfield.mgz --reg hsf.reg.dat --s subject --regheader --fstarg
It will bring up the tkregister2 GUI and just double check that the subfields are where they need to be. Hit "Save Reg" and exit. In the future, you can run the tkregister2 command with --noedit and it will not bring the GUI up (and will save the registration). hipposubfield.mgz is the HSF segmentation. Now run mri_matrix_multiple -im register.dof6.dat -iim hsf.reg.dat -om func2hsf.reg.dat where register.dof6.dat is the registration between the functional and anatomical Check that it looks ok tkregister2 --mov func.nii.gz --targ hipposubfield.mgz --reg func2hsf.reg.dat I'm not sure what your final plans are, but you can use func2hsf.reg.dat with mri_vol2vol (similar to the tkregister2 cmd above) doug On 04/03/2014 05:23 AM, Erik O'Hanlon wrote: > Hi Doug, > > Thanks for that, I will give that a shot and see how it looks. > > As for my highres hippo images, I ran the recon-all with the -hippo-subfields > setting on my T1 highres whole brain anatomy file. This gave me the usual FS > outputs and the extra hippo subfield volumes. I can look at these with > Freeview and when I load the anatomy, the aseg and the hippo subfields, > everything is fine. I then want to transform these to my diffusion space for > tractography, and managed to get the anat and aseg images to align with my > diffusion space B0 image but just can't get the subfields to align. I think > this is due to the smaller fov of the subfields as they appear a small cubes > with the hippo structures inside in the Freeview screen. > > Thanks again for the direction, I haven't tried the tkregister2 tool so I'll > play with it and see > > Much appreciated. > > best regards > > 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: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 02 April 2014 22:35 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: registration difficulty > >>> 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 > > _______________________________________________ > 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
