yep, can you upload the relevant datato our file drop? On 05/09/2013 05:52 AM, Johannes Klein wrote: > Hi Doug, > Thanks! I've tried that now, but it didn't help. Looking at the output, I get > the impression that some of the axes might be swapped over. I've done a > manual registration now to process my subject. > Maybe it's worth following this up for future use of FSL-supplied matrices - > however, the problem only applies to XFM-style output, and e.g. mri_vol2vol > works fine, so I guess there aren't many other users affected. If you like, I > can send you a few volumes and the associated registration matrix. > Thanks for your help! > Cheers, > Johannes > > Douglas N Greve Wed, 08 May 2013 12:16:36 -0700 > > Hi Johannes, as a quick fix can you try inverting the matrix? > doug > > On 05/08/2013 01:31 PM, Johannes Klein wrote: >> Hi Doug, >> Thanks for your reply! I'm getting closer to a solution now, with >> tkregister2's display showing a correctly transformed mni305 file, >> but I still cannot get a valid talairach.xfm file out of this. >> >> Here's what I tried: >> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz >> --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg >> works fine. >> >> Next, to obtain a suitable .xfm file, I ran >> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz >> --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg --xfmout >> testtal.xfm --noedit >> and copied the output (testtal.xfm) into mri/transforms/talairach.xfm >> >> Now, when I view the result with >> tkregister2 --s test --fstal --mgz >> the transform is way off again. Apparently, tkregister2 reads and >> interprets the FSL matrix correctly, but the output transform that I >> get is not in the right format for transforms/talairach.xfm. >> I wonder if I'm using the wrong output switch now - but looking at >> tkregister2's documentation, it seems to be the one to use? >> Thanks, >> Johannes >> >> >> >> Date: Tue, 07 May 2013 14:11:27 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> < > mailto:gr...@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform >> To: freesurfer@nmr.mgh.harvard.edu < > mailto:freesurfer@nmr.mgh.harvard.edu >> Message-ID: <518943cf.7050...@nmr.mgh.harvard.edu >> < > mailto:518943cf.7050...@nmr.mgh.harvard.edu >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure >> what regdat2xfm is doing. >> doug >> >> On 05/07/2013 12:42 PM, Johannes Klein wrote: >>> Dear all, >>> I have some tricky subjects that I cannot get to register properly >>> with the standard Talairach process, or even the use-mritotal option. >>> However, with some fiddling, I've produced a reasonable registration >>> matrix with FSL's FLIRT. >>> >>> I'm now looking to convert my FSL registration matrix, and use it as >>> Freesurfer's Talairach transform. From the documentation, I gathered >>> that I need to get it into Freesurfer's xfm format, and I suppose >>> this is a two step process. >>> >>> I converted the FLIRT-provided matrix cor2raw.xfm like so: >>> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz >>> --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat >>> >>> I then converted register.dat to the xfm data format: >>> regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz >>> register.dat tal.xfm >>> >>> and finally replaced talairach.xfm in the transforms directory with >>> the output of the last command. Unfortunately, this doesn't work, and >>> the transform is very much off target when I view it in tkregister2. >>> Obviously, I've made a mistake when converting between the different >>> transforms - could anybody point me in the right direction? >>> Thanks all, >>> Johannes >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu < > mailto: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 < > mailto: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 >> < > http://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
-- 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 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.
