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Yeah - sorry, I'm not sure I do agree with Gwen on that one - though for affine registration either brain-extracted nodif or the FA should work fine. I think you're right - that in the past I've recommended using the nodif image, and that's what FDT registration uses by default. Cheers. On 7 Apr 2008, at 15:29, Lindgren, Kristen, Ann wrote: > Is that true? I thought one time when I sent an e-mail outlining my > steps Steve told me not to use the dti_FA but rather the nodif_brain > within the FDT gui. I'd be curious to hear what others think about > this since I'm doing something similar to what Ravi is doing. Thanks! > > Kristen > > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD > Sent: Mon 4/7/2008 8:45 AM > To: [log in to unmask] > Subject: Re: [FSL] T1 and DTI Registration problems > > Hi Ravi, > > here is my take. > > First, Kristen is not right: you should definitely go for the image > that shows a better contrast, so the FA rather than the B0 (it's all > the more true if you use non-linear registration). > > Second, if I understand you correctly, you want to register T1 and > FA to possibly draw some ROIs on the T1 and transfer them on the DW > space... > > So what you should do is: > flirt -in T1 -ref FA -omat T1_to_FA.mat > > then: > flirt -in T1 -ref FA -o T1_to_FA -init T1_to_FA.mat -applyxfm (to > check first for the flirt registration) > then for your ROIs: > flirt -in my_ROI_on_T1 -ref FA -o my_ROI_on_FA -init T1_to_FA.mat - > applyxfm > > Hope this helps, > Gwenaelle > > > > --- En date de : Lun 7.4.08, Lindgren, Kristen, Ann <[log in to unmask]> a > écrit : > >> De: Lindgren, Kristen, Ann <[log in to unmask]> >> Objet: Re: [FSL] T1 and DTI Registration problems >> À: [log in to unmask] >> Date: Lundi 7 Avril 2008, 14h31 >> I'm not sure if there's more you should be doing, >> but you shouldn't be using the dti_FA image in FLIRT to >> get the str2diff.mat. Instead you should be using the >> nodif_brain image. Not sure if that will solve your >> problem but it might help. Good luck! >> >> Kristen >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library on behalf of Ravi >> Shetty >> Sent: Mon 4/7/2008 4:40 AM >> To: [log in to unmask] >> Subject: Re: [FSL] T1 and DTI Registration problems >> >> Sorry I am not sure if I quite follow. I have been >> registering my diffusion >> data(dti_FA) to the reference image(T1 weighted) and I >> believe that would >> give me the equivalent of the str2diff.mat. From there I >> use that matrix to >> convert the ROI mask I created on my T1 weighted image into >> diffusion space. >> I then overlay that new diffusion space ROI mask onto my >> original diffusion >> image and see if the images are being registered correctly. >> I use this >> method to check because the images outputed after >> registration always seem >> to line up pretty well but once I run probtrackx my results >> were very off. >> This just seemed a faster way to check the registrations >> accuracy. Please >> let me know if I seem to be missing a step. Thanks. >> >> On Mon, 7 Apr 2008 08:33:21 +0100, Steve Smith >> <[log in to unmask]> wrote: >> >>> Just a quick sanity check - you _are_ inverting the >> DTI->structural >>> transform before using it to transform structural-space >> ROIs back to >>> DTI space? >>> Cheers. >>> >>> >>> On 7 Apr 2008, at 03:03, Ravi Shetty wrote: >>>> Hi I have been using FLIRT to register my T1 and >> DTI images to each >>>> other but keep running into >>>> problems. The registered images produced are >> always very close to >>>> what they should be when I >>>> overlay them onto the T1 image. The problem I have >> is the matrixes >>>> don't always reflect the >>>> registration image. I create a CC ROI mask on the >> T1 image/ >>>> registered image and use the matrix I >>>> produced to convert it back into difusion space. >> Now when I do this >>>> with some subjects the ROI will >>>> be spot on the CC and for others it will be off >> somewhere in the >>>> cortex or even just into the black >>>> void. I can't seem to find any rhyme or reason >> for this and the >>>> variation of how off the matrix is does >>>> not seem to be consistent, any help figuring this >> out would be >>>> appreciated. Thanks. >>>> >>> >>> >>> --------------------------------------------------------------------------- >>> Stephen M. Smith, Professor of Biomedical Engineering >>> Associate Director, Oxford University FMRIB Centre >>> >>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>> +44 (0) 1865 222726 (fax 222717) >>> [log in to unmask] >> http://www.fmrib.ox.ac.uk/~steve >>> --------------------------------------------------------------------------- >>> = >>> = >>> = >>> = >>> = >>> ==================================================================== > > > > _____________________________________________________________________________ > Envoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.yahoo.fr > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------