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Excellent, that should help a lot. Usually when I do get an error, its in the first stage of registration, and the brain has been tilted up (visual area has been registered to the templates frontal lobes). -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Brian Patenaude Sent: Thursday, September 27, 2007 3:59 PM To: [log in to unmask] Subject: Re: [FSL] first_flirt fslswapdim can switch the dimension. You'll have to figure out the appropriate dimensions to swap/reverse. fslswapdim will give you a warning if you've flipped the left/right orientation (which you should not do). Cheers, Brian > Yes those were from FSLview, and no they didn't start in the same > orientation as the standard. Actually that's true for all of our > images. Is there a utility in the fsl toolbox to easily flip the > orientation of the images, that would be helpful? Its easy enough in > matlab, but I don't want to mess up the header information. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Brian Patenaude > Sent: Thursday, September 27, 2007 3:16 PM > To: [log in to unmask] > Subject: Re: [FSL] first_flirt > > Out of curiosity, were those images generated using FSLview? If so, it > doesn't look like it starts off in the same orientation as the MNI > template. > > Generally, I've never had to crop quite so high with the neck mask, > but I'm glad it works. > > Cheers, > > > Brian > > > >> >> The brains are our typical "LPS" axial. The neck goes to the bottom >> of the brain stem. I made a new mask, which masked out more of the >> neck/brain stem and it ran after that. >> >> I've attached a screenshot of a scan, with the successful mask. Is >> this the level I should be aiming for, or any other suggestions? >> >> Thanks, >> >> Chris >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf Of Brian Patenaude >> Sent: Wednesday, September 26, 2007 4:57 PM >> To: [log in to unmask] >> Subject: Re: [FSL] first_flirt >> >> Does the brain within the image have an odd orientation? I'm just >> trying to figure out why flirt would fail. Is there any strong bias >> field effects? The ones that failed, did they have a significant >> amount of neck? If so, for the mask used, does it extend far below >> the cerebellum (preferably not)? >> >> Cheers, >> >> Brian >> >> >>> No, just 256x256x166 1x1x1mm axial. >>> >>> -----Original Message----- >>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >>> Behalf Of Brian Patenaude >>> Sent: Wednesday, September 26, 2007 4:35 PM >>> To: [log in to unmask] >>> Subject: Re: [FSL] first_flirt >>> >>> Do they have any strange orientation to begin with? >>> >>> Cheers, >>> >>> Brian >>> >>>> Yes the failure(s) have been at the first level. Sometimes the >>>> brain ends upside-down and flipped, sometimes it appears zoomed in >>>> and skewed. >>>> >>>> >>>> -----Original Message----- >>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >>>> Behalf Of Brian Patenaude >>>> Sent: Wednesday, September 26, 2007 1:41 PM >>>> To: [log in to unmask] >>>> Subject: Re: [FSL] first_flirt >>>> >>>> Hi, >>>> >>>> >>>>> Is the outcome of run_first_all supposed to be in standard mni >>>>> space, or native subject space? >>>> >>>> All the segmentations should be in native space. The FIRST takes >>>> the transformation matrix inputed, inverts it, then applies it to >>>> the model prior to fitting. >>>> >>>> >>>>> Also, any suggestions as what to do when first_flirt fails to >>>>> register even after masking out the neck? >>>> >>>> Does the failure occur at the first stage (use -d option)? >>>> >>>> Cheers, >>>> >>>> Brian