 |
 |
Hi, If FLIRT works well on the brain extracted images, why not just use that? Or is the brain extraction unreliable? Also, have you tried the -usesqform option in FLIRT or cutting down the original field of view (using fslroi) to eliminate the majority of the neck? All the best, Mark On 27 Jul 2012, at 10:01, Westeneng, H.J. wrote: > Hi Mark, > > I used FLIRT to create linear registrations of brain and that performed well but if I used FLIRT to create linear registrations of whole head images it performed really bad in some cases and even if I changed many options of FLIRT, no good registration could be obtained (I used the general checklist on the FSL FAQ page without effect in some cases). Therefore I tried minc-tools. So, my question is, do you know if there are other linear registration tools (maybe in Freesurfer) that create registrations that can be used in FLIRT (with applyxfm)? Or if you have suggestions about how to get better registrations of whole head images in FLIRT, I will try that. > > Thanks, > Henk-Jan > > Van: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Namens Mark Jenkinson > Verzonden: vrijdag 27 juli 2012 10:09 > Aan: [log in to unmask] > Onderwerp: Re: [FSL] .xfm to .mat > > Hi, > > I'm afraid we don't have any tools to convert from minc to FSL format. > Maybe you can ask the minc developers and see if they have any conversion tools. > Or someone on the list might have done this before and could help. > > All the best, > Mark > > On 27 Jul 2012, at 09:06, Westeneng, H.J. wrote: > > > Hi Mark, > > FLIRT was used to generate .mat files and minc-tools (mincresample and minctracc) was used to generate .xfm files. > > Thanks in advance, > Henk-Jan > > Van: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Namens Mark Jenkinson > Verzonden: vrijdag 27 juli 2012 10:00 > Aan: [log in to unmask] > Onderwerp: Re: [FSL] .xfm to .mat > > Hi, > > What tools were used to generate these files? > Outputs from FLIRT can be called anything (there is no restriction on the filenames) and so both .mat and .xfm might have been generated by FLIRT. If not, then we can't help unless you tell us how they were generated. > > All the best, > Mark > > > On 27 Jul 2012, at 08:17, Westeneng, H.J. wrote: > > > > Dear FSL users, > > I have a short question. How can I convert an .xfm transformation matrix to a .mat transformation matrix? If this is not possible, is there another way to concat a .mat and an .xfm transformation matrix? > > Thank you in advance, > > Henk-Jan Westeneng > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > >