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Hi, In fact, I have tried the first option already without success. I can send the MRI to you (via ftp?) if you want to take a look at it (I will appreciate a lot if you can). How about the possibility to run 'first_flirt' by myself using GUI FLIRT? thank you, Buyean -----Original Message----- From: Brian Patenaude <[log in to unmask]> To: [log in to unmask] Sent: Mon, 10 Sep 2007 11:56 am Subject: Re: [FSL] Correction: [FSL] FIRST failed to segment a T1 MRI Hi, Is there a much neck in the image? If so, this is probably the reason for the failure at the first stage. If this is the case you have 2 options: 1) Crop the image. If you use this option you must input the cropped image into run_first. 2) To create a mask omitting the lower portion of the image containing neck (i.e. zero for neck region and 1 elsewhere ). Then use the -inweight option in first_flirt, this will apply weighting mask to the input image such that the region where the mask is 0 will not contribute to the cost function. In this case run_first still takes in the uncropped image. Hope this helps, Cheers, Brian > > Hi, > > The registered MRI image after first stage registration is not correctly > registered to the standard. After second stage registration, the MRI is > distorted, cut, and zoomed. Since the MRI is not registered at all, all > structures fail; all structures are located in wrong place. > > I am wondering if I can run these two step registrations (only the > 'first_flirt') step by step using the GUI FLIRT. It looks like the > advanced option in FLIRT helps register this specific T1 MRI to the > standard (the first stage registration). > > Thank you, > > Buyean > > > > > > > > > -----Original Message----- > From: Brian Patenaude <[log in to unmask]> > To: [log in to unmask] > Sent: Mon, 10 Sep 2007 7:33 am > Subject: Re: [FSL] Correction: [FSL] FIRST failed to segment a T1 MRI > > > > > > > > > > > Hi, > > The registered image, how well do the subcortical structures align? Is > it visible where the registration does not match up? Also, do all the > structures fail? When it fails are segementations was off or do they > mostly overlap except the boundaries are clearly not well aligned? > > Cheers, > > Brian > > P.S. The is no GUI version for the first_flirt script. > > >> >> >> >> >> >> Dear FSL users, >> >> >> >> I have very limited experience in FSL and have been trying out FIRST >> to generate the ROIs for my PET image analysis. >> FIRST did good job in segmenting the subcortical regions (20 T1 MRIs >> out of 21 T1 MRIs). >> But, it failed to segment the regions in one T1 MRI. >> >> When I ran 'first_flirst' with -d option, the image after the first >> stage looks OK, but it is not right; the image was not registered to >> the standard. The image after the second stage is not a mess. >> >> I will appreciate any suggestions to run 'first_flirt' successfully >> with this T1 image. >> >> Is there any way to run 'first_flirt' using GUI version FLIRT? >> >> >> Thank you, >> >> Buyean >> >> >> >> >> >> >> ________________________________________________________________________ >> Check Out the new free AIM(R) Mail -- Unlimited storage and >> industry-leading spam and email virus protection. > > > > > > > ________________________________________________________________________ > Check Out the new free AIM(R) Mail -- Unlimited storage and > industry-leading spam and email virus protection. ________________________________________________________________________ Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection.