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Hi Brain, It seems like that I can run the two stage registrations if where the subcortical mask, which is being used during the second registration, is. Would you let me know where it is? 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.