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Dear Stamatios, If i understand correctly the steps you described above are the ideal way to save time preprocessing. I have tried to preprocess again following your instructions and I don't see apparent difference in the outcome for dtifit. Is the way i have run first correct for my posterior analisys (i.e. dtifit or tractography)? On the other way i don't understand what bet2 does. Thank you very much. Patricia. 2011/1/20 Stamatios Sotiropoulos <[log in to unmask]> > Hi Patricia, > > Step 2 is not necessary. If you give the full 4D image as input to BET, it > will extract a mask using the first T2-volume. Furthermore, you should > replace Steps 3 and 4 (not sure why you have used Bet2) by calling bet with > the fractional intensity threshold option -f 0.3. > > Step 5 can be run either before or after bet, given that you use the same > T2 volume for bet and as a reference for eddy_correct. > > Cheers, > Stam > > > On 20 Jan 2011, at 16:05, Patricia Pires wrote: > > * > Dear Mark, > > Thanks for your replies. The steps in my preprocessing analisis are: > > 1.- I have a 4D nifty image with 16 volumes (first volume is a simple 3D > image (T2) without diffusion-weighted (i.e. b=0 s/mm2); the others 15 > volumes are b=800 s/mm2 (i.e. gradient volumes). > > 2.- I need a nodif_brain_mask.nii for dtifit process so ,the first step is > to extract the first volume (i.e. the T2, b=0 s/mm2) as the referent volume. > This process (extract the first volume = nodif) is Fslroi: > > fslroi <sto1.nii.gz> nodif 0 1 > > 3.- In order to create a mask in this nodif i run BET and i get > nodif_brain.nii. > > bet nodif nodif_brain -m > > 4.- BET creates a mask (nodif_brain) but it's not exactly the same > dimensions as the nodif. So, BET2 modifies the nodif_brain and creates the > nodif_brain_mask: > > bet2 <sto1.nii.gz> nodif_brain_mask -f 0.3 > > 5.- Then i run eddy current correction: > > eddy_correct <sto1.nii.gz> data 0 > > > * > Is this preprocessing correct in order to run dtifit with this data? > > Thanks again, > > Patricia. > > 2011/1/17 Mark Jenkinson <[log in to unmask]> > >> Dear Patricia, >> >> I'm still not sure what "adjusting the mask to the original image" >> does. Can you be more specific about which images you run >> BET and BET2 on and how these are used later on? >> >> All the best, >> Mark >> >> >> On 17 Jan 2011, at 15:59, Patricia Pires wrote: >> >> > Dear Mark, >> > >> > I use bet2 to adjuts the mask to the original image. >> > >> > I am seeing in the website that eddy current is first than bet but I >> have already run all the study by eddy at the end of the preprocessing. Can >> this affect my results? Should I run it again or it is not necessary? >> > >> > Thanks, >> > >> > Patricia. >> > >> > >> > 2011/1/17 Mark Jenkinson <[log in to unmask]> >> > Dear Patricia, >> > >> > The recommended order on the website I sent was eddy_correct and then >> bet. >> > If you running fslroi too then have this first (so fslroi, then >> eddy_correct and then bet). >> > >> > Also, why are you running bet2? >> > >> > All the best, >> > Mark >> > >> > >> > On 17 Jan 2011, at 14:22, Patricia Pires wrote: >> > >> > > Hi Mark, >> > > >> > > i am doing these steps in preprocessing for dtifit analisys or >> tractography. I proceed fslroi, bet and bet2 just for construct the >> nodif_brain_mask in my 4D image; then i apply eddy current correction in the >> original 4D image to get the data for dtifit/tractography. >> > > >> > > Is that correct? >> > > >> > > Thank you, >> > > >> > > Patricia. >> > > >> > > 2011/1/17 Mark Jenkinson <[log in to unmask]> >> > > Hi, >> > > >> > > Are you trying to do an analysis of diffusion data? >> > > If so see: >> > > http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_pipeline.html >> > > >> > > I'm not sure what reason you are doing the fslroi extraction >> > > for, but if it is to remove excessive neck from the image then >> > > I would do that first, before anything else, as you have it here. >> > > >> > > Also, why are you using bet2? >> > > >> > > All the best, >> > > Mark >> > > >> > > >> > > On 17 Jan 2011, at 08:57, SUBSCRIBE FSL Patricia Pires wrote: >> > > >> > > > Hello fslexperts, >> > > > >> > > > i wondering if preprocessing is correct if i follow these steps: >> > > > >> > > > 1) Fslroi extraction >> > > > 2) Bet >> > > > 3) Bet 2 >> > > > 4) Eddy current correction >> > > > >> > > > I have proceeded in this order for my studies, is that correct or >> eddy current correction must to be the firt step. >> > > > >> > > > Thank you very much. >> > > > >> > > > Patricia. >> > > > >> > > >> > >> > > >