 |
 |
* 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. > > > > > > > > > >