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Hi, I've got a question. I opened nodif_brain_mask image in fslview. It was yellow in color. How is it supposed to look like? Thanks, Mi Jung On Wed, Mar 11, 2009 at 9:12 AM, Matt Glasser <[log in to unmask]> wrote: > If you intend to do fiber tracking, you will need more than 6 directions. > 30 is good, 60 is great. Most of the greater than 1 FA values are probably > clustered around the rim of the brain where the brain is incompletely > extracted, and should not cause you any problem. You could threshold the FA > in fslview at min =1 max =1.22 to see where these voxels are located. > > > > Peace, > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *Mi Jung Kim > *Sent:* Wednesday, March 11, 2009 10:52 AM > *To:* [log in to unmask] > *Subject:* Re: [FSL] capillary phantom for muscle dti2 > > > > I got you. > > > But my SNR is pretty high. How high SNR is required when I have few > gradient directions for this algorithm. I know that it is recommended use > more than 25 gradient directions for this calculation. Do you think that > getting more gradient directions is only way to solve this isse? > > Thanks, > > Mi Jung > > On Wed, Mar 11, 2009 at 8:45 AM, Saad Jbabdi <[log in to unmask]> wrote: > > DTIFIT does not impose that the fitted tensor is positive definite, so you > may have negative eigenvalues (i.e. negative Ls, which can produce FA>1). > > Since you only have 6 data points to calculate your tensor, your chances of > getting negative tensors are higher, esp if SNR is low.. > > > > > > Saad. > > > > > > On 11 Mar 2009, at 15:40, Mi Jung Kim wrote: > > > > Yes, I can see V1 and FA. But when I check the values with fslstats they > seemed to be odd to me. Because FA has max of 1, but it was more than 1 > something like that. Here is my question. I do not think that lamdas can > have negative values, but fslstats shows them in negative min as well. Why > is that? > > Thanks, > > Mi Jng > > On Wed, Mar 11, 2009 at 8:22 AM, Saad Jbabdi <[log in to unmask]> wrote: > > They look all right to me. > > Why are you saying they are not right? > > Did you have a look at FA and V1 in fslview? > > > > Saad. > > > > On 11 Mar 2009, at 15:18, Mi Jung Kim wrote: > > > > Hi, > > These are my outputs from dtifit. > I did a carriage return in bvals. > Are they right? They do not seem to be right values to me. > Any thought? > > Sincerely, > > Mi Jung > computer-four:~/data macadmin$ fslstats dti_FA.nii.gz -R > 0.000000 1.224744 > computer-four:~/data macadmin$ fslstats dti_V1.nii.gz -R > -0.999986 0.999999 > computer-four:~/data macadmin$ fslstats dti_L1.nii.gz -R > -0.000893 0.003149 > computer-four:~/data macadmin$ fslstats dti_L2.nii.gz -R > -0.001136 0.002519 > computer-four:~/data macadmin$ fslstats dti_L3.nii.gz -R > -0.002149 0.002262 > computer-four:~/data macadmin$ fslstats dti_V2.nii.gz -R > -0.999982 0.999999 > computer-four:~/data macadmin$ fslstats dti_V3.nii.gz -R > -0.999986 1.000000 > computer-four:~/data macadmin$ fslstats dti_MD.nii.gz -R > -0.001113 0.002447 > computer-four:~/data macadmin$ fslstats dti_S0.nii.gz -R > 0.000000 16406.000000 > > On Wed, Mar 11, 2009 at 8:01 AM, Mark Jenkinson <[log in to unmask]> > wrote: > > Hi, > > Just add a blank line at the end with a text editor. > > All the best, > Mark > > > > > On 11 Mar 2009, at 14:49, Mi Jung Kim wrote: > > Hi Sadd, > > How can I add a carriage return? > > Thanks, > > Mi Jung > > On Wed, Mar 11, 2009 at 1:54 AM, Saad Jbabdi <[log in to unmask]> wrote: > Yes, it sounds like you have a version which still had the bvals bug. > Just add a carriage return at the end of your bvals file and that should > solve the problem. > > Saad. > > On 10 Mar 2009, at 18:00, Mi Jung Kim wrote: > > Hi, > > I am using FSL4.0 on Mac. > > Thanks, > > Mi Jung > > On Tue, Mar 10, 2009 at 10:19 AM, Saad Jbabdi <[log in to unmask]> wrote: > I suspect this is because you need to add a carriage return at the end of > your bvals file (which version of FSL are you using?) > > Saad. > > > On 10 Mar 2009, at 16:29, Mi Jung Kim wrote: > > Hi, > > I have been working capillary phantom for muscle DTI. > > I just was able to run all procedures, but after dtifit, outputs are > blank..Do you have any thought on that? > > One more question right now is that since I am dealing with phantom data, > do > I still go though all steps before probtrack? > > > Thanks, > > Mi Jung > > > Saad Jbabdi > Oxford University FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > +44 (0) 1865 222545 (fax 717) > www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> > > > Saad Jbabdi > Oxford University FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > +44 (0) 1865 222545 (fax 717) > www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> > > > > > > > > > > > Saad Jbabdi > > Oxford University FMRIB Centre > > > > JR Hospital, Headington, OX3 9DU, UK > > +44 (0) 1865 222545 (fax 717) > > www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> > > > > > > > > > > > > > > > > > > Saad Jbabdi > > Oxford University FMRIB Centre > > > > JR Hospital, Headington, OX3 9DU, UK > > +44 (0) 1865 222545 (fax 717) > > www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> > > > > > > > > > > > > > > >