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Hi All, When you run 'bedpost', the result of precessing steps is shown. Mine is showing like '0 slices processed' line after line. Is it ok? Previous run showed '0 slices processed','4slices processed', and so on but not all '0slices processed'. Is anybody there has seen these before? Sincerely, Mi Jung On Wed, Mar 11, 2009 at 10:58 AM, Mark Jenkinson <[log in to unmask]>wrote: > Hi, > > You can change the colourmap used by using the "i" button at the bottom > left > corner of the list of images. By default all masks (images with "mask" in > the > name are assumed to be masks) come up with the red-yellow colourmap. > See the FSLView documentation for more information about this. > > All the best, > Mark > > > > On 11 Mar 2009, at 17:33, Mi Jung Kim wrote: > > 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> >> >> >> >> >> >> >> >> >> >> >>