According to the bedpostx_datacheck info you posted earlier, your resolution
is 0.5x0.5x2.4. This is also not ideal for tractography as your ability to
resolve the superior to inferior component of fibers in much worse than your
ability to resolve the other components. Better is 2mmX2mmX2mm, which has
both good resolution and SNR. At a minimum you should turn off
interpolation on the scanner (and then your resolution would be 1x1x2.4mm).
Peace,
Matt.
_____
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Mi Jung Kim
Sent: Wednesday, March 11, 2009 11:02 AM
To: [log in to unmask]
Subject: Re: [FSL] capillary phantom for muscle dti2
Hello,
When you run FDT, how isotropic voxel has to be? I am dealing with 1x1x2.4.
Is it too non-isotropic?
Thanks,
Mi Jung
On Wed, Mar 11, 2009 at 8:52 AM, Mi Jung Kim <[log in to unmask]> wrote:
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>
