You may have to give up the arcuate (slft) too, since part of the temporal
lobes are chopped off. Although it didn't get to that tract so it's just a
guess.
Yes, you should be fine by removing from pathlist (and the respective
entries in ncpts) any tracts that are partly cut off in your imag
Many thanks Anastasia.
So, do you think it would work if I exclude this tracts from the analysis
and ask for the remaining ones?
thanks again,
Gari
On Fri, Sep 27, 2013 at 4:35 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Gari - Just looked at your subject. The bottom of
Hi Gari - Just looked at your subject. The bottom of the brain is
truncated in the DWIs. The slices stop in the middle of the angular
bundle, which is why the -prior step failed in that pathway. But I expect
there'd be problems with other tracts that reach that inferior, even if
they didn't f
Hi Gari - It looks from the output like something has gone wrong with the
registration, either diffusion to anatomical, or individual to atlas. If
you upload for me here all the directories that tracula has created so far
(dmri, dmri.bedpostX, dlabel), I'll take a look.
http://gate.nm
Hi Gari - Yes, that's your best option right now. Sorry for the
inconvenience. I'll make sure to add the option to have one gradient file
per subject in the next version.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi! Thanks for the fast answer. If I do: diff id1.bvec id2.bve
Hi! Thanks for the fast answer.
If I do: diff id1.bvec id2.bvec
I can see some clear differences.
I was told that in FSL I should use the bvecs and bvals created in dcm2nii
per subject, so I understand I should do the same now?
Do you think an option would be to script the creation of a dmrirc fil
Hi Gari - Sorry, right now the assumption is that the gradient vectors are
the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using
Siemens Dicoms, so I did not specify
Hi Anastasia,
I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms,
so I did not specify any setting for bval and bvec, but when trac-all -prep
starts running it gives the following error: mv: cannot stat
'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or
dir
