Hi Jacek - I looked at the data that you uploaded. The problem is that
both the b-value table and the gradient table that you were using were
assuming that the b=0 images were interspersed throughout your scan, when
in fact based on your dicoms they are all in the begining of the scan. So
the 10 entries of 0.000 need to be in the beginning of the b-value table,
not one every 7th image. Same with the gradient table. The gradient table
also had some flipped coordinates that would cause a different problem
down the line.
I was able to get the right tables by using mri_convert from the
development version of freesurfer. The 5.3 version doesn't have the
capability to read these tables from the dicoms but the 6.0 version will.
In the meantime you can download the dev version and use mri_convert from
that version.
Best,
a.y
On Sun, 14 Feb 2016, Jacek Manko wrote:
Dear Freesurfer experts,
I have also noticed something wrong with the tracts I reconctructed. There were
no erroors during the processing, but when I visualized all tracts in
Freeview according to your command "freeview -tv
my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say
the least. Please
have a look at the attached image.
I have also notice abnormal volumes of these tracts in comparison to your
elmo-subjects. For example the volume of left uncinate for your tutorial
subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy seems
to coincide with with what you can spot in my screen, because it was my
first impression that these tracts are extremely large.
I run tracula with default commands as you stated in your tutorial, no major
changes were made. If there is anything you could advise me, I will very
grateful. Are these results ok or I should udertake some steps? If you perhaps
need some additional information I will be pleased to provide you with
that as well.
Cheers,
Jacek
Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
Dear Anastasia and Tracula users,
I succesfully ran the longitudinal Tracula procedure for one subject. However,
when I visualized the tracts, they look a bit weird (not smooth).
Even if I played with the threshold on freeview, I couldn't make them look nice
as in the wiki page. I checked the registration and it looks
accurate, so I am not sure what could be wrong. I am attaching the messy
looking tracts for your reference.
Could you tell me if I should run again with reinit=1 for these tracts?
Thank you very much for your time.
Best regards,
--
D.
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