Dear FSL list,
I am running tbss on 825 individuals (age between 50 and 65), and I have
got as far as tbss_3_postreg without problems or any error messages. I
am using the tbss_2_reg -T option with the FMRIB58_FA as the target, and
the tbss_3_postreg -S option.
But when I looked at the results in the stats file from tbss_3_postreg,
my mean_FA_mask coveres a small area of the brain (it covers the corpus
callosum and almost the whole brain from inferior to superior, but much
the right and left sides of the brain is missing). And since the
mean_FA_mask is used for the all_FA, mean_FA and mean_FA_skeleton, these
also covers a small part of the brain.
I searched the FSL archives, and found the following answer to what
seems to be the same problem:
"On Thu, May 21, 2009 at 12:05 PM, Gwenaëlle DOUAUD <[log in to unmask]
<https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind0905%26L%3DFSL%26E%3Dquoted-printable%26P%3D2234062%26B%3D--0016e645fa8a7fec87046a6ea584%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D>>
wrote:
Hi again Sushravya,
I think I know what's going on: in the most recent version of TBSS,
Steve has changed the way to create the mask for the analyis. Basically,
it now takes the *intersection* of all your FA maps.
This is a good way to be aware of some data truncated and lack of
overlap across subjects etc...
So it might be the case that your mean_FA_mask is actually correct and
points out as one image (possibly several?) being truncated... What
happens if you load your all_FA in FSLview and turns on the movie loop?
You should be able to spot the images contributing to the reduced
mean_FA_mask and either remove them or try to fix what is wrong with
them if possible.
Cheers,
Gwenaelle"
So based on this does this mean that some of my images are being
"truncated", and that I need to find these images? Before I ran the tbss
analysis, I looked through all the FA images in all the individuals, and
to me it looked fine.
Do you have a solution to my problem?
Best regards,
Live Eikenes.
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