Flipping the sign of the x row will fix the gradient directions and the
results.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Ting-Shuo Yo
Sent: Monday, June 30, 2008 4:52 AM
To: [log in to unmask]
Subject: Re: [FSL] Strange probtrackx results
Hi,
Thanks for all the answering, it took me some time to re-run the analysis
following the suggestions. I have tried the following (mainly what Tim has
suggested):
(1) use "fslorient" to convert my data in the very first stage (data.nii.gz,
nodif_brain_mask.nii.gz, and nodif.nii.gz).
(2) use the data I have (in neurological convention), change signs of the
x-direction in "bvecs"
With the two settings, I re-do the BEDPOSTX and then PROBTRACKX. However,
the tracking results look just as the previous run, except this time the
arrows indeed correspond to the tracts. ((1)
http://lh4.ggpht.com/tingshuo.yo/SGir9f9mQBI/AAAAAAAACk0/40Hngsx68ww/fsl_pro
btrackx_03.jpg?imgmax=576, and
(2)
http://lh5.ggpht.com/tingshuo.yo/SGir9S23NOI/AAAAAAAACk8/FibZvIw4IsI/fsl_pro
btrackx_04.jpg?imgmax=576)
Now I am trying the (1) with a flipped x, I will post the results once I get
it. Thanks.
Ting
=============================================================
Ting-Shuo Yo
Max Planck Institute for Human Cognitive and Brain Sciences
E-mail: [log in to unmask]
=============================================================
----- Original Message -----
From: "Tim Behrens" <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, June 25, 2008 6:31:51 AM (GMT+0100) Europe/Berlin
Subject: Re: [FSL] Strange probtrackx results
Ah - sorry I didn't read far enough to get to the screenshots. Dumbass!
The reason for this will be that the data is stored in neurological
format -
There is currently an inconsistency between fslview and fdt wrt
neurological data unfortunately - this will be fixed in the next
release. Sorry.
At present The safest thing to do is to change the data ordering to
radiological at the very first stage of processing - then to run
dtifit on the new radiological data check the arrows. If the arrows
are wrong, flip your vectors in x (change the sign of the x elements).
fslorient -forceradiological myimage
make sure you do this on data, nodif, and nodif_brain_mask
The alternative is to get the arrows looking correct in neurological
format (as you have done), and _then_ to flip your bvecs in x (again
change the sign of every x element). So that if you run dtifit again,
the new arrows will look wrong - however the internal processing for
tractography will work.
Sorry about this - it is only very recently that we have started
supporting neurological data, and this inconsistency slipped through
the net!
Cheers
T
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