Dear fsl users,
I want to evaluate Controls and Patients and i want to ask some questions(
regarding the data acquisition) in order to have valid analysis results
after the use of sienax, siena and randomise.
As far as it concerns the data parameters the data should have (among them)
the same:
pulse sequence
TE
TR
T1
Matrix size
FOV
B field strength
Acquisition plane
for accurate analysis with the fsl tools? or it's only enough for the data
just to have the same modality, resolution in-plane size which is less than
2mm and slice thickness that can vary among 1 and 6mm?
As far as it concerns the relation between the data and the MNI152 standard
image that sienax and randomise use, the data should use the same parameters
as the MNI152? And if yes which ones of the previous mentioned should be the
same? If for instance we have sagittaly data acquisitions then if we
analyse them with sienax that registers them to the axially oriented MNI152,
will this cause some trouble?
The data should be as close as possible to the MNI152 standard image
resolution in both the in-slice resolution and slice thickness? In FSL-FAQ
you mention that it's better to use in plane resolution of less than 2mm and
slice thickness between 1 to 6 mm. So at least the slice thickness in not an
important issue if it's between some limits (as it is also mentioned in
Smith et. al 2002). Suppose that our data are of 1.7x1.7x1.7 mm. Is it the
same to use the MNI152 of 1.5x1.5x1.5 or 2.0x2.0x2.0 or even the 1x1x1 as
the standard image for our comparisons? Or we have to choose the one that is
as close as possible to our data resolution (which is 1.5x1.5x1.5 in the
previous example)?
Generally is it better to use the MNI152 template as the standard template
or to create our own template for analyzing our data? (since sienax and
randomise need a standard space template).If the second case is the
preferred one then we can make our own template by just averaging our
controls, do cross sectional analysis (sienax) and then repeat the same
step with a patients template? Is this the best way? Where can i find info
on how to make my own template?
What abour randomise? Since with randomise we register the flow images of
our groups (in our case controls and Parkinsons patients) that are derived
from siena in a standard space image (MNI152) is it better to use this
default randomise template as the standard one or our own one? And in this
case if it's better to make our own template, this template should be an avg
image of both our controls and patients? where can i also find some more
info about this topic?
Finally is the MNI (2x2x2) which is the default standard image used by all
applications of siena: flirt siena and randomise etc in the fsl 4 version?
Thanks in advance
Antonios-Constantine Thanellas
|