Hi Takafumi,
Firstly, you may want to consider trying 12 degrees of freedom for the T1 → MNI template registration. 6 degrees of freedom is really for intra-subject registration; you can see in some of your images that there are still clear gross misalignments between your subject-s T1 image and the overlaid parcels, probably due to the fact that your registration doesn’t include scaling components.
Regarding this:
Next, I created the LUT file. and I executted the labelconvert command.
But unfortunately, the obtained AAL atlas was discontinuous.
The original value of AAL file was continuous, then I think this error was caused.
If anyone know the solution to overcome this error, please explain it.
It’s not entirely clear what the problem is that you’re encountering; I’ll make a couple of stabs in the dark, but if I don’t hit the mark you’ll need to explain the issue more precisely.
-
Your registration of AAL parcellation to subject space appears to be using tri-linear interpolation. For re-gridding a parcellation image, nearest-neighbour interpolation must be used.
-
For label images being used in connectome construction,
tck2connectomeexpects an image where the label numbers increment continuously from 1 upwards. This is the purpose of thelabelconvertcommand: to manipulate any arbitrary label image into this form. I have however seen the AAL image provided via some sources where the image values already increment continuously from 1; if this is the case for you, then thelabelconvertstep may not be necessary for your data.
If none of this makes sense to you, there’s a page in the online documentation that will hopefully help explain the purpose of this command, how it works, and therefore possibly how to get it to work for your data.
Cheers
Rob