I've tried using the --dist option in the mne_add_patch_info program but
it's not being recognized; the program doesn't run and prompts an error. I
invoked help for this command (--help) and --dist isn't listed as a valid
option, contrary to what the user guide for v2.7.3 states. How can I use
this option?
Also, I'm having trouble viewing the patches I create with both the
formerly mentioned program or by using the --cps option within the source
space creation.
How can I display the patches in mne_analyze. Additionally, how can I read
the cortical patch statistics from the different patch files? Do I need to
use the Matlab Toolbox for this purpose?
Finally, does anyone know if some of the vertices along the patch
boundaries are shared between different patches?
I've tried using the --dist option in the mne_add_patch_info program but
it's not being recognized; the program doesn't run and prompts an error. I
invoked help for this command (--help) and --dist isn't listed as a valid
option, contrary to what the user guide for v2.7.3 states. How can I use
this option?
You need to use the nightly build of MNE.
Also, I'm having trouble viewing the patches I create with both the
formerly mentioned program or by using the --cps option within the source
space creation.
How can I display the patches in mne_analyze. Additionally, how can I read
the cortical patch statistics from the different patch files? Do I need to
use the Matlab Toolbox for this purpose?
With the --w option to mne_add_patch_info you can produce w files which can be loaded to mne_analyze to show the patches.
Finally, does anyone know if some of the vertices along the patch
boundaries are shared between different patches?
I dont know about mne_add_patch_info function, but I have some matlab
functions that can give you patch statistics, feel free to visit my
cubicle,
I am in south central 1115-Seat B.
I dont know about mne_add_patch_info function, but I have some matlab
functions that can give you patch statistics, feel free to visit my
cubicle,
I am in south central 1115-Seat B.
The pinfo field of the source spaces loaded with mne_read_source_spaces contains the information about the composition of the patches as vertex numbers.
Thanks a lot for your help. I already tried overlaying the .w files
created with mne_add_patch_info on the WM surface using mne_analyze, but I
don't know how to interpret the output (my basic understanding about these
type of files was that they merely contained the patch area information,
complementary to the .fif files created with the --srcp option, which I
thought were the ones included the most info.). When I overlay the .w
files on the WM surface, my surface suddenly gets completely filled in
with color and there are almost no (if there are any) fluctuations with
respect to the color scale. I've played around with the threshold but
can't notice any change.
There are three pairs of w files produced, they contain one of the following in their names:
patches These contain a colored picture of the patches. Each patch will be shown with a random color.
rad These are the radiuses of the patches.
dev These are the surface normal standard deviations within a patch.
Regarding your other answer, if I invoke mne_add_patch_info without the
--dist option and with an ico-4 source space as input, what will be the
resulting geometry of my patches? How can I find out about the way in
which vertices are being assigned to the different, non-overlapping
patches? i.e., if there are two adjacent patches, how will the vertices on
their common boundary be assigned to one or the other?
Conceptually, the vertices are not on the boundary, the boundary is between the vertices. All vertices in a patch share the same closest vertex among those belonging to the ico-4 source space.