[Mne_analysis] visualizing "activation" regions with MNE

[Dan Wakeman]

Hi,

Well, given what you want to do you can simply type in the vertex
numbers and draw it like that (i.e. not by hand in theory, but in
practice it would involve some work by hand). Theoretically, you can
even write a tcl script to create them. There is information, in the
MNE files about the downsampling, if you used the --cps option (lookup
"--cps" in the manual  and "nearest" in the matlab toolbox chapter),
however, adding those vertices will only change the way your ROIs
appear not what they are i.e. the data will still come from the
individual points you have at the moment (as those vertices are the
ones, which have been removed by downsampling). Drawing by hand either
with mne_analyze or tksurfer is really the only way I know of to
generate these (without writing complex code from scratch). I would
also point out that it is possible that depending on your criteria,
you could put yourself in some tricky statistical situations due to
issues of double dipping or selecting strange data points i.e. the
distributions could be bizarre etc.

HTH
D

On Tue, Jan 31, 2012 at 11:35 AM, Mingbo Cai <mcai at cpu.bcm.edu> wrote:
> Thanks Dan!
> I tried tksurfer but it is less intuitive for me to draw ROI there by hand. Does anyone know if there is information of neighborhood between vertices so that we can include neighbor vertices of each activated vertices in order to obtain a continuous "activation" patch?
>
> Mingbo
>
> -----Original Message-----
> From: Dan Wakeman [mailto:dgwakeman at gmail.com]
> Sent: Monday, January 30, 2012 3:59 PM
> To: Mingbo Cai
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] visualizing "activation" regions with MNE
>
> Hi Mingbo,
>
> This will depend on how the ROIs look from the criteria. You could try
> to go through and generate a label using the vertex numbers you have
> produced and tksurfer. i.e. select each of the vertices one by one and
> use the draw line features to generate a closed ROI. This will likely
> end up including more vertices than the ones, which have "passed the
> criteria". It may also be influenced by the size of the source space
> you use.
>
> D
>
> On Mon, Jan 30, 2012 at 4:52 PM, Mingbo Cai <mcai at cpu.bcm.edu> wrote:
>> Dear colleagues,
>> I have a question of visualizing interesting regions. I identified a group
>> of vertices of which the time course of mne pass certain criterion, saved
>> these vertices to a label file, and viewed them with mne_analyze. But
>> probably because the vertices that have mne estimation are only a subset of
>> all the vertices on the cortex, they appear as isolated dots within a
>> constrained area. So my question is: is there any way that I can find all
>> the vertices that are within the region this group of “activated” vertices
>> span? In this way, instead of showing many isolated dots, I can show a small
>> region on the inflated brain just as what we usually see when we load a
>> label file from freesurfer parcellation.
>>
>>
>>
>> Mingbo Cai
>>
>> Department of Neuroscience
>>
>> Baylor College of Medicine
>>
>>
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