[FieldTrip] What does minimum-norm estimate tell me + correlation in the source space
CRN
runna90 at 126.com
Tue Mar 15 09:45:16 CET 2016
Dear Jan-Mathijs,
Thank you very much for your reply! I have been halted in this problem for a few days… And I am really looking forward urgently to get the source localization result. So I am sorry to bother you again!
But there is still something wrong with followed steps in this page.
1. The built of volume conduction model. I noticed that it is required to create the volume model with same coordinate system as MEG sensor positions were defined. The ‘or-nomask.mgz’ file was asked to provide again to be used as anatomical data. I chose to replace this file with ‘orig.mgz’ first, but I got bad outcome as displayed below:
the code I applied was copied from the web:
mri_nom = ft_read_mri('orig.mgz');
cfg = [];
cfg.coordsys = 'spm';
cfg.output = {'brain'};
seg = ft_volumesegment(cfg, mri_nom);
seg = ft_convert_units(seg,'cm');
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg,seg);
vol.bnd = ft_transform_geometry(T, vol.bnd);
save vol vol;
So should I use the mri data with ctf coordinate system to build the model and then transform it to spm system with the ’T’ metric?
2. When I did Forward solution, I could not find sourcespace.pnt, parameters I got in the sourcespace as below:
what is the definition of ‘.pnt’? Why it was lost in my sourcespace data?
Thank you for your help!
Best
Runnan
> On Mar 14, 2016, at 16:40, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl> wrote:
>
> Hi Runnan,
>
> Sorry for the confusion. The part of the documentation you are working with is currently being improved, but not finalized yet.
> In particular, the part you refer to ‘Source model: co-registration of the source space to the sensor-based coordinate system’ needs a heavy update. I would assume that you have done the tutorial up until there. In particular, if you have done the preprocessing of the anatomical MRI, where you have created 2 transformation matrices (using the same anatomical volume), you’re almost there. So please forget about the orig.mgz, either nomask or not, and please be a bit patient until we (i.e. I) find time to update the documentation.
>
> This is how you get the appropriate coregistration:
>
> (Note: I assume that all the objects are defined in ‘mm’, otherwise it won’t work. To get all things in ‘mm’, use ft_convert_units).
>
> Preliminaries:
> -we know how to get from an arbitrary voxel-space to the sensor-based coordinate system: transform_vox2ctf
> -we know how to get to the ‘mni’ coordinate system from the same arbitrary voxel-space: transform_vox2spm
> -we know that the sourcespace is expressed in the ‘mni’ coordinate system (check the units, is it mm?)
>
> Based on the first two points above, we can easily construct a transformation matrix that goes from ‘mni’ to ‘ctf’:
>
> T = transform_vox2ctf/transform_vox2spm
>
> We can now use T to transform the sourcespace:
>
> sourcespace = ft_transform_geometry(T, sourcespace);
>
> I am pretty sure that this will do the trick.
>
> Best,
> Jan-Mathijs
>
>
>
>
>> On 13 Mar 2016, at 13:20, Harold Cavendish <harold.cav89 at gmail.com <mailto:harold.cav89 at gmail.com>> wrote:
>>
>> Dear Runnan,
>>
>> I'd be happy to help, but sadly, I have no experience with FreeSurfer and skipped that portion of the tutorial entirely (instead, I used files from fieldtrip/template).
>>
>> However, using just common sense, I believe there's an error in the tutorial because orig-nomask.mgz is mentioned for the first time where you need to load it but it isn't present in any of the outputs or in the Subject01 directory. I believe it's just a renamed copy of orig.mgz which is created as explained in the tutorial.
>>
>> As far as I understand, you take an anatomical MRI image (e.g. Subject01.mri), use FT to do some preprocessing and get Subject01.mgz (a FreeSurfer-compatible format), then do some segmentation and get Subject01masked.mgz, then do some conversion in FreeSurfer and transform those two into orig.mgz and brainmask.mgz respectively, and to make it even more convoluted, some filled.mgz pops up as well. To be honest, I don't follow… I have zero experience with FreeSurfer as well as MRI/fMRI analysis.
>>
>> Briefly, try using orig.mgz instead of orig-nomask.mgz whenever you need to use ft_read_mri('orig-nomask.mgz'). If it doesn't do the job, hopefully someone else will come to the rescue.
>>
>> Best regards,
>> Harold
>>
>>
>> On 12 March 2016 at 01:02, <runna90 at 126.com <mailto:runna90 at 126.com>> wrote:
>> Dear Harold,
>> I am very sorry that I am not writing to reply your question but to request you something about minimum norm estimate because I am a rather new fieldtripper. I noticed that you have got results applying MNE, thus I think you must be more experienced! I followed the tutorial at http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate <http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate> and did source reconstruction with MEG data acquired from ctf 275 system. But I got stuck in here
>> . Source model: Co-registration of the source space to the sensor-based head coordinate system, <>
>> I could not find the file named ‘orig-nomask.mgz’ under the mir folder. Would you tell me in which step should this file be created? And how to create this file?
>>
>> Best regards,
>>
>> Runnan
>>
>>
>>
>>
>>
>>
>>> 在 2016年3月10日，08:40，Harold Cavendish <harold.cav89 at gmail.com <mailto:harold.cav89 at gmail.com>> 写道：
>>>
>>> Dear FieldTrip users,
>>>
>>> I have a few questions regarding source localisation and statistics:
>>>
>>> 1. Suppose I'm doing source reconstruction of ERP using minimum-norm estimate; one condition, multiple subjects. I'm using ft_sourceanalysis() and getting rather meaningful results which I visualise via ft_plot_mesh().
>>>
>>> What is the validity of this result? I understand there are many individual dipoles spread over the cortical sheet and we're estimating best fit to the data given the conductance model while minimising overall power, but what does this actually tell us? If I find an area with higher power, what conclusions can I draw?
>>>
>>> 2. Can I compute a correlation between the result in the source space and a behavioural variable? Perhaps even specify a region of interest? If yes, is this approach considered to be valid?
>>>
>>> I want to see if e.g. the power of the reconstructed activity in the source space averaged over a time window correlates with my behavioural variable.
>>>
>>> Thank you!
>>>
>>> Best regards,
>>> Harold
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>>
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