[FieldTrip] Official Fieldtrip Courses/Meetings in Europe this year?

Diego Lozano-Soldevilla dlozanosoldevilla at gmail.com
Thu Oct 6 11:47:29 CEST 2016 

Hi,

Take a look here: http://www.fieldtriptoolbox.org/workshop

There's one in Tuebingen and another in Marseille. Ask the organizers to
see if there're available seats

best,

Diego



On 6 October 2016 at 11:24, parham hashemzadeh <ph442 at cam.ac.uk> wrote:

> Dear Fieldtrippers
>  I was wondering if there are any official Fieldtrip courses/Meetings in
> Europe this year or early next year?
> best regards parham
>
> On 2016-10-05 02:15, Schoffelen, J.M. (Jan Mathijs) wrote:
>
>> Hi Parham,
>>
>> Sorry for sounding cryptic earlier, I was just reciprocating the
>> crypticity of the question.
>> I think that the suggestion made in the previous e-mail is an
>> excellent one.
>> With the addition that, rather than using ft_determine_coordsys, you
>> could use ft_plot_ortho to visualize an arbitrary cross-cut through
>> your volumetric image.
>> Note however, that the MR and the sourcespace should be in the same
>> coordinate system for this to work.
>>
>> Best,
>> Jan-Mathijs
>>
>> On 05 Oct 2016, at 00:47, A. Donda <a.donda at hotmail.com> wrote:
>>>
>>> Hi Parham,
>>>
>>> if you wanna plot it in FieldTrip, these commands worked well for
>>> me, but in my case (MEG data) I had to make sure first that these
>>> data were on the same coordinate system (co-registration of MRI and
>>> MEG sensor-data). If you do not have this issue, then you can simply
>>> plot an MRI and a mesh obtained from freesurfer the following way
>>> (make sure that both MRI and the mesh are in the same units, e.g. cm
>>> or mm):
>>>
>>> ft_determine_coordsys(mricor_cm, 'interactive', 'no')
>>>
>>> hold on
>>>
>>> ft_plot_mesh(sourcespace);
>>>
>>> Alternatively, if you want to plot the vertices of the mesh as dots,
>>> you can use
>>>
>>> ft_plot_mesh(sourcespace.pnt,'vertexcolor','b');
>>>
>>> sourcespace has the following structure (in case this is helpful for
>>> you):
>>>
>>> pnt: [8196x3 double]
>>> tri: [16384x3 double]
>>> area: [16384x1 double]
>>> orig: [1x1 struct]
>>> unit: 'm'
>>>
>>> I obtained sourcespace by loading the boundary element model (bem)
>>> surface, created with the watershed algorthim of Freesurfer:
>>>
>>> sourcespace =
>>> ft_read_headshape([subjectname/bem/subjectname-oct-6-src.fif'],
>>> 'format', 'mne_source'); %in meters
>>>
>>> Note that I had to transform the sourcespace dataset to the right
>>> coordinate system and units.
>>>
>>> Finally I plotted the mri and mesh in cm
>>>
>>> To convert units in Fieldtrip, as you know, use X_cm =
>>> ft_convert_units(X,'cm');
>>>
>>> I hope this is helpful.
>>>
>>> Best
>>>
>>> A.Donda
>>>
>>> -------------------------
>>>
>>> FROM: fieldtrip-bounces at science.ru.nl
>>> <fieldtrip-bounces at science.ru.nl> on behalf of parham hashemzadeh
>>> <ph442 at cam.ac.uk>
>>> SENT: Tuesday, October 4, 2016 6:08 PM
>>> TO: FieldTrip discussion list
>>> SUBJECT: Re: [FieldTrip] plotting freesurfer mesh on the
>>> mri_aligned.
>>>
>>> Dear Darren
>>> Thank you very much, and I will try to give it a go.
>>> In the event that I can not. You are a life saver if you can help
>>> me
>>> out. Everything is in place except this incredibly important item.
>>> I
>>> have noticed that you are in Cambridge, maybe we can meet at some
>>> point.
>>> I am close by at the mathematics department.
>>> Many many thanks
>>> best regards parham
>>>
>>> On 2016-10-04 17:45, Darren Price wrote:
>>>
>>>> Hi Parham
>>>>
>>>> For a non-linear interpolation onto a regular grid,
>>>>
>>> spm_mesh_to_grid
>>>
>>>> might be ideal (from the spm package of course). I don't have a
>>>> working example to hand, but I may be able to dig one out if you
>>>>
>>> can't
>>>
>>>> get it working.
>>>>
>>>> Darren
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> Dr. Darren Price
>>>> Investigator Scientist and Cam-CAN Data Manager
>>>> MRC Cognition & Brain Sciences Unit
>>>> 15 Chaucer Road
>>>> Cambridge, CB2 7EF
>>>> England
>>>> EMAIL: darren.price at mrc-cbu.cam.ac.uk
>>>> URL: http://www.mrc-cbu.cam.ac.uk/people/darren.price [1]
>>>> TEL +44 (0)1223 355 294 x202
>>>> FAX +44 (0)1223 359 062
>>>> MOB +44 (0)7717822431
>>>> -------------------------------------------------------
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: fieldtrip-bounces at science.ru.nl
>>>> [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of parham
>>>> hashemzadeh
>>>> Sent: 04 October 2016 16:59
>>>> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>>>> Subject: Re: [FieldTrip] plotting freesurfer mesh on the
>>>>
>>> mri_aligned.
>>>
>>>>
>>>> Hi Jan
>>>> Thank you, my functional data are the function values of some
>>>> function (irrotational component of the current). From my limited
>>>> experience of Fieldtrip, your explanation feels (to myself) a bit
>>>> cryptic at the moment.
>>>>
>>>> You see if my inversion strategy was one of the classical ones
>>>> such as the ones provided by "ft_sourceanalysis" lcmv,sam,...,
>>>>
>>> eloreta
>>>
>>>> then the available fieldtrip tutorials are great in showing
>>>> how to plot functional values on the top of anatomical values.
>>>> But, since, I work on inversion methods, then I need a hacking
>>>> strategy to be able to plot functional values of "some
>>>> function"(estimated) on top of anatomical data MRI.
>>>>
>>>> I would appreciate if you would kindly let me know, if there is
>>>>
>>> hack
>>>
>>>> to it such that
>>>> ft_sourceplot can accept the input.
>>>> best regards parham
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 2016-10-04 16:29, Schoffelen, J.M. (Jan Mathijs) wrote:
>>>>
>>>>> Hi Parham,
>>>>>
>>>>> It is possible, but certainly not pain free, nor
>>>>>
>>>> straightforward.
>>>
>>>> I think this is not really a fieldtrip question, but more a
>>>>>
>>>> general
>>>
>>>> matlab related issue.
>>>>>
>>>>> It should be possible to plot a slice through an MRI volume as a
>>>>> MATLAB patch, where the coordinates of the voxels are expressed
>>>>>
>>>> in
>>>
>>>> some coordinate system. Then, it is possible to generate and
>>>>> intersection of the freesurfer mesh through the plane of
>>>>> visualization.
>>>>>
>>>>> Best,
>>>>> Jan-Mathijs
>>>>>
>>>>>
>>>>>
>>>>> On 04 Oct 2016, at 16:41, parham hashemzadeh <ph442 at cam.ac.uk>
>>>>>>
>>>>> wrote:
>>>
>>>>
>>>>>> Dear Fieldtrippers
>>>>>> Is there a straightforward pain free method ( I appreciate if
>>>>>>
>>>>> you can
>>>
>>>> give me the command)
>>>>>> to plot arbitrary points such as the vertices of the freesurfer
>>>>>>
>>>>>
>>> output
>>>>>> (mesh) onto the MRI image?
>>>>>> The reason that I ask is that I would like to plot my solution
>>>>>>
>>>>> on the
>>>
>>>> MRI image.
>>>>>> Unfortunately I do not use dipoles. In EEG, I model the
>>>>>>
>>>>> irrotational
>>>
>>>> component of the current as a scalar function and therefore I
>>>>>>
>>>>> am
>>>
>>>> doing
>>>>>> function estimation.
>>>>>> IF you use dipoles, it is straightforward because you follow
>>>>>>
>>>>> one of
>>>
>>>> the tutorials.
>>>>>> But if you do not use dipoles and model the current as the
>>>>>>
>>>>> gradient
>>>
>>>> of the irrotational component of the current in EEG then one
>>>>>>
>>>>> can get
>>>
>>>> lost.
>>>>>> Any help would be appreciated.
>>>>>> Many thanks
>>>>>>
>>>>>> --
>>>>>> best regards
>>>>>> Parham Hashemzadeh
>>>>>> Research Associate
>>>>>> Department of Applied Mathematics and Theoretical Physics
>>>>>> University of Cambridge, UK.
>>>>>> email: hashemzadeh at damtp.cam.ac.uk
>>>>>> _______________________________________________
>>>>>> fieldtrip mailing list
>>>>>> fieldtrip at donders.ru.nl
>>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>>>>
>>>>
>>>> --
>>>> best regards
>>>> Parham Hashemzadeh
>>>> Research Associate
>>>> Department of Applied Mathematics and Theoretical Physics
>>>> University of Cambridge, UK.
>>>> email: hashemzadeh at damtp.cam.ac.uk
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>>>
>>>
>>> --
>>> best regards
>>> Parham Hashemzadeh
>>> Research Associate
>>> Department of Applied Mathematics and Theoretical Physics
>>> University of Cambridge, UK.
>>> email: hashemzadeh at damtp.cam.ac.uk
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip [2]
>>>
>>
>>
>>
>> Links:
>> ------
>> [1] http://www.mrc-cbu.cam.ac.uk/people/darren.price
>> [2] https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> --
> best regards
> Parham Hashemzadeh
> Research Associate
> Department of Applied Mathematics and Theoretical Physics
> University of Cambridge, UK.
> email: hashemzadeh at damtp.cam.ac.uk
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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