CMCorig data, Coherence Tutorial

[jan-mathijs schoffelen]

Dear Nathan,

Indeed, the flipping as applied in the tutorial should be applied for
volumes, segmented from .mri files. This has an obscure reason, which
I never managed to find. Importantly, the flipping has to be applied
in order for the transformation-matrix, as stored in mri.transform
(or segment.transform), to correctly transform from volume-based
voxel indices into head-space.
Did you check, whether the segmentation itself worked? In other
words, do the gray/white/csf volumes look reasonable with respect to
the anatomy from which it is derived?
As far as I know, the spm segmentation routine which is used by
fieldtrip, matches the input anatomy to some gray/white/csf template
volumes, but assumes a quite good coregistration between the
templates and the input volume, both in terms of coordinate-frame
(which should be spm-based), and in the way the volumetric data are
stored physically in the data-matrix. These issues are taken care of
when volumesegment is instructed to interpret the coordinate-system
as being 'ctf'-based, either by some user-interactions prompted when
the function is executed, or by explicitly putting cfg.coordinates to
'ctf'.
You mention you convert your dicoms to analyze format, but this step
in itself does not tell fieldtrip how to interpret the volumetric
data. Does the image have a transformation matrix attached when
loaded in? If not, you should probably first need to use
volumerealign to specify the fiducial locations. This will give you a
transformation matrix attached to the mri according to ctf-conventions.
Next volumesegment should be called with cfg.coordinates = 'ctf'.

Hope this helps,

Jan-Mathijs

On Jun 16, 2008, at 6:59 PM, Nathan Dees wrote:

> Jan-Mathijs -
>
> Thank you for responding.  I have waited to reply as I have
> steadily worked my way through the Coherence
> Tutorial, and most all of the beamforming tutorial - there a major
> question at this point:
>
> My segmented MRI is never aligned with the MRI image it is derived
> from.  I am using the program MRIcro to convert *.dcm files to an
> *.img file before I read it into fieldtrip using the
> read_fcdc_mri.m function.  Then I segment using spm2 through
> fieldtrip's volumesegment.m function, and flip dimensions as
> discussed in the tutorial.  This works correctly for the sample
> data, file Subject01.mri, but for my *.img files, when I use
> sourceplot to see if the segmented brain fits and the MRI are
> aligned correctly, they are unfortunately not.  I have tried
> different flipping methods to no avail.
>
> Any suggestions?
>
> Thank you in advance,
> Nathan Dees
>
>
>
> ----- Original Message ----- From: "jan-mathijs schoffelen"
> <j.schoffelen at PSY.GLA.AC.UK>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Friday, May 09, 2008 3:39 AM
> Subject: Re: [FIELDTRIP] CMCorig data, Coherence Tutorial
>
>
>> Dear Nathan,
>>
>> Indeed the CMCorig mat-file is missing from the ftp-server, but in
>> principle it can be generated by executing the preceding steps in the
>> tutorial. We will change the tutorial accordingly. Historically, the
>> tutorials have been used at the FCDC toolkit-courses for data
>> analysis,
>> and students had the mat-file available to save some time.
>> However, from your mail I conclude that you had some problems
>> running  the
>> tutorial itself, probably unrelated to the (un)availability of  the
>> CMCorig file. If so, could you just retry running the tutorial
>> and let us
>> know whether and where specified problems arise?
>>
>> Thanks,
>>
>> Jan-Mathijs
>>
>> On May 7, 2008, at 12:54 AM, Nathan Dees wrote:
>>
>>> How can one gain access to the dataset 'CMCorig' discussed in the
>>> tutorials, specifically the tutorial on Coherence?  This file is not
>>> included in the SubjectCMC data posted on the tutorial data
>>> section  of
>>> the
>>> website.
>>>
>>> Has anyone else had trouble running the Coherence tutorial from
>>> start to
>>> finish - I thought having access to this data might help me get
>>> through
>>> certain sections?
>>>
>>> Thank you
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between
>>> users  of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>> for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the
>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG
>> and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.