CMCorig data, Coherence Tutorial

[Nathan Dees]

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.