[FieldTrip] Question about minimum norm estimate pipeline
Stephen Politzer-Ahles
politzerahless at gmail.com
Fri May 31 05:53:45 CEST 2013
Hello all,
I have not yet gotten a response to my question below, but in the meantime
I have another question about the minimum norm estimate
workflow--specifically, about the coordinate system for the skull-stripped
anatomy in the step described at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk.
I'm confused by the following bit of code:
% ensure that the skull-stripped anatomy is expressed in the same
coordinate system as the anatomy
seg.transform = mri_tal.transform;
In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
re-aligning to Talairach in the previous step?) whereas seg.coordsys is
'ctf' (as a result of re-aligning to CTF several steps earlier). (But
mri_tal also has a field mri_tal.transformorig, which seg does not have.)
So should I really be using the same transform for both, as shown in the
tutorial?
Apologies if this question is pretty basic; I'm just trying to pinpoint
where the mis-alignment described in my message below occurred, so I want
to make sure I understand each step of the workflow correctly
Best,
Steve
> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
> <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
On Sat, May 25, 2013 at 1:56 PM, <fieldtrip-request at science.ru.nl> wrote:
>
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> Today's Topics:
>
> 1. Sourcespace and volume conductor misaligned
> (Stephen Politzer-Ahles)
> 2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
> <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
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> Message: 2
> Date: Sat, 25 May 2013 20:54:59 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> Message-ID:
> <CAL4kA6eTL_TwECF62W-OoWY=
Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> 1. Every MRI scanner is different, so I'm not familiar with that naming
> scheme, but it seems the 'GAD' at the end of the file name indicates that
> was with the Gadolinium contrast agent, so I would suggest to not use
that,
> but instead use the first (plain) T1.
>
> 2. I'm not sure what to suggest. I assume you can see the vitamin E
marker
> clearly when viewing the DICOM file? Is the issue that some slices are
> missing in the conversion, or that the contrast on the image is not the
> same? or right/left flipped?
>
> Best,
> Johanna
>
>
> 2013/5/23 WangJing <13681530640 at 139.com>
>
> > Dear Johanna,
> >
> > Thank you for your suggestion.
> > 1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > t1_vibe_traGAD-5. which one is best?
> > 2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> > didn't be found. what can I do?
> >
> > Best Regards,
> > Jing Wang
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-22 15:33:13
> > Subject?fieldtrip Digest, Vol 30, Issue 31
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
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> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
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> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: question About head model (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 22 May 2013 09:30:17 +0200
> > From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] question About head model
> > Message-ID:
> > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > It is best to use the T1 MRI rather than the other scans. To open a
DICOM
> > format file, you can try one of these options:
> >
> > % read the DICOM files
> > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > % or use a graphical file selection[f, p] = uigetfile
> > <
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > >('*');
> > mri = ft_read_mri(fullfile
> > <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > >(p,
> > f));
> >
> >
> > I copied the above from documentation on the FieldTrip wiki:
> >
> >
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> >
> >
> > Then you can save the 'mri' into a *.mat file for future use with
FieldTrip.
> >
> > Best regards,
> > Johanna
> >
> >
> > 2013/5/22 WangJing <13681530640 at 139.com>
> >
> > > Hi
> > > I am a freshman about field trip.
> > > I am trying to build the forward model. but my mri data is different
from
> > > the data in the tutorial. So I don't know how to bulid the head
model. I
> > > use the date which is from the paper "Open Database of Epileptic EEG
with
> > > MRI and Postoperational Assessment of Foci?a Real World Verification
for
> > > the EEG Inverse Solutions",http://eeg.pl/epi
> > . MRI recordings containing a
> >
> > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain
scans
> > > with morphologic substrate of the epilepsy (mostly cortical
dysplasias,
> > > dysplastic tumors etc.). In some cases there is also a scan with the
> >
> > > gadolinium (GAD) contrast. The images were collected by Siemens
Sonata 1.5T
> > > scanner. The data is stored in the Digital Imaging and Communications
in
> > > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > > weighting.The scans have the following resolutions: T1: 512 ? 512
pixels,
> > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> >
> > > In the tutorial,the mri data stored in only one file, while the data
which
> >
> > > I used have many files, I don't know how to process. who can help
me,Thanks1
> > > Thanks very much!
> > > Best Reagards
> > > Jing Wang
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > > To?fieldtrip<fieldtrip at science.ru.nl>
> > > Date?2013-05-21 23:59:18
> > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Thank you so much for your answer J?rn,
> > >
> > >
> >
> > > Now I got it, so, I will let the 'fourier' as input to
ft_connectivityanalysis, because for some indices I will need the
auto-spectrum, and if I fully undertood what you said, it will be the same,
as they always take the phase information from the fourier transform. And
fieltrip will automatically compute the csd if the input is the frequency
data.
> > >
> > >
> >
> > > Nevertheless, it give me some error when I tried to use the output
from 'powandcsd' of freqanalysis, always gives me a matrix dimensions
error, and when I use the output 'fourier' from connectivityanalysis, it
computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they
are signed, so this is ok), the problem are the ImC ranging from -inf to
inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier'
the values are. Which for me is really weird.
> > >
> > >
> > >
> >
> > > I have checked internally, and even when I always use the 'fourier'
as input, when it internally calculates cross-spectrum for the ImC and PLV,
the data.crsspctrm is different, e.g:
> > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > ans size(data.crsspctrm) = [1 7 59 59];
> > >
> >
> > > So, both are apparently the same, but the data inside this matrices
is different,
> > >
> > >
> >
> > > for example, when calculating the ImC the first 7 columns for the
first two rows are:
> > > val(:,:,1,1)
> > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i?
0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > >
> > > while when calculating the PLV are:
> > > val(:,:,1,1)
> > > ?[1? 1? 1? 1? 1? 1? 1]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i?
0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > >
> > >
> > >
> >
> > > I'm pretty sure I'm doing something wrong here, but I don't really
have a clue,
> > >
> > >
> >
> > > If I use the fourier transform to calculate the 'csd' in
ft_connectivity analysis and use this csd as input to all other
ft_connectivityanalysis indices all of them are set to NaN or 1, not
ranging between any numbers.
> > >
> > >
> > >
> > >
> > >
> >
> > > On the other hand, I have seen searching on the net, that fieltrip is
capable of create surrogate data, by shifting the phase information on
every trial for only one electrode of each pair while using the original
samples of each trials on the second channel, but I couldn't find on the
manual how to do such a thing. Is there any way to compute this kind of
surrogates for every sensor? or was it something that some one suggest to
somebody?
> > >
> > >
> > > Many thanks in advanced,
> > > Gabriel.
> > >
> > >
> > >
> > >
> > > ----- Mensaje original -----
> > > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > >
> > >
> > >
> > >
> > >
> > > > Dear Gabriel,
> > > >
> > >
> >
> > > > A) As you see, this makes an average over the
epochs of each channel, and not over the samples (which in this
case are the 9 frequencies of the FFT), And I would like to
have the opposite, this is, to get the imaginary part of coherence for
each epoch (repetition) on all my channels
and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,
Is this possible?
> > > >
> > >
> >
> > > > No. You should think of coherence more as a measure for the
consistency of the phase relation between channels across trials,
so coherence is just not defined per trial,neither would it make
sense to compute coherence for a single trial.
> > > >
> > >
> >
> > > > B) Another question I have is: for the
Imaginary part of Coherence is not necessary to compute
the cross-spectrum with 'powandcsd', only the FFT, but
for the PLV, PPC or WPLI is that way too? I see
some terminology issues here. Let me try to explain in a simple (aka
least-mathematical I can think of) way:
> > > >
> > >
> >
> > > > For all these connectivity measures, we need the phase
information from the Fourier transform (FFT) to compute the
cross-spectral density matrix (CSD). The CSD can be regarded as the
equivalent in the frequency domain to the covariance matrix in the
time domain, thus it is a measures how a certain channels activity is
co-modulated with another channels activity (for a particular
frequency) - makes pretty much sense to make use of this when
computing connectivity, right? :)
> > >
> >
> > > > As you might know, a Fourier transform returns complex
numbers, where the imaginary part of this number contains phase
information. When calling ft_freqanalysis, you can decide if it shall
only return the (squared) real part of the frequency spectrum
(cfg.output='pow'), or instead the full CSD (cfg.output =
'powandcsd'). Alternatively, you can also let ft_freqanalysis return
the raw Fourier coefficients (cfg.output='fourier'). From the Fourier
coefficients, however, you can easily obtain the CSD or the power
spectrum basically by multiplication the Fourier matrix with itself
(transposed). All of these measures quantify the phase relation
between channels across trials, and as phase information is coded in
the imaginary part of the fourier output, thus for
connectivityanalysis you need the CSD which can be obtained either by
'powandcsd' or by 'fourier'.
> > > >
> > > > I hope that somehow clarifies your questions.
> > > >
> > > > Best,
> > > > J?rn
> > > >
> > > > On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > > > Dear Fieltrip experts,
> > > >
> > >
> >
> > > > I have my continuous data imported to fieldtrip with
matlab, I'm looking for performing connectivity analysis between
pairs of sensors, I have succed as:
> > >
> >
> > > > data.trials {1xNepochs}; % Nepochs = 7, each epoch
with 59 channels and 2000 samples
> > > > data.label {59x1};
> > > > data.time {1xNepochs};
> > > >
> > > > then, calculate only the FFT of all sensors as:
> > > > cfg=[];
> > > > cfg.output='fourier';
> > > > cfg.method='mtmfft';
> > > > cfg.taper='hanning';
> > > > cfg.foilim=[8.5 9.5];
> > > > cfg.tapsmofrq=0;
> > > > cfg.trials='all';
> > > > cfg.keeptrials='yes';
> > > > cfg.channel='all';
> > > > fourier=ft_freqanalysis(cfg, data)
> > > > as output I get:
> > > > dimord = 'rpttap_chan_freq'
> > > > freq= [1x9]
> > > > fourierspctrm=[7x59x9 double]
> > > >
> > > > Then compute the imaginary part of coherency as:
> > > > cfg=[];
> > > > cfg.method ='cohe';
> > > > cfg.complex='imag';
> > > > cfg.channelcbm={'all' 'all'};
> > > > coher = ft_connectivityanalysis (cfg, fourier)
> > > > as output get:
> > > > dimord='chan_chan_freq';
> > > > cohspctrm=[59x59x9 double];
> > > > dof=7;
> > > >
> > > > I have two main questions:
> > > >
> > >
> >
> > > > A) As you see, this makes an average over the
epochs of each channel, and not over the samples (which in this
case are the 9 frequencies of the FFT), And I would like to have
the opposite, this is, to get the imaginary
part of coherence for each epoch (repetition) on all my
channels and not for each frequency, something like: chan_chan_rpt or
chancbm_rpt, Is this possible?
> > > >
> > > >
> > > >
> > >
> >
> > > > B) Another question I have is: for the
Imaginary part of Coherence is not necessary to
compute the cross-spectrum with 'powandcsd', only the
FFT, but for the PLV, PPC or WPLI is that way too?
> > > >
> > > >
> > > >
> > > >
> > > > Many thanks in advanced,
> > > > Gabriel.
> > > >
> > > >
> > > >
> > >
> >
> > > > _______________________________________________ > fieldtrip
mailing list >
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > >
> >
> > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for
Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging >
Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip
Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands
> > Contact: > E-Mail:
> > > jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:
> > > http://www.ru.nl/donders
> >
> > > > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
NL-6525 EN Nijmegen > The Netherlands >
_______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > >
> >
> > > <font size="3">--------------------------<br />PhD. student Gabriel
Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain
-<br /><br />Email:
> > > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> > >
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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