[FieldTrip] fieldtrip Digest, Vol 30, Issue 45

[Stephen Politzer-Ahles]

Hi Arjen,

Thanks for your message; I did indeed re-align to Talairach after
reslicing, although I can't be sure it was "correct" (the page linked from
the tutorial, http://neuroimage.usc.edu/brainstorm/CoordinateSystems,
didn't give guidelines on how anterior/posteriorly to place the
interhemispheric point, so I just placed it near the top of the head on
about the same plane as the commisures). But it wasn't until the end of the
anatomical processing that I noticed the issue, so I'm wondering if there's
a way to re-align the source space and volume conduction model to each
other without going back to the beginning of the pipeline.

Best,
Steve


> Message: 1
> Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
> From: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about minimum norm estimate pipeline
> Message-ID:
>         <
1914237354.1292588.1369980683984.JavaMail.root at sculptor.zimbra.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve, A quick guess; did you correctly align your resliced mri to
Talairach space by indicating the commissures (
http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm
correct, a point in the same place, e.g. between the hemispheres? This
should update the transformation matrix. Best regards, Arjen -----
Oorspronkelijk bericht -----
> > Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> > Aan: fieldtrip at science.ru.nl
> > Verzonden: Vrijdag 31 mei 2013 05:53:45
> > Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> > 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/
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