[FieldTrip] Question about minimum norm estimate pipeline

Sat Jun 1 23:22:34 CEST 2013

hi Steve,

yes, it is possible that the tutorial is slightly out of the date. I can
look at your problem and the tutorial around the end of the next week.
Thanks a lot for the detailed email!

Lilla

> Hi Arjen,
>
> Thanks for your message. I did align the mri to Talairach; as you can see
> from http://i.imgur.com/26nyHYZ.png, the volume conduction model and
> sourcespace are both expressed in the same coordinate system (i.e.,
> everything's pointing in the same direction) but they're just not sitting
> on top of one another. If anyone has any ideas on where that problem was
> introduced (or how to re-align them now), I would greatly appreciate it.
> Below I have some more details about how I processed that data, if it
> helps.
>
> I'm trying to go through the data one step at a time and track where the
> problem might have happened. When I compare the sourcespace before having
> applied any transformation (i.e., the headshape from
> <subject>-oct-6-src.fif) to the original mri (orig-nomask.mgz), they look
> ok (I don't know how to plot them together, but see
> http://i.imgur.com/LGW7YnJ.png and http://i.imgur.com/JUoTxc9.png --
> things
> at least look like they're on more or less the same plane). Then I
> re-register the mri to CTF (
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#source_modelco-registration_of_the_source_space_to_the_sensor-based_head_coordinate_system);
> after that, in mri_nom_ctf, the axes are all going in the right direction
> but the whole head is tilted forward and the origin of the axes is no
> longer at the anterior commisure (see http://i.imgur.com/CTZNOTk.png for
> the realigned MRI).  Applying the transformation matrix T to the
> sourcespace also seems to tilt it like that
> (http://i.imgur.com/bcNIpf3.png),
> although as can be seen from the first image in this message it doesn't
> quite line up with the volume conduction model in the end. As for the
> volume conduction model, here is what it looks like at first (
> http://i.imgur.com/ZX3m38b.png) and here is what it looks like after
> applying the transformation matrix (http://i.imgur.com/vXa3Cnc.png).
> Obviously the transformation matrix is doing something, but it's not
> getting the sourcespace and volume conduction model lined up; since it's
> the same transformation matrix, all I can guess is that there was some
> pre-existing difference between the source mesh (the .fif file) and the
> anatomical mri (orig-nomask.mgz), but I'm not sure when that came in.
>
> Another minor issue: when I first compared the volume conduction model and
> the sourcespace, they were expressed in different units even though I
> followed the code in the tutorial. See http://i.imgur.com/orwgcTJ.png: the
> sourcespace looks 10x smaller than the volume conduction model, which I
> assume is because it is expressed in cm whereas the volume conduction
> model
> is expressed in mm. To get the figure linked at the very beginning of this
> message, I had to convert the units of the volume conduction model to cm,
> even though that's not in the tutorial.
>
> I notice that the tutorial on the wiki hasn't been edited since October
> 2012 (other than a few edits I made this month which were just correcting
> typos in the prose). Is it possible that what's on the wiki is out of
> date?
> (Also cc'ing Lilla on this.)
>
> Thanks,
> 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/
>> > On Sat, May 25, 2013 at 1:56 PM, < fieldtrip-request at science.ru.nl >
>> > wrote:
>> > >
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>> > > than "Re: Contents of fieldtrip digest..."
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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/
>