[FieldTrip] channel_repair bug

["Jörn M. Horschig"]

Hi Frederic,

The one Google Code is the most recent version. My guess would be that 
it was introduced beginning of July in revision 3807 (apologies for that ).
Any version after that had this bug, I cannot tell for the versions 
before (but doubt).

Best regards,
Jörn

On 9/15/2011 4:07 PM, Frederic Roux wrote:
>
> Hi Jorn,
>
> I was wondering if the bug you reported concerning the channel_repair
> function also applied to older versions of fieldtrip and in which
> cases this bug appears.
>
> This would be important for me to know as I have been using the function
> in the past and would like to know if it affects my results or not.
>
> Best,
>
> Frederic
>
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
>
> > From: fieldtrip-request at donders.ru.nl
> > Subject: fieldtrip Digest, Vol 10, Issue 18
> > To: fieldtrip at donders.ru.nl
> > Date: Thu, 15 Sep 2011 12:00:17 +0200
> >
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> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Critical bug in ft_channelrepair fixed (J?rn M. Horschig)
> > 2. Fwd: AW: Forward solution using concentric spheres and BEM
> > models (Micheli, C.)
> > 3. cortical time-course reconstruction (Paolo Belardinelli)
> > 4. Re: interaction within-subject indepsamplesT (Eric Maris)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 14 Sep 2011 15:41:45 +0200
> > From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > To: Email discussion list for the FieldTrip project
> > <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Critical bug in ft_channelrepair fixed
> > Message-ID: <4E70AF19.2040003 at donders.ru.nl>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hey everyone,
> >
> > we found a critical bug in ft_channelrepair, which we fixed now. The 
> bug
> > caused wrong channels to be chosen for interpolation in some 
> situations,
> > meaning that the timecourse your repaired channel did not make sense.
> > Please be aware of this, check your reconstructed channels and re-run
> > your channel reconstruction if you are in doubt with the newest
> > FieldTrip version!
> >
> > For more information, check Google code:
> > http://code.google.com/p/fieldtrip/source/detail?r=4158
> > and Bugzilla:
> > http://bugzilla.fcdonders.nl/show_bug.cgi?id=941
> >
> > Best regards,
> > J?rn
> >
> >
> > --
> > J?rn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen
> > Neuronal Oscillations Group
> >
> > 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
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 14 Sep 2011 17:56:38 +0200 (CEST)
> > From: "Micheli, C." <c.micheli at fcdonders.ru.nl>
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Fwd: AW: Forward solution using concentric
> > spheres and BEM models
> > Message-ID:
> > <1624476173.1270054.1316015798685.JavaMail.root at draco.zimbra.ru.nl>
> > Content-Type: text/plain; charset=utf-8
> >
> > Hi Margit and Juan Pablo
> > see my answers below.
> >
> > ----- "Margit Sch?nherr" <Margit.Schoenherr at uk-erlangen.de> schreef:
> >
> > > Van: "Margit Sch?nherr" <Margit.Schoenherr at uk-erlangen.de>
> > > Aan: "c micheli" <c.micheli at fcdonders.ru.nl>
> > > Verzonden: Woensdag 7 september 2011 09:33:53
> > > Onderwerp: AW: [FieldTrip] Forward solution using concentric 
> spheres and BEM models
> > >
> > > Hello Cristiano,
> > >
> > > thank you for your email. I have tried the code, but I have 2 problems
> > > with it.
> > > 1) When I do it exactly as suggested in the email, I get the following
> > > error when using ft_prepare_mesh:
> > >
> > > bnd = ft_prepare_mesh(cfg, mri_segment);
> > > ??? Error using ==> ft_prepare_mesh at 159
> > > unsupported cfg.method and/or input
> > >
> > > I think, this is simply a problem concerning the naming of the
> > > variables. The segmented mri is called 'seg', the labels are assigned
> > > to 'mri_segment'. I think, this is the wrong input for
> > > ft_prepare_mesh, because 'mri_segment' does not contain any mri
> > > information. Putting the labels into a new field 'seg.seg' and calling
> > > bnd = ft_prepare_mesh(cfg, seg) solves this.
> > >
> >
> > I could replicate the error and this is due to the fact that 
> ft_prepare_mesh accepts inputs of FieldTrip type 'volume'. See 
> ft_datatype_volume. The function crashed because I simply used an old 
> version of the test file where I inputted the volume matrix only, 
> whereas three fields are required (dim, transform and anatomy), that's 
> why the input should look like this:
> >
> > mri2 = [];
> > mri2.anatomy = mri_segment;
> > mri2.dim = mri.dim;
> > mri2.transform = mri.transform;
> >
> > I patched the correct code at the end of the mail.
> >
> > > 2) However, there is still only one surface triangulated. So as I
> > > wrote in my last email, I still believe that line 25 in
> > > prepare_mesh_segmentation needs to be commented. What do you mean?
> >
> >
> > I agree. This function needs a general review altogether and at the 
> moment I committed your correction. In the future I'll restructure the 
> whole function taking care of the more recent guidelines. Thanks for 
> your suggestion.
> >
> > Try this:
> >
> > % download from the FieldTrip ftp site
> > % (ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip)
> >
> > % load the MRI
> > mri = ft_read_mri('Subject01.mri');
> >
> > % segment it
> > cfg = [];
> > cfg.output = {'scalp', 'skull', 'brain'};
> > seg = ft_volumesegment(cfg, mri);
> >
> > % volumetric preprocessing
> > % Note: the three compartments have to be 'filled' otherwise the 
> triangulation won't work correctly. The output of ft_volumesegment 
> will change soon, making it compatible with ft_prepare_mesh. As of 
> today we need the following:
> >
> > mri_segment{1} = seg.scalp;
> > mri_segment{2} = imfill(seg.skull,'holes'); % you need the image 
> processing toolbox here!
> > mri_segment{3} = seg.brain;
> >
> > % triangulation (from volumes to surfaces)
> > % Note: now the volumes are inputted one at a time
> > mri2 = mri;
> > cfg=[];
> > cfg.sourceunits = 'mm';
> > cfg.mrinuits = 'mm';
> > cfg.tissue = 1;
> > cfg.numvertices = 1000;
> > for i=1:3
> > mri2.seg = mri_segment{i};
> > mesh{i} = ft_prepare_mesh(cfg,mri2);
> > end
> >
> > % visualization of the triangulated surfaces
> > 
> figure,ft_plot_mesh(mesh{1},'edgecolor','none','facecolor','w','facealpha',0.5)
> > ft_plot_mesh(mesh{2},'edgecolor','none','facecolor','g','facealpha',0.7)
> > ft_plot_mesh(mesh{3},'edgecolor','none','facecolor','r','facealpha',1)
> >
> >
> > > Thank you.
> >
> > Be my guest.
> > Cheers,
> > Cristiano
> >
> > >
> > > Best regards,
> > > Margit
> > >
> > >
> > > ***********************************
> > > Margit Sch?nherr
> > > Universit?tsklinikum Erlangen
> > > Neurologische Klinik
> > > Epilepsiezentrum (Biomagnetismus)
> > > Schwabachanlage 6
> > > 91054 Erlangen
> > > Telefon: ++49 9131 / 85 36921
> > > Email: margit.schoenherr at uk-erlangen.de
> > > ***********************************
> > > ________________________________________
> > > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
> > > im Auftrag von Micheli, C. [c.micheli at fcdonders.ru.nl]
> > > Gesendet: Montag, 5. September 2011 12:59
> > > An: Email discussion list for the FieldTrip project
> > > Betreff: Re: [FieldTrip] Forward solution using concentric spheres
> > > and BEM models
> > >
> > > Dear Juan Pablo and Margit
> > >
> > > The function 'ft_prepare_mesh' takes care of triangulating every
> > > compartment via the cfg.tissue option. This option contains the
> > > integers which describe a type of tissue, given that the user
> > > beforehand defined all voxels of the segmented MRI compartment as
> > > having that particular value.
> > > As an example, download the sample MRI in FieldTrip ftp location:
> > >
> > > ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip
> > > Create a folder and unzip these files.
> > >
> > > % read in the mri
> > > mri = ft_read_mri('Subject01.mri');
> > >
> > > % segment it
> > > cfg = [];
> > > cfg.output = {'scalp', 'skull', 'brain'};
> > > seg = ft_volumesegment(cfg, mri);
> > >
> > > % assign a label
> > > scalp = (seg.scalp) & ~(seg.skull | seg.brain);
> > > skull = 2*(seg.skull);
> > > brain = 3*(seg.brain);
> > > mri_segment = scalp + skull + brain;
> > >
> > > % build the meshes
> > > cfg = [];
> > > cfg.method = 'segmentation';
> > > cfg.tissue = [1 2 3]; % scalp = 1; skull = 2; brain = 3;
> > > cfg.numvertices = [2000 1000 800];
> > > cfg.sourceunits = 'mm';
> > > cfg.mriunits = 'mm';
> > > bnd = ft_prepare_mesh(cfg, mri_segment);
> > >
> > > If any of the tissues has a different value from cfg.tissues this
> > > won't be triangulated. To check for this use ft_sourceplot in the
> > > interactive mode. By clicking around you can see the tissue's value in
> > > the command window:
> > >
> > > % view the labelled segmentations
> > > mri2 = mri;
> > > mri2.seg = mri_segment;
> > > cfg=[];
> > > cfg.interactive = 'yes';
> > > cfg.funparameter = 'seg';
> > > ft_sourceplot(cfg,mri2);
> > >
> > > About the concentric spheres:
> > > both ways to derive a concentric spheres model are correct. In one
> > > case you directly build the vol structure and you assume you know the
> > > radiuses of your spheres. In the other case you allow the
> > > ft_prepare_concentricspheres function to build the spheres starting
> > > from realistic geometrical boundaries.
> > > The second approach is my favorite because the ft_prepare function
> > > contains a function that fits a sphere to each boundary and I don't
> > > have to do it myself.
> > > The first approach (directly force the radiuses in your vol structure)
> > > is preferable if you derive the information from other software (e.g.
> > > CTF's MRIView) or if you fit the sphere yourself.
> > >
> > > @Pablo
> > > If the sphere is fitted inside the brain it is correct. You do not
> > > want the sphere to include other tissues, because your assumption for
> > > the construction of the forward model is that the tissue inside the
> > > sphere is homogeneous.
> > > For a more realistic model (encompassing the whole brain volume) I
> > > would rather use a BEM model.
> > >
> > > I hope this helps,
> > > Cristiano
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 14 Sep 2011 18:18:36 +0200
> > From: Paolo Belardinelli <paolo.belardinelli at med.uni-tuebingen.de>
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] cortical time-course reconstruction
> > Message-ID: <4E70D3DC.4060403 at med.uni-tuebingen.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi Robert.
> > We have some nice coherence maps with peaks in M1 for a finger tapping
> > task. We were wondering how to properly reconstruct the power
> > time-course in the M1 area in order to use it as a further reference
> > signal.
> >
> > -Is the code necessary for the approach described in (Schoffelen et 
> al.,
> > NeuroImage 2008) already implemented in ft (we observed in the code 
> that
> > it is possible in ft_sourceanalysis.m to give a location for a
> > reference dipole but we found no documentation)?
> >
> > -Is the only reliable solution for reconstructing a time-course to
> > project the activity in the dominant direction? We have the eigenvalues
> > of the first dipole which are normally 3 to 6 times larger
> > than the ones of the second. We are not sure this is enough to neglect
> > the second component.
> >
> > - One last technical question: in the mailing list it is said that the
> > orientation of the dipole is saved in source.avg.ori but it doesn't 
> seem
> > like that to us. Maybe we are doing something wrong.
> >
> > Best regards and thank you for your work,
> >
> > Paolo and Erick
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 15 Sep 2011 10:10:36 +0200
> > From: "Eric Maris" <e.maris at donders.ru.nl>
> > To: "'Email discussion list for the FieldTrip project'"
> > <fieldtrip at donders.ru.nl>
> > Subject: Re: [FieldTrip] interaction within-subject indepsamplesT
> > Message-ID: <008d01cc737e$f6192ba0$e24b82e0$@maris at donders.ru.nl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear Kathrin,
> >
> > > I need your advice on how to correctly test the interaction 
> effects in a
> > 2x2
> > > within-subject design with cluster-based randomization tests. I 
> have two
> > > factors A and B with the levels a1/a2 and b1/b2. In addition, the 
> number
> > of
> > > trials in A are about twice as much as in B.
> > >
> > > The procedure would be totally clear in a between-subject design 
> (as in a
> > > previous post on the list:
> > > 
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html)
> >
> > This post is about a WITHIN-subjects design.
> >
> > > because I could easily compute the differences of the factor levels
> > > A_diff=a1-a2 and B_diff=b1-b2 and then run ft_freqstatistics on the
> > > differences. However, since I have to run the statistics across 
> trials and
> > not
> > > subjects I have independent samples and not dependent samples.
> >
> > So, you have a between-trials design.
> >
> > If it is
> > > possible at all, how can I calculate the differences A_diff and B_diff
> > across
> > > trials? Is it a problem that the number of trials are not equal?
> >
> > This is not possible. Permutation tests cannot be used for testing
> > interactions in a multi-factorial between-subjects/trials design. 
> Michael
> > Wibral has a post in which he refers to a nice statistics paper on the
> > issue.
> >
> > A proxy that is possible (but not statistically sound) is to perform two
> > statistical tests of the first factor, once at the first level of second
> > factor and once at the second level.
> >
> >
> > Best,
> >
> > Eric Maris
> >
> >
> >
> >
> >
> >
> >
> >
> > >
> > > Any help is appreciated!
> > >
> > > Best,
> > > Kathrin
> > >
> > > _____________________________________
> > > Kathrin M?sch
> > >
> > > Dept. of Neurophysiology and Pathophysiology
> > > University Medical Center Hamburg-Eppendorf
> > > Martinistr. 52
> > > 20246 Hamburg
> > > Germany
> > > Phone: +49-40-7410-54680
> > > Fax: +49-40-7410-57752
> > > E-Mail: k.muesch at uke.uni-hamburg.de
> > > _____________________________________
> > >
> > >
> > > --
> > > Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und
> > > Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> > >
> > > Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen
> > > Rechts; Gerichtsstand: Hamburg
> > >
> > > Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender), Dr.
> > Alexander
> > > Kirstein, Joachim Pr?l?, Prof. Dr. Dr. Uwe Koch-Gromus
> > >
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 10, Issue 18
> > *****************************************
>
>
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-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group

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

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