<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'><div dir='ltr'>
<br>Hi Jorn,<br><br>I was wondering if the bug you reported concerning the channel_repair<br>function also applied to older versions of fieldtrip and in which<br>cases this bug appears.<br><br>This would be important for me to know as I have been using the function<br>in the past and would like to know if it affects my results or not.<br><br>Best,<br><br>Frederic<br><br>-- <br>Frédéric Roux, PhD student<br>Department of Neurophysiology<br>Max Planck Institute for Brain Research<br>D-60529 Frankfurt am Main<br>Frederic.Roux@brain.mpg.de<br>+49(0)69630183225<br><br><br><br><br><div>> From: fieldtrip-request@donders.ru.nl<br>> Subject: fieldtrip Digest, Vol 10, Issue 18<br>> To: fieldtrip@donders.ru.nl<br>> Date: Thu, 15 Sep 2011 12:00:17 +0200<br>> <br>> Send fieldtrip mailing list submissions to<br>> fieldtrip@donders.ru.nl<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> or, via email, send a message with subject or body 'help' to<br>> fieldtrip-request@donders.ru.nl<br>> <br>> You can reach the person managing the list at<br>> fieldtrip-owner@donders.ru.nl<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of fieldtrip digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. Critical bug in ft_channelrepair fixed (J?rn M. Horschig)<br>> 2. Fwd: AW: Forward solution using concentric spheres and BEM<br>> models (Micheli, C.)<br>> 3. cortical time-course reconstruction (Paolo Belardinelli)<br>> 4. Re: interaction within-subject indepsamplesT (Eric Maris)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Wed, 14 Sep 2011 15:41:45 +0200<br>> From: "J?rn M. Horschig" <jm.horschig@donders.ru.nl><br>> To: Email discussion list for the FieldTrip project<br>> <fieldtrip@donders.ru.nl><br>> Subject: [FieldTrip] Critical bug in ft_channelrepair fixed<br>> Message-ID: <4E70AF19.2040003@donders.ru.nl><br>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> <br>> Hey everyone,<br>> <br>> we found a critical bug in ft_channelrepair, which we fixed now. The bug <br>> caused wrong channels to be chosen for interpolation in some situations, <br>> meaning that the timecourse your repaired channel did not make sense. <br>> Please be aware of this, check your reconstructed channels and re-run <br>> your channel reconstruction if you are in doubt with the newest <br>> FieldTrip version!<br>> <br>> For more information, check Google code:<br>> http://code.google.com/p/fieldtrip/source/detail?r=4158<br>> and Bugzilla:<br>> http://bugzilla.fcdonders.nl/show_bug.cgi?id=941<br>> <br>> Best regards,<br>> J?rn<br>> <br>> <br>> -- <br>> J?rn M. Horschig<br>> PhD Student<br>> Donders Institute for Brain, Cognition and Behaviour<br>> Centre for Cognitive Neuroimaging<br>> Radboud University Nijmegen<br>> Neuronal Oscillations Group<br>> <br>> P.O. Box 9101<br>> NL-6500 HB Nijmegen<br>> The Netherlands<br>> <br>> Contact:<br>> E-Mail: jm.horschig@donders.ru.nl<br>> Tel: +31-(0)24-36-68493<br>> Web: http://www.ru.nl/donders<br>> <br>> Visiting address:<br>> Trigon, room 2.30<br>> Kapittelweg 29<br>> NL-6525 EN Nijmegen<br>> The Netherlands<br>> <br>> <br>> <br>> ------------------------------<br>> <br>> Message: 2<br>> Date: Wed, 14 Sep 2011 17:56:38 +0200 (CEST)<br>> From: "Micheli, C." <c.micheli@fcdonders.ru.nl><br>> To: fieldtrip@donders.ru.nl<br>> Subject: [FieldTrip] Fwd: AW: Forward solution using concentric<br>> spheres and BEM models<br>> Message-ID:<br>> <1624476173.1270054.1316015798685.JavaMail.root@draco.zimbra.ru.nl><br>> Content-Type: text/plain; charset=utf-8<br>> <br>> Hi Margit and Juan Pablo<br>> see my answers below.<br>> <br>> ----- "Margit Sch?nherr" <Margit.Schoenherr@uk-erlangen.de> schreef:<br>> <br>> > Van: "Margit Sch?nherr" <Margit.Schoenherr@uk-erlangen.de><br>> > Aan: "c micheli" <c.micheli@fcdonders.ru.nl><br>> > Verzonden: Woensdag 7 september 2011 09:33:53<br>> > Onderwerp: AW: [FieldTrip] Forward solution using concentric spheres and BEM models<br>> ><br>> > Hello Cristiano,<br>> > <br>> > thank you for your email. I have tried the code, but I have 2 problems<br>> > with it.<br>> > 1) When I do it exactly as suggested in the email, I get the following<br>> > error when using ft_prepare_mesh:<br>> > <br>> > bnd = ft_prepare_mesh(cfg, mri_segment);<br>> > ??? Error using ==> ft_prepare_mesh at 159<br>> > unsupported cfg.method and/or input<br>> > <br>> > I think, this is simply a problem concerning the naming of the<br>> > variables. The segmented mri is called 'seg', the labels are assigned<br>> > to 'mri_segment'. I think, this is the wrong input for<br>> > ft_prepare_mesh, because 'mri_segment' does not contain any mri<br>> > information. Putting the labels into a new field 'seg.seg' and calling<br>> > bnd = ft_prepare_mesh(cfg, seg) solves this.<br>> > <br>> <br>> 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:<br>> <br>> mri2 = [];<br>> mri2.anatomy = mri_segment;<br>> mri2.dim = mri.dim;<br>> mri2.transform = mri.transform;<br>> <br>> I patched the correct code at the end of the mail.<br>> <br>> > 2) However, there is still only one surface triangulated. So as I<br>> > wrote in my last email, I still believe that line 25 in<br>> > prepare_mesh_segmentation needs to be commented. What do you mean?<br>> <br>> <br>> 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.<br>> <br>> Try this:<br>> <br>> % download from the FieldTrip ftp site <br>> % (ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip)<br>> <br>> % load the MRI<br>> mri = ft_read_mri('Subject01.mri');<br>> <br>> % segment it<br>> cfg = [];<br>> cfg.output = {'scalp', 'skull', 'brain'};<br>> seg = ft_volumesegment(cfg, mri);<br>> <br>> % volumetric preprocessing<br>> % 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:<br>> <br>> mri_segment{1} = seg.scalp;<br>> mri_segment{2} = imfill(seg.skull,'holes'); % you need the image processing toolbox here!<br>> mri_segment{3} = seg.brain;<br>> <br>> % triangulation (from volumes to surfaces)<br>> % Note: now the volumes are inputted one at a time<br>> mri2 = mri;<br>> cfg=[];<br>> cfg.sourceunits = 'mm';<br>> cfg.mrinuits = 'mm';<br>> cfg.tissue = 1;<br>> cfg.numvertices = 1000;<br>> for i=1:3<br>> mri2.seg = mri_segment{i};<br>> mesh{i} = ft_prepare_mesh(cfg,mri2);<br>> end<br>> <br>> % visualization of the triangulated surfaces<br>> figure,ft_plot_mesh(mesh{1},'edgecolor','none','facecolor','w','facealpha',0.5)<br>> ft_plot_mesh(mesh{2},'edgecolor','none','facecolor','g','facealpha',0.7)<br>> ft_plot_mesh(mesh{3},'edgecolor','none','facecolor','r','facealpha',1)<br>> <br>> <br>> > Thank you.<br>> <br>> Be my guest.<br>> Cheers,<br>> Cristiano<br>> <br>> > <br>> > Best regards,<br>> > Margit<br>> > <br>> > <br>> > ***********************************<br>> > Margit Sch?nherr<br>> > Universit?tsklinikum Erlangen<br>> > Neurologische Klinik<br>> > Epilepsiezentrum (Biomagnetismus)<br>> > Schwabachanlage 6<br>> > 91054 Erlangen<br>> > Telefon: ++49 9131 / 85 36921<br>> > Email: margit.schoenherr@uk-erlangen.de<br>> > ***********************************<br>> > ________________________________________<br>> > Von: fieldtrip-bounces@donders.ru.nl [fieldtrip-bounces@donders.ru.nl]<br>> > im Auftrag von Micheli, C. [c.micheli@fcdonders.ru.nl]<br>> > Gesendet: Montag, 5. September 2011 12:59<br>> > An: Email discussion list for the FieldTrip project<br>> > Betreff: Re: [FieldTrip] Forward solution using concentric spheres <br>> > and BEM models<br>> > <br>> > Dear Juan Pablo and Margit<br>> > <br>> > The function 'ft_prepare_mesh' takes care of triangulating every<br>> > compartment via the cfg.tissue option. This option contains the<br>> > integers which describe a type of tissue, given that the user<br>> > beforehand defined all voxels of the segmented MRI compartment as<br>> > having that particular value.<br>> > As an example, download the sample MRI in FieldTrip ftp location:<br>> > <br>> > ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/Subject01.zip<br>> > Create a folder and unzip these files.<br>> > <br>> > % read in the mri<br>> > mri = ft_read_mri('Subject01.mri');<br>> > <br>> > % segment it<br>> > cfg = [];<br>> > cfg.output = {'scalp', 'skull', 'brain'};<br>> > seg = ft_volumesegment(cfg, mri);<br>> > <br>> > % assign a label<br>> > scalp = (seg.scalp) & ~(seg.skull | seg.brain);<br>> > skull = 2*(seg.skull);<br>> > brain = 3*(seg.brain);<br>> > mri_segment = scalp + skull + brain;<br>> > <br>> > % build the meshes<br>> > cfg = [];<br>> > cfg.method = 'segmentation';<br>> > cfg.tissue = [1 2 3]; % scalp = 1; skull = 2; brain = 3;<br>> > cfg.numvertices = [2000 1000 800];<br>> > cfg.sourceunits = 'mm';<br>> > cfg.mriunits = 'mm';<br>> > bnd = ft_prepare_mesh(cfg, mri_segment);<br>> > <br>> > If any of the tissues has a different value from cfg.tissues this<br>> > won't be triangulated. To check for this use ft_sourceplot in the<br>> > interactive mode. By clicking around you can see the tissue's value in<br>> > the command window:<br>> > <br>> > % view the labelled segmentations<br>> > mri2 = mri;<br>> > mri2.seg = mri_segment;<br>> > cfg=[];<br>> > cfg.interactive = 'yes';<br>> > cfg.funparameter = 'seg';<br>> > ft_sourceplot(cfg,mri2);<br>> > <br>> > About the concentric spheres:<br>> > both ways to derive a concentric spheres model are correct. In one<br>> > case you directly build the vol structure and you assume you know the<br>> > radiuses of your spheres. In the other case you allow the<br>> > ft_prepare_concentricspheres function to build the spheres starting<br>> > from realistic geometrical boundaries.<br>> > The second approach is my favorite because the ft_prepare function<br>> > contains a function that fits a sphere to each boundary and I don't<br>> > have to do it myself.<br>> > The first approach (directly force the radiuses in your vol structure)<br>> > is preferable if you derive the information from other software (e.g.<br>> > CTF's MRIView) or if you fit the sphere yourself.<br>> > <br>> > @Pablo<br>> > If the sphere is fitted inside the brain it is correct. You do not<br>> > want the sphere to include other tissues, because your assumption for<br>> > the construction of the forward model is that the tissue inside the<br>> > sphere is homogeneous.<br>> > For a more realistic model (encompassing the whole brain volume) I<br>> > would rather use a BEM model.<br>> > <br>> > I hope this helps,<br>> > Cristiano<br>> <br>> <br>> <br>> ------------------------------<br>> <br>> Message: 3<br>> Date: Wed, 14 Sep 2011 18:18:36 +0200<br>> From: Paolo Belardinelli <paolo.belardinelli@med.uni-tuebingen.de><br>> To: fieldtrip@donders.ru.nl<br>> Subject: [FieldTrip] cortical time-course reconstruction<br>> Message-ID: <4E70D3DC.4060403@med.uni-tuebingen.de><br>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> <br>> Hi Robert.<br>> We have some nice coherence maps with peaks in M1 for a finger tapping <br>> task. We were wondering how to properly reconstruct the power <br>> time-course in the M1 area in order to use it as a further reference<br>> signal.<br>> <br>> -Is the code necessary for the approach described in (Schoffelen et al., <br>> NeuroImage 2008) already implemented in ft (we observed in the code that <br>> it is possible in ft_sourceanalysis.m to give a location for a<br>> reference dipole but we found no documentation)?<br>> <br>> -Is the only reliable solution for reconstructing a time-course to <br>> project the activity in the dominant direction? We have the eigenvalues <br>> of the first dipole which are normally 3 to 6 times larger<br>> than the ones of the second. We are not sure this is enough to neglect <br>> the second component.<br>> <br>> - One last technical question: in the mailing list it is said that the <br>> orientation of the dipole is saved in source.avg.ori but it doesn't seem <br>> like that to us. Maybe we are doing something wrong.<br>> <br>> Best regards and thank you for your work,<br>> <br>> Paolo and Erick<br>> <br>> <br>> ------------------------------<br>> <br>> Message: 4<br>> Date: Thu, 15 Sep 2011 10:10:36 +0200<br>> From: "Eric Maris" <e.maris@donders.ru.nl><br>> To: "'Email discussion list for the FieldTrip project'"<br>> <fieldtrip@donders.ru.nl><br>> Subject: Re: [FieldTrip] interaction within-subject indepsamplesT<br>> Message-ID: <008d01cc737e$f6192ba0$e24b82e0$@maris@donders.ru.nl><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> Dear Kathrin,<br>> <br>> > I need your advice on how to correctly test the interaction effects in a<br>> 2x2<br>> > within-subject design with cluster-based randomization tests. I have two<br>> > factors A and B with the levels a1/a2 and b1/b2. In addition, the number<br>> of<br>> > trials in A are about twice as much as in B.<br>> > <br>> > The procedure would be totally clear in a between-subject design (as in a<br>> > previous post on the list:<br>> > http://mailman.science.ru.nl/pipermail/fieldtrip/2011-January/003447.html)<br>> <br>> This post is about a WITHIN-subjects design.<br>> <br>> > because I could easily compute the differences of the factor levels<br>> > A_diff=a1-a2 and B_diff=b1-b2 and then run ft_freqstatistics on the<br>> > differences. However, since I have to run the statistics across trials and<br>> not<br>> > subjects I have independent samples and not dependent samples. <br>> <br>> So, you have a between-trials design.<br>> <br>> If it is<br>> > possible at all, how can I calculate the differences A_diff and B_diff<br>> across<br>> > trials? Is it a problem that the number of trials are not equal?<br>> <br>> This is not possible. Permutation tests cannot be used for testing<br>> interactions in a multi-factorial between-subjects/trials design. Michael<br>> Wibral has a post in which he refers to a nice statistics paper on the<br>> issue.<br>> <br>> A proxy that is possible (but not statistically sound) is to perform two<br>> statistical tests of the first factor, once at the first level of second<br>> factor and once at the second level.<br>> <br>> <br>> Best,<br>> <br>> Eric Maris<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> > <br>> > Any help is appreciated!<br>> > <br>> > Best,<br>> > Kathrin<br>> > <br>> > _____________________________________<br>> > Kathrin M?sch<br>> > <br>> > Dept. of Neurophysiology and Pathophysiology<br>> > University Medical Center Hamburg-Eppendorf<br>> > Martinistr. 52<br>> > 20246 Hamburg<br>> > Germany<br>> > Phone: +49-40-7410-54680<br>> > Fax: +49-40-7410-57752<br>> > E-Mail: k.muesch@uke.uni-hamburg.de<br>> > _____________________________________<br>> > <br>> > <br>> > --<br>> > Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und<br>> > Genossenschaftsregister sowie das Unternehmensregister (EHUG):<br>> > <br>> > Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen<br>> > Rechts; Gerichtsstand: Hamburg<br>> > <br>> > Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender), Dr.<br>> Alexander<br>> > Kirstein, Joachim Pr?l?, Prof. Dr. Dr. Uwe Koch-Gromus<br>> > <br>> > <br>> > _______________________________________________<br>> > fieldtrip mailing list<br>> > fieldtrip@donders.ru.nl<br>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> <br>> <br>> <br>> <br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> fieldtrip mailing list<br>> fieldtrip@donders.ru.nl<br>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> <br>> End of fieldtrip Digest, Vol 10, Issue 18<br>> *****************************************<br></div> </div></body>
</html>