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<body class='hmmessage'><div dir='ltr'><br>Dear fieldtriper,<br><br>How can I plot the ROC curve if I want to compare different inverse problems?<br>if dipole is active or not.<br>what should be the threshold?<br>I have the simulated and estimated data on the mesh as an input<br><br>thank you<br><br><br><div>> From: fieldtrip-request@science.ru.nl<br>> Subject: fieldtrip Digest, Vol 67, Issue 12<br>> To: fieldtrip@science.ru.nl<br>> Date: Mon, 13 Jun 2016 11:10:44 +0200<br>> <br>> Send fieldtrip mailing list submissions to<br>> fieldtrip@science.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@science.ru.nl<br>> <br>> You can reach the person managing the list at<br>> fieldtrip-owner@science.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. Re: help diagnosing issues with source analysis (pathological<br>> brain) (Vitoria Piai)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Mon, 13 Jun 2016 11:02:11 +0200<br>> From: Vitoria Piai <v.piai.research@gmail.com><br>> To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>> Subject: Re: [FieldTrip] help diagnosing issues with source analysis<br>> (pathological brain)<br>> Message-ID:<br>> <CADAXq1R_6ZCan=fXW2Vg4hbixeqdMKW0auOr1vMLvk6CBSA5Uw@mail.gmail.com><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Hi Cris,<br>> <br>> that makes sense, except that the .mri file I'm getting from the hospital<br>> should already contain the right fiducial coordinates (or so I was told by<br>> the MEG technician). Maybe the issue is that FieldTrip is not getting these<br>> coordinates right from the .mri file if I don't run it through<br>> ft_volumerealign first.<br>> Any thoughts anyone?<br>> <br>> Thanks again<br>> <br>> On 12 June 2016 at 13:55, Cristiano Micheli <michelic72@gmail.com> wrote:<br>> <br>> > Dear Vitoria<br>> ><br>> > I had the same problem when I tried to coregister functional and<br>> > anatomical data without transitioning through a head-referenced coordinates<br>> > system.<br>> > I solved the problem by using ft_volumerealign and selecting comparable<br>> > anatomical fiducials for different subjects (nasion, left, right,..) BEFORE<br>> > volume normalization.<br>> ><br>> > Maybe a hint towards the solution?<br>> ><br>> > Cheers<br>> > Cris<br>> ><br>> ><br>> > On Sat, Jun 11, 2016 at 8:50 PM, Vit?ria Piai <v.piai.research@gmail.com><br>> > wrote:<br>> ><br>> >> Hi everyone,<br>> >><br>> >> I was hoping someone could help me figure out where my source analysis is<br>> >> going wrong.<br>> >> I have data on brain tumour patients (MRIs are from prior to tumour<br>> >> resection). From the hospital (using CTF), I receive .mri files that<br>> >> already have fiducial points saved as far as I was told. I then reslice and<br>> >> segment the .mri file, after reading it with ft_read_mri<br>> >> mri_reslice = ft_volumereslice([], mri);<br>> >> segmentedmri = ft_volumesegment([], mri_reslice);<br>> >> This seems to be working:<br>> >><br>> >><br>> >> Plotting headmodel and sensors, it looks like they are aligned:<br>> >><br>> >> If I compute the source model with MNI-warping (non-linear<br>> >> transformation), I get something that doesn't seem right. I don't know if<br>> >> this is because these are not normal brains to start with:<br>> >><br>> >> With linear transformation, things look better:<br>> >><br>> >> One of my questions is what the consequences are of using linear<br>> >> transformation for the MNI warping given the pathological nature of these<br>> >> brains.<br>> >><br>> >> Then, the next issue is this result when projecting the source to the<br>> >> surface:<br>> >><br>> >> This happens regardless of whether I use the MNI-warped grid interpolated<br>> >> to the MNI template, or the patient's individual grid skipping the MNI<br>> >> normalisation step, interpolated to the patient's own T1.<br>> >> But if I plot with 'ortho' method, then I see that the MNI-warped and<br>> >> interpolated source data is misaligned, but the patient-native space one<br>> >> isn't.<br>> >><br>> >><br>> >> I can't make sense of this anymore; I've been trying all kinds of things<br>> >> that don't work, so I was wondering whether anyone has an idea of what<br>> >> could be going on by looking at these figures. Is it an error already at<br>> >> the level of alignment of the fiducials? Or is it due to the MNI-warping?<br>> >> Or a combination of issues?<br>> >><br>> >> Thanks very much for any kind of help!<br>> >> Vitoria<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>> > fieldtrip mailing list<br>> > fieldtrip@donders.ru.nl<br>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> ><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment.html><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: jidhfdhd.png<br>> Type: image/png<br>> Size: 4722 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment.png><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: ebfighdf.png<br>> Type: image/png<br>> Size: 9956 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment-0001.png><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: bfejiccb.png<br>> Type: image/png<br>> Size: 75399 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment-0002.png><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: dffeehgc.png<br>> Type: image/png<br>> Size: 274137 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment-0003.png><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: dcigdbdi.png<br>> Type: image/png<br>> Size: 150070 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment-0004.png><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: ehffjdea.png<br>> Type: image/png<br>> Size: 10561 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160613/da0b30ab/attachment-0005.png><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 67, Issue 12<br>> *****************************************<br></div> </div></body>
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