[FieldTrip] typo in ft_sourceplot ?

Eelke Spaak eelke.spaak at donders.ru.nl
Thu Sep 29 09:49:03 CEST 2011 

Hi Sebastien,

That indeed looks like a typo. It was, however, fixed in revision 3744
(see http://code.google.com/p/fieldtrip/source/diff?spec=svn4313&r=3744&format=side&path=/trunk/ft_sourceplot.m&old_path=/trunk/ft_sourceplot.m&old=3674),
on June 29, so if you update your FT version it should disappear.

Best,
Eelke

2011/9/29  <miellet at psy.gla.ac.uk>:
> Hello,
> I think there is a typo in ft_sourceplot at line 205.
>
> cfg.funcolrolim = ft_getopt(cfg,'funcolorlim', 'auto');
>
> Sorry if it's not the case or if this typo has already been corrected (I am
> not sure that I'm using the exact last version, I'm using fieldtrip on
> Glasgow grid).
>
> Sebastien
>
> ----------------------------------------------
> Dr. Sébastien Miellet, Lecturer
>
> Department of Psychology
> University of Fribourg
> Faucigny 2
> 1700 Fribourg
> Switzerland
>
> tel: +41 (0)77 489 6468
> ----------------------------------------------
>
>
>
> Quoting Kanal Eliezer <ekanal at cmu.edu>:
>
>> Thanks for the clarification. The problem seemed to be that the function
>> was ignoring the input I was providing to `cfg.coordsys`; hopefully the fix
>> you described below will address that. Note that it should also recognize
>> coordsys of `ras`, `als`, and whatever else can be outputted from the
>> interactive alignment process.
>>
>> Thanks,
>> Elli
>>
>>
>> On Sep 28, 2011, at 6:15 AM, jan-mathijs schoffelen wrote:
>>
>>> Dear Elli,
>>>
>>> Your proposed fix is equivalent to swapping the first 2 columns in your
>>> tmp.bnd.pnt matrix, i.e. swapping the y and x axis. To me this seems that
>>> you can also alleviate this by specifying the proper cfg.coordsys prior to
>>> your call to ft_volumerealign. The idea is the following: by specifying the
>>> location of nasion/lpa/rpa a transformation matrix can be computed. This
>>> transformation matrix will assign the X,Y, and Z axes of the coordinate
>>> system. According to different conventions, the X-axis either goes anterior
>>> (leading to a 'ALS'-like coordinate system, e.g. used in the CTF-systems and
>>> 4D neuroimaging systems), or the X-axis goes to the right (leading to a
>>> 'RAS'-like coordinate system, e.g. used in the Neuromag system). This
>>> specification will have an effect on the transformation matrix only at the
>>> level of ft_volumerealign. Specifying the coordinate system later on
>>> (through ft_estimate_coordsys) only adds the field coordsys to the
>>> mri-structure, without affecting the tran!
>>> sformation matrix. Adding the coordsys-field just gives an interpretation
>>> to the coordinate system (and thus to the transformation matrix). To
>>> summarize, I expect that your expectation of the coordinate system in which
>>> the sensors are expressed, don't coincide with the coordinate system in
>>> which (according to the transformation matrix in combination with the
>>> coordsys) the MRI is expressed. See for the different coordinate systems
>>> definitions:
>>>
>>>
>>> http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
>>>
>>> For your call to ft_volumerealign you need to specify cfg.coordsys = 'one
>>> of the meg-systems'. At the moment this at least works for 'ctf' and 'itab'
>>> as strings. These reflect the two major conventions, i.e. X-axis anterior,
>>> or X-axis to the right. To de-confuse it a bit, I will add the other
>>> MEG-systems also as supported strings. For the time being you can look up in
>>> the table in the linked web-page which one you need. I suspect it is 'itab',
>>> because the default is ctf-convention.
>>>
>>> Best wishes,
>>>
>>> Jan-Mathijs
>>>
>>>
>>> On Sep 27, 2011, at 9:23 PM, Kanal Eliezer wrote:
>>>
>>>> Unfortunately, it looks like redoing the alignment didn't help. I re-ran
>>>> `ft_volumerealign` in interactive, and it did add the correct field to the
>>>> output structure, but the brain is still facing the wrong way.
>>>>
>>>> Is it possible that FieldTrip is ignoring this field when plotting? The
>>>> plotting functions are pretty complex, and are even more obfuscated than
>>>> usual due to all the transforms used in aligning everything, so I don't want
>>>> to try to troubleshoot this one myself since I'd almost certainly find the
>>>> wrong thing.
>>>>
>>>> In the end, I fixed the problem by simply taking vol.bnd.pnt and
>>>> vol.bnd.tri, applying cart2sph, adding pi/2, and applying sph2cart. However,
>>>> this is a workaround rather than a direct fix. Still, if anyone else has
>>>> this problem, I'm attaching the code below... it seems to have worked.
>>>>
>>>> Elli
>>>>
>>>> ~~~
>>>>
>>>> tmp = vol;
>>>>
>>>> % transform to spherical coords
>>>> [tmp.bnd.pnt(:,1) tmp.bnd.pnt(:,2) tmp.bnd.pnt(:,3)] ...
>>>> = cart2sph( ...
>>>>  tmp.bnd.pnt(:,1), ...
>>>>  tmp.bnd.pnt(:,2), ...
>>>>  tmp.bnd.pnt(:,3) );
>>>> [tmp.bnd.tri(:,1) tmp.bnd.tri(:,2) tmp.bnd.tri(:,3)] ...
>>>> = cart2sph( ...
>>>>  tmp.bnd.tri(:,1), ...
>>>>  tmp.bnd.tri(:,2), ...
>>>>  tmp.bnd.tri(:,3) );
>>>>
>>>> % rotate as necessary
>>>> tmp.bnd.pnt(:,1) = tmp.bnd.pnt(:,1) + pi()/2;
>>>> tmp.bnd.tri(:,1) = tmp.bnd.tri(:,1) + pi()/2;
>>>>
>>>> % transform back to cartesian
>>>> [tmp.bnd.pnt(:,1) tmp.bnd.pnt(:,2) tmp.bnd.pnt(:,3)] ...
>>>> = sph2cart( ...
>>>>  tmp.bnd.pnt(:,1), ...
>>>>  tmp.bnd.pnt(:,2), ...
>>>>  tmp.bnd.pnt(:,3) );
>>>> [tmp.bnd.tri(:,1) tmp.bnd.tri(:,2) tmp.bnd.tri(:,3)] ...
>>>> = cart2sph( ...
>>>>  tmp.bnd.tri(:,1), ...
>>>>  tmp.bnd.tri(:,2), ...
>>>>  tmp.bnd.tri(:,3) );
>>>>
>>>> vol = tmp;
>>>>
>>>>
>>>>
>>>> On Sep 27, 2011, at 2:14 PM, Belluscio, Beth (NIH/NINDS) [E] wrote:
>>>>
>>>>> OK, Elli, I think you have the source of your problem - I'm glad that
>>>>> helped.  To redefine the alignment, you can use ft_volumerealign in
>>>>> interactive mode.  Be sure to read the instructions that come up in your
>>>>> matlab workspace simultaneously with the image so that you mark your volume
>>>>> as you wish (I found this a little confusing initially). As you mark your
>>>>> landmarks (eg l, r, n or a,p,s) you should also see the coordinates written
>>>>> out in the workspace.  This should confirm that your realignment is taking
>>>>> place.  After you have done this, you can check it again with the
>>>>> ft_determine_coordsys to make sure.
>>>>> Beth.
>>>>>
>>>>> -----Original Message-----
>>>>> From: Kanal Eliezer [mailto:ekanal at cmu.edu]
>>>>> Sent: Tuesday, September 27, 2011 1:41 PM
>>>>> To: Email discussion list for the FieldTrip project
>>>>> Subject: Re: [FieldTrip] Fwd: source localization difficulties
>>>>>
>>>>> Hello Beth -
>>>>>
>>>>> I actually hadn't tried using `ft_determine_coordsys` on the
>>>>> `ft_prepare_headmodel` output, and it turns out that it's incorrect; it has
>>>>> the anterior along the Y axis, when it should be along the Y. However,
>>>>> changing it doesn't seem to do anything! I.e., using `ft_determine_coordsys`
>>>>> to redefine the alignment, and then re-running `ft_plot_vol` - or even
>>>>> re-running `ft_determine_coordsys` on the new structure - doesn't seem to
>>>>> change anything! The field `coordsys` has been added (and now reads "ras"),
>>>>> but this doesn't seem to affect anything. Is this a bug? Do I need to apply
>>>>> a transformation function to make the new coordsys take effect? Thanks -
>>>>>
>>>>> Elli
>>>>>
>>>>>
>>>>> On Sep 27, 2011, at 9:35 AM, Belluscio, Beth (NIH/NINDS) [E] wrote:
>>>>>
>>>>>> Elli-
>>>>>> I had similar problems at one point.  You may already have tried this,
>>>>>> but for what it's worth, here are a couple of suggestions:  you can check
>>>>>> each type of volume or array with ft_determine_coordsys.  This will give you
>>>>>> an image with the x,y,z coordinates superimposed so that you can check
>>>>>> directly what type of coordinate system is attached to the volume.
>>>>>>  Secondly, when using ft_volumerealign, interactive, make sure you are not
>>>>>> incorrectly identifying right and left.  Sometimes in the conversion of
>>>>>> DICOM to another system, left and right are switched.
>>>>>> Hope this helps.
>>>>>> Beth.
>>>>>>
>>>>>>
>>>>>> Beth Belluscio MD-PhD
>>>>>> Clinical Fellow
>>>>>> Human Motor Control Section
>>>>>> NINDS, NIH
>>>>>> 301-402-3495
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Kanal Eliezer [mailto:ekanal at cmu.edu]
>>>>>> Sent: Tuesday, September 27, 2011 8:50 AM
>>>>>> To: Email discussion list for the FieldTrip project
>>>>>> Subject: Re: [FieldTrip] Fwd: source localization difficulties
>>>>>>
>>>>>> Thanks for forwarding the message to the list.
>>>>>>
>>>>>> Just to clarify, the reconstruction worked fine; the brain looks good.
>>>>>> The problem is that it's facing the wrong way; in the, the helmet is facing
>>>>>> left/back, and the brain is turned 90 degrees to the right (facing forward
>>>>>> in the image). If anyone knows how to either correct it as it is or how to
>>>>>> re-run the analysis to prevent it from happening I'd be most appreciative.
>>>>>> If any more details are needed, please just ask! Thanks -
>>>>>>
>>>>>> Elli
>>>>>>
>>>>>>
>>>>>> --------------------
>>>>>> Eliezer Kanal, Ph.D.
>>>>>> Postdoctoral Fellow
>>>>>> Center for the Neural Basis of Cognition
>>>>>> Carnegie Mellon University
>>>>>> 4400 Fifth Ave, Suite 110A
>>>>>> Pittsburgh PA 15213
>>>>>> P: 412-268-4115
>>>>>> F: 412-268-5060
>>>>>>
>>>>>>
>>>>>> On Sep 27, 2011, at 2:51 AM, jan-mathijs schoffelen wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Begin forwarded message:
>>>>>>>
>>>>>>>> From: Kanal Eliezer <ekanal at cmu.edu>
>>>>>>>> Date: September 26, 2011 9:45:00 PM GMT+02:00
>>>>>>>> To: jan-mathijs schoffelen <jan.schoffelen at DONDERS.RU.NL>
>>>>>>>> Subject: Re: [FieldTrip] source localization difficulties
>>>>>>>>
>>>>>>>> Hello Dr Schoffelen -
>>>>>>>>
>>>>>>>> Thanks for the advice. The way I got this part to work was to use
>>>>>>>> SPM to convert my DICOM files to NIfTI ('*.img') and use `ft_read_mri` on
>>>>>>>> that file, instead of reading the DICOM files directly. Using this method, I
>>>>>>>> was able to reconstruct well.
>>>>>>>>
>>>>>>>> However, it seems that there's another related issue. When running
>>>>>>>> the
>>>>>>>>        ft_plot_sens(data_preprocessed.hdr.grad);
>>>>>>>>        hold on;
>>>>>>>>        ft_plot_vol(vol);
>>>>>>>> check, I got the attached image. Do you have any idea why it's doing
>>>>>>>> that? Please let me know if I can provide any more details which could help
>>>>>>>> troubleshoot.
>>>>>>>>
>>>>>>>> In case it's relevant, I did notice that the output structure of the
>>>>>>>> `ft_volumerealign` function (run with method='interactive') contained the
>>>>>>>> following field:
>>>>>>>>        mri_realign.coordsys = 'ctf';
>>>>>>>> That can't be correct. I'm pretty sure it should be 'nifti'.
>>>>>>>> However, I tried re-running `ft_volumesegment` after manually changing that
>>>>>>>> value, and the figure looks the same.
>>>>>>>>
>>>>>>>> Any help would be most appreciated! Thanks -
>>>>>>>>
>>>>>>>> Elli
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> <check.jpg>
>>>>>>>> On Sep 24, 2011, at 3:09 AM, jan-mathijs schoffelen wrote:
>>>>>>>>
>>>>>>>>> Hi Elli,
>>>>>>>>>
>>>>>>>>>> Hello Dr. Schoffelen -
>>>>>>>>>>
>>>>>>>>>> I sent a response to the below email, but I think it got lost in
>>>>>>>>>> the shuffle. I tried what you suggested, and I got the image attached below
>>>>>>>>>> (matlab figure).
>>>>>>>>>>
>>>>>>>>>> Two questions: (1) What could be the cause of this poor alignment?
>>>>>>>>>> This isn't right/left flipping, as the nose also looks to be in the back.
>>>>>>>>>> (2) Do you have any idea why the reconstruction of the MRI looks so poor?
>>>>>>>>>> FreeSurfer reconstructions looked much "healthier".
>>>>>>>>>
>>>>>>>>> To combine both questions into 1 answer, I wouldn't say that the
>>>>>>>>> alignment is bad, it's the segmentation that seems to be completely off.
>>>>>>>>> This usually happens, when FieldTrip assigns the wrong coordinate system to
>>>>>>>>> the MRI. For the segmentation to work, SPM needs an approximate
>>>>>>>>> coregistration of the MRI in MNI-space. FieldTrip tries to achieve this, and
>>>>>>>>> needs the tag mri.coordsys for this. This tag is usually set after a pass
>>>>>>>>> through ft_volumerealign, where you can specify a cfg.coordsys (I just
>>>>>>>>> noticed this as an undocumented option: perhaps that needs to change). By
>>>>>>>>> default, this tag is set to 'ctf', see
>>>>>>>>> http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
>>>>>>>>> for a definition of the coordinate systems. If the coordinate system in
>>>>>>>>> which the sensors are defined differs from the ctf coordinate system,
>>>>>>>>> causing a bad initial alignmnent prior to the segmentation and a worthless
>>>>>>>>> segmentation.
>>>>>>>>>
>>>>>>>>>> You mentioned below that I could simply load the up freesurfer
>>>>>>>>>> files and go from there. All the *.mgz files I've found from freesurfer
>>>>>>>>>> processing are simply volumetric MRI files. The surface files are stored in
>>>>>>>>>> a variety of formats with seemingly no file extension. Is there a way to
>>>>>>>>>> load FreeSurfer surfaces, or should I be using `ft_prepare_headmodel` to do
>>>>>>>>>> that?
>>>>>>>>>
>>>>>>>>> The ft_read_headshape function should be able to read freesurfer
>>>>>>>>> triangle and quadrangle files. Use it as ft_read_headshape(filename,
>>>>>>>>> 'fileformat', 'freesurfer-triangle_binary');
>>>>>>>>>
>>>>>>>>>> Thanks -
>>>>>>>>>>
>>>>>>>>>> Eliezer Kanal
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Jan-Mathijs
>>>>>>>
>>>>>>> Jan-Mathijs Schoffelen, MD PhD
>>>>>>> Donders Institute for Brain, Cognition and Behaviour,
>>>>>>> Centre for Cognitive Neuroimaging,
>>>>>>> Radboud University Nijmegen, The Netherlands
>>>>>>> J.Schoffelen at donders.ru.nl
>>>>>>> Telephone: +31-24-3614793
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> fieldtrip mailing list
>>>>>>> fieldtrip at donders.ru.nl
>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>
>>>>>>
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>>>>>
>>>>>
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>>>>
>>>>
>>>> _______________________________________________
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>>>
>>> Jan-Mathijs Schoffelen, MD PhD
>>> Donders Institute for Brain, Cognition and Behaviour,
>>> Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl
>>> Telephone: +31-24-3614793
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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