Hi Gustavo,
As stated below, MaxFilter 2.0 sphere fitting does some iterations and
drops worst fitting points one by one. Still, if there are several points
that were digitized on the face or below ears, the fit may produce a sphere
which seems to extend outside the nearest sensor.
Have you tried to set the origin manually, e,g, as:
-frame head -origin 0 0 45 (or via the GUI oirigin dialog)?
Best regards, Jukka Nenonen
Gustavo Sudre wrote:
> Hello,
>
> I get the same error messages about the fitted sphere extending outside of
> the sensors for 2 of my subjects. I was wondering if I can get some help
> because I still can't find an answer based on the previous e-mails on the
> subject.
>
> 1) What points are used to fit the sphere? Is the sphere fitted using only
> the HPI coil measurements and the cardinal points? Are the additional points
> we digitize after the HPI coils used at all? If yes, can we not use them?
>
> 2) Based on the e-mail below, I think I have good transformation numbers for
> these two files (two different subjects):
>
> 222 = transform device -> head
> 0.995393 -0.075930 0.058547
> 0.073332 0.996278 0.045314
> -0.061770 -0.040812 0.997256
> 2.820464 1.565292 45.885883 (inv. -0.087904 0.527397 -45.996021)
>
> 222 = transform device -> head
> 0.995131 -0.025254 -0.095275
> 0.021956 0.999129 -0.035499
> 0.096088 0.033235 0.994818
> 2.770155 -9.265076 44.514574 (inv. -6.830577 7.847536 -44.348873)
>
> Still, I get the error running Maxfilter. Are these numbers OK? If yes, what
> are my other options to still run Maxfilter in these subjects and not get
> the error?
>
> Thanks,
>
> Gus
>
> On Tue, 18 Mar 2008 11:28:34 +0200, Jukka Nenonen <[log in to unmask]> wrote:
>
>> Hello Max,
>>
>> I presume that the coordinate transformation in the input file has a problem
>> if you still get the message "sphere fitted to isotrak extends outside
>> of the sensors!"
>>
>> You can check it by typing /neuro/bin/util/show_fiff -vt222 input_file.fif
>>
>> The output looks like
>> 222 = transform device -> head
>> 0.991323 0.122468 0.047753
>> -0.117611 0.988611 -0.093888
>> -0.058708 0.087457 0.994436
>> -3.402352 -11.903301 61.529018 (inv. 5.585114 6.803262 -62.141802)
>>
>> In normal adult cases, the rotation (first 3x3 numbers) should be fairly
>> close
>> to a unit 3x3 matrix, and the translation (first 3 numbers on last row)
>> approximately near to 0 0 40 (in the above example, x = -3.4 mm, y =
>> -11.9 mm,
>> z = 61.5 mm).
>>
>> If HPI fit failed during acquisition, the rotation may show coordinate
>> inversions
>> or swaps, the translation x or y may be larger than 20-30 mm from the
>> origin,
>> or the translation z may become larger.
>>
>> In such cases you may try to redo hpi fitting by applying (on a HP-UX
>> machine)
>> /neuro/dacq/bin/hpifit -file input_file.fif
>>
>> If the fit succeeds, you will get an output file hpi_coils.fif.
>> You can check the new transformation: /neuro/bin/util/show_fiff -vt222
>> hpi_coils.fif
>> If it looks better than the old one, just replace it:
>> /neuro/bin/util/copy_trans_fiff -f hpi_coils.fif input_file.fif
>>
>> If not, there are unfortunately no ways to improve the bad head position
>> determination...
>>
>> Best regards, Jukka
>>
>> Max Garagnani wrote:
>>> Hello Jukka,
>>>
>>>> 1) message "sphere fitted to isotrak extends outside of the sensors!"
>>>> usually indicates that the initial head position determined during the
>>>> recording may have a problem, and the resulting transformation may
>>>> put the head in a wrong position. Thus, sphere fit to isotrak may be OK,
>>>> but the radius extending outside of sensors indicates that also the
>>>> head 'pierces' through the dewar bottom.
>>>>
>>> In these cases I provided the sphere origin by specifying
>>>
>>> -frame head
>>> -origin 0 0 45
>>>
>>> Are there any alternatives that I should be aware of?
>>> (Sorry if this point was discussed before but I don't seem to have any
>>> records of it..)
>>>
>>> Many thanks,
>>> Max
>>>
>>>> 2) maxfilter origin fit does some iterations, on each roundthe point
>>>> furthest
>>>> from the sphere is dropped. Thus, points on the nose and gace are
>>>> typically
>>>> omitted, and therefore the result may deviate from 'fit_sphere_to_points'.
>>>>
>>>> Best regards, Jukka
>>>>
>>>> Rik Henson wrote:
>>>>> Dear Neuromeg list.
>>>>>
>>>>> We have two questions about the centre of the spherical expansions in
>>>>> Maxfilter:
>>>>>
>>>>>
>>>>> 1. Occasionally MaxFilter bails out with the error:
>>>>>
>>>>> "ERROR: sphere fitted to isotrak extends outside of the sensors! (r0
>>>>> = (14 3 36) mm, rad = 11 cm)"
>>>>>
>>>>> However, when we run the Neuromag utiltity:
>>>>>
>>>>> /neuro/bin/util/fit_sphere_to_points
>>>>>
>>>>> (or our own sphere-fitting code), we seem to get sensible fits, eg
>>>>> Centre = [1.347 7.374 42.871] (Radius=98.608).
>>>>>
>>>>> The MaxFilter manual implies that the MaxFilter sphere-fitting is more
>>>>> sophisticated/robust than simple methods, so should we not trust the
>>>>> "fit_sphere_to_points" results above? Or is the error actually with
>>>>> MaxFilter? If the latter, should we just "bypass" this MaxFilter bug by
>>>>> passing "-frame head -origin 1.347 7.374 42.871" (in this example)?
>>>>>
>>>>>
>>>>> 2. Related to question 1 above, we have noticed that the sphere fit by
>>>>> MaxFilter and the sphere fit by fit_sphere_to_points tend to differ,
>>>>> sometimes vastly so, with the origins differing by 10mm in one or
>>>>> another dimension. (When we independently fit a sphere using SPM
>>>>> functions in matlab, the origin is consistently very close (within 1 mm)
>>>>> to the fit_sphere_to_points result). Here are some examples:
>>>>>
>>>>> Subject 1:
>>>>> -0.7770 5.3440 35.9980 fit_sphere_to_points origin
>>>>> -0.9496 5.1591 36.2188 SPM origin
>>>>> 2.2 6.2 38.6 MaxFilter Inside Origin
>>>>>
>>>>> Subject 2:
>>>>> -9.5500 0.8510 39.8750
>>>>> -9.5891 1.4581 39.3087
>>>>> -10.1 5.5 36.9
>>>>>
>>>>> Subject 3:
>>>>> -0.6850 11.9050 51.6610
>>>>> -0.5834 11.6485 51.4186
>>>>> -10.4 12.5 46.6
>>>>>
>>>>> So should we ALWAYS use independent sphere fitting, rather than relying
>>>>> on MaxFilter? (we expect not, but just wanted to get your attention! ;-)
>>>>> Or are we misunderstanding what MaxFilter actually does?
>>>>>
>>>>> Many thanks
>>>>> Rik Henson, Jason Taylor, Danny Mitchell
>>>>>
>>>> --
>>>>
>>>> ================================
>>>> Dr. Jukka Nenonen
>>>> Manager, Method development
>>>> Elekta Neuromag Oy
>>>> Street address: Siltasaarenkatu 18-20A, Helsinki, Finland
>>>> Mailing address: P.O. Box 68, FIN-00511 HELSINKI, Finland
>>>> Tel: +358 9 756 240 85 (office), +358 400 249 557 (mobile),
>>>> +358 9 756 240 11 (fax), +358 9 756 2400 (operator)
>>>> E-mail: [log in to unmask]
>>>> http://www.neuromag.com
>>>>
>>>
>>> ------------------
>>> Max Garagnani, PhD.
>>> MRC - Cognition & Brain Sciences Unit
>>> 15 Chaucer Rd.
>>> Cambridge - CB2 7EF
>>> UK
>>> Tel. +44 1223 273730 (direct)
>>> Fax: +44 1223 359062
>>>
>>
>> --
>>
>> ================================
>> Dr. Jukka Nenonen
>> Manager, Method development
>> Elekta Neuromag Oy
>> Street address: Siltasaarenkatu 18-20A, Helsinki, Finland
>> Mailing address: P.O. Box 68, FIN-00511 HELSINKI, Finland
>> Tel: +358 9 756 240 85 (office), +358 400 249 557 (mobile),
>> +358 9 756 240 11 (fax), +358 9 756 2400 (operator)
>> E-mail: [log in to unmask]
>> http://www.neuromag.com
--
================================
Dr. Jukka Nenonen
Manager, Method development
Elekta Neuromag Oy
Street address: Siltasaarenkatu 18-20A, Helsinki, Finland
Mailing address: P.O. Box 68, FIN-00511 HELSINKI, Finland
Tel: +358 9 756 240 85 (office), +358 400 249 557 (mobile),
+358 9 756 240 11 (fax), +358 9 756 2400 (operator)
E-mail: [log in to unmask]
http://www.neuromag.com
|
