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
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 =
z = 61.5 mm).
If HPI fit failed during acquisition, the rotation may show coordinate
or swaps, the translation x or y may be larger than 20-30 mm from the
or the translation z may become larger.
In such cases you may try to redo hpi fitting by applying (on a HP-UX
/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
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
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,
>> 2) maxfilter origin fit does some iterations, on each roundthe point
>> from the sphere is dropped. Thus, points on the nose and gace are
>> 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
>>> 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:
>>> (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]
> Max Garagnani, PhD.
> MRC - Cognition & Brain Sciences Unit
> 15 Chaucer Rd.
> Cambridge - CB2 7EF
> 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]