JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for NEUROMEG Archives


NEUROMEG Archives

NEUROMEG Archives


NEUROMEG@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

NEUROMEG Home

NEUROMEG Home

NEUROMEG  March 2008

NEUROMEG March 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: MaxFilter HPI Sphere Centres

From:

Jukka Nenonen <[log in to unmask]>

Reply-To:

Jukka Nenonen <[log in to unmask]>

Date:

Tue, 18 Mar 2008 11:28:34 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (169 lines)

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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

July 2020
May 2020
April 2020
January 2020
December 2019
June 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
May 2018
April 2018
March 2018
February 2018
January 2018
November 2017
October 2017
September 2017
August 2017
March 2017
December 2016
September 2016
July 2016
April 2016
January 2016
August 2015
July 2015
June 2015
March 2015
December 2014
August 2014
May 2014
April 2014
January 2014
December 2013
November 2013
October 2013
September 2013
June 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
July 2012
May 2012
March 2012
February 2012
September 2011
July 2011
June 2011
May 2011
April 2011
March 2011
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
February 2010
January 2010
December 2009
November 2009
October 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
March 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager