Hi Max,
1) MaxFilter 2.0 supports only 'neuromag-style' bad channel marking
provided by DACQ and utility program /neuro/bin/util/mark_bad_fiff.
Such bad channels are set permanently bad ones in maxfilter.
Using mark_bad_fiff requires that the file has a bad channel tag
generated during data acquisition. You can check it by running
/neuro/bin/util/show_fiff -v <file.fif> | grep bad
which should report
220 = bad chs 315 ints
In this case, you can always re-run mark_bad_fiff to overwrite the
previous bad channel selection. For example, command
/neuro/bin/util/mark_bad_fiff -1 <file.fif>
removes all bad channels.
If the input file does not have the bad channel tag, mark_bad_fiff reports
an error and does not do the job. In such cases you have to give the
bad channels separately on maxfilter command-line or gui.
NOTE: the result file after maxfilter does not have the bad channels tag,
because the program reconstructs all MEG channels.
2) MNE software of Matti Hämäläinen uses a different bad channel
marking, /neuro/bin/util/show_fiff -v <file.fif> reports:
...
104 = { Cannot explain: 359
Cannot explain: 3507 MEG 2443:EEG 053
105 = } Cannot explain: 359
Unfortunately, MaxFilter 2.0 does not recognize this extension, and you
need to run mark_bad_fiff. In the above example:
/neuro/bin/util/mark_bad_fiff 53 2443 <file.fif>.
If it fails, you have to give the channnel 2443 as a bad one when starting
maxfilter.
MaxFilter 2.1 can handle both styles of bad channels (but I haven't decided
yet if style 1) is ignored when style 2) is present...)
Best regards, Jukka
Max Garagnani wrote:
> Hello,
>
> Thanks for your reply.
>
> After marking with "mark_bad_fiff", is it possible to "unmark" channels
> previously marked as bad on the fif file? If so, how?
>
> Many thanks,
> Max
>
> On Mon, November 19, 2007 12:08, Jukka Nenonen wrote:
>> Hello Yury,
>>
>> We are aiming to release maxfilter 2.1 during the spring, and the new
>> version can handle also bad channels marked by the MNE software.
>>
>> While waiting for it, the quickest 'workaround' would be to write down
>> the list of bad channels identified in the MNE software, and then apply
>> Neuromag utility program mark_bad_fiff, e.g.
>> /neuro/bin/util/mark_bad_fiff 632 741 2211 <filename.fif>
>>
>> Best regards, Jukka
>>
>>
>> Yury Shtyrov wrote:
>>> Hi Jukka -
>>>
>>> Thanks a lot for your quick reply! I think this explains it all: we
>>> did the marking in MNE - pretty much the only program where you can
>>> comfortably view and mark raw data in the same time - under the
>>> assumption that it uses native fiff-file format for everything
>>> (something I would expect from Matti). Too bad this is not the case -
>>> but good that you are fixing this in the second version. Any chance
>>> to have it soon? (we are beta testers anyway)
>>>
>>> yury
>>>
>>> 2007/11/19, Jukka Nenonen <[log in to unmask]>:
>>>> Hi Yury,
>>>>
>>>> How did you mark the bad channel in the FIFF file?
>>>>
>>>> Pneuromag utility program 'mark_bad_fiff' generates a list
>>>> of logical channel numbers, which maxfilter automatically
>>>> adds to permanently bad channels:
>>>> show_fiff -v filename.fif
>>>> ...
>>>> 220 = bad chs 315 ints
>>>> ...
>>>>
>>>> On the other hand, some programs (e.g. MNE software by Matti
>>>> Hämäläinen) may use a different bad channel marking (such as
>>>> a list of bad channel names). In such cases maxfilter 2.0 does
>>>> not recognize the bad channel settings.
>>>>
>>>> I have added the latter list to the new maxfilter.
>>>>
>>>> Can you email me a short evoked-format example file where the bad
>>>> channel marking seems to fail?
>>>>
>>>> Best regards, Jukka
>>>>
>>>> Yury Shtyrov wrote:
>>>>> Hello -
>>>>>
>>>>> The maxfilter manual seems to imply that if the channel has been
>>>>> marked bad in the fif-file previously, it will be automatically
>>>>> recognised as bad by maxfilter, regardless of the -bad option.
>>>>> However, this does not seem to be the case, and the bad channels (if
>>>>> marked bad in fiff but not entered in -bad) seem to badly influence
>>>>> good channels after maxfiltering.
>>>>>
>>>>> Has anyone else encountered this problem and is there a remedy -
>>>>> except manually entering all channels using -bad (which is time
>>>>> consuming and error-prone, to say the least)?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> -yury-
>>
>> --
>>
>> ===============================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
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