Hello Raj,
I presume that you have the proper fine-calibration available
(/neuro/database/sss/sss_cal.dat)?
It is difficult to tell what causes the trouble without seeing the data,
and I would like to have a closer look
on an example file.
Best regards, Jukka
Raj Rajagovindan wrote:
> Hi folks,
> I have been recently running into some Maxfilter-related issues, and I was wondering if anybody else has faced this or has any thoughts.
>
> Maxfilter Usage:
> {ExecDir}maxfilter-2.1 -f <InputFileName> -o <OutputFileName> -in 8 -out 3 -autobad off –bad <BadSensorList> -st 10 -trans default -frame head -origin 0 0 40
>
> Issue: Maxfilter aborts on 5-10% of the files.
> However, upon including ‘-magbad’ option many of the files execute successfully.
> Suspecting some issue with the magnetometer data, I ran (separately) maxfilter with '-autobad on' to identify if there were excessive bad sensors. It turned out that some files had >20 bad magnetometer sensors (identified by maxfilter), however there were many other files where the number of bad magnetometer sensors were only a few (<3). So it is not clear to me what the exact problem is.
> Further, this doesn’t appear to be related to the MaxST buffer length since I have tried different values for it.
>
> Related questions:
> 1. What is the best way to salvage these data (either gradiometer or magnetometer data)?
> 2. In such cases, is the use of ‘-magbad’ recommended, so that I could salvage at least the gradiometer data.
> 3. Is Lin=8 and Lout=3 still optimal for performing maxfiltering with the ‘-magbad’ option, since in this case only gradiometer data is used.
> 4. I had compared the performance of maxfiltering with and without ‘-magbad’ on gradiometer time series, I notice that the variance of the resulting time series differs by upto 4 folds ( i.e variance of tsssed data with –magbad option is 4 times that of variance of data with regular usage (as included above), with other parameters kept constant). Further the correlation between the tsssed time series with and without –magbad option is at best around 0.5. These comparisons were performed on files that did not have any other issues (such as maxfilter abortions). Given such drastic differences, I am concerned as to which time series to use.
> 5. With ‘-magbad’ option I notice that the tsssed file has both gradiometer and magnetometer data in it. It is not clear as to how this magnetometer time series was derived / processed. Correlation between this magnetometer time series and the original non-tsssed time series is < 0.5, which indicates that despite all magnetometers being marked bad, there is some processing that happens on these sensors. Are these estimates for the magnetometer derived based on expansions of the gradiometer data?
>
> Any assistance will be greatly appreciated! Please let me know if you need any further information or clarifications.
>
> Thank you!
> Raj
>
--
================================
Dr. Jukka Nenonen
Manager, Method development
Elekta Oy
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