Dear Matthew

It's been a week since I uploaded the analysis output onto the fsl website. Could you please tell me whether there are any updates on this?

Many thanks
Anja
________________________________________
From: Andreja Varjacic
Sent: 12 September 2014 16:42
To: FSL - FMRIB's Software Library
Subject: RE: [FSL] FEAT: Errors at the first level

Hi

I've uploaded a tar of the whole folder "RUN1_FULL_SAMPLE_GR.tar.gz" onto the system.

Many thanks
Anja
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 12 September 2014 15:58
To: [log in to unmask]
Subject: Re: [FSL] FEAT: Errors at the first level

Hello,
          Thank you for the upload - it looks like I will need a tar of the whole folder though.

Kind Regards
Matthew
> Dear FSL developers
>
> I am writing because I am experiencing a number of errors when running first level analysis using FEAT.
>
> Looking at the log, there appears to be an error at the end of the preprocessing, a 'fatal error' at the end of the stats stage and a warning about smoothing in the poststats. This is what the log reads:
>
> PREPROCESSING STAGE 2:
>
> [...]
>
> /usr/local/fsl-5/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
>
> /usr/local/fsl-5/bin/fslmaths filtered_func_data -Tmean mean_func
>
> /bin/rm -rf prefiltered_func_data*
> Completed
>    while executing
> "if { [ catch {
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>    switch -- [ lindex $argv $argindex ] {
>
>       -I {
>           incr arginde..."
>    (file "/usr/local/fsl-5/bin/feat" line 310)
> -stats
> Completed
>
> STATS:
>
> /usr/local/fsl-5/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
> Log directory is: stats
> paradigm.getDesignMatrix().Nrows()=491
> paradigm.getDesignMatrix().Ncols()=27
> sizeTS=491
> numTS=39675
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 9966.43
> sig = 1261
> Spatially smoothing auto corr estimates
> .....................
> Completed
> Tukey M = 22
> Tukey estimates... Completed
> Completed
> Prewhitening and Computing PEs...
> Percentage done:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
> Saving results...
> Completed
>
> FATAL ERROR ENCOUNTERED
>
> (then it carries on to the post stats)
>
> POST-STATS:
>
> /usr/local/fsl-5/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
>
> /usr/local/fsl-5/bin/smoothest -m mask -z stats/zstat1 > stats/zstat1.smoothness
> WARNING: Extreme smoothness detected in X - possibly biased global estimate.
> WARNING: Extreme smoothness detected in Y - possibly biased global estimate.
> WARNING: Extreme smoothness detected in Z - possibly biased global estimate.
>
>
> The confusing part is that feat carries on with the next stage of the analysis as if the errors were not detected at all. When the analysis is completed, I get the motion/stats/post stats/registration outputs I would expect in the error-free analysis. Technical staff from our department tried to track the errors but to no avail: it looks like feat reports errors which, when inspected, do not exist.
>
> I have ran this analysis protocol on over 50 subjects in the past two years and I had no issues like this at all. I started getting these errors after fsl update in the mid July. This may have caused the errors, but nobody understands how.
>
> Could you please help? Would you advise me carrying on with the analysis despite the errors (as they *appear* not to affect the data very much) or can these errors be tracked and resolved?
>
> Thanks very much,
> Anja