Any help would be so appreciated!
I am trying to run a seed-based resting state analysis in FSL. I have my preprocessed data and am attempting to:
L1 step 1: input preprocessed image, regress nuisance regressors (motion, WM, CSF) as EVs.
L1 step 2: use res4d file from step 1, add time series seed text file (created using fslmeants) as EV and select main effects contrast.
Group step 1: use cope1 file from L1 step 2 above to run a group level analysis with each subject's cope1.nii.gz file and get a seed correlations map.
Group step 2: binarize the thresh_zstat1.nii.gz file that is output from Group step 1 and extract time series using fslmaths.
Group step 3: Rerun Group step 1 using the thresholded correlation mask created at Group step 2.
Registration question: I am not sure whether I should attempt to register at L1 step 1 or 2 above?
Empty mask error: Regardless of whether I register or not, when I try to use the res4d file at L1 step 2, I get an error at Preprocessing: Stage 2 that says
/space/raid/fmri/fsl-5.0.9-centos6_64/bin/fslstats filtered_func_data -k mask -R | awk '{ print }'
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
[EMPTY MASK ERROR CONTINUES]
0.000000
/space/raid/fmri/fsl-5.0.9-centos6_64/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*
Stats error: In stats processing I get a smoothness error even though I have not done any additional smoothing (after preprocessing) in the Feat GUI
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.
Any assistance as to whether my process seems correct and as to what I can do to rectify the empty mask error would be most appreciated.
Thank you!
Sarah
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