Hi FSL gurus:
I have some resting data that has been preprocessed in the HCP Minimal Preprocessing Pipeline (up through the ICA-FIX) stage. The data is a nifti file (in MNI space) that has been cleaned in a number of ways, and I am trying to run it through FEAT in order to create some seed maps.
To this end, I’m using a first-level design file that does Stats only, but it aborts while doing setup processes in Prestats:
Prestats
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslmaths prefiltered_func_data filtered_func_data
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslmaths filtered_func_data -Tmin -bin mask -odt char
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslstats filtered_func_data -k mask -R | awk '{ print }' -
0.000000
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
….
I tried manually running the different steps of the second statement above (ie, first running the -Tmin operation, then –bin, then –odt). The “-Tmin” alone appears to yield a reasonable file, but the “-bin” operation results in an empty mask. It is possible that the –Tmin results were all negative, but that should be allowed, shouldn’t it?
Could you please advise how to get around this problem? I found a similar question on the listserv (user: lu.hraskova@gmail), but no one appears to have answered her query.
Thanks very much,
Christina Fales
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P.S. I am using FSL version 5.06, which I need in order to be compatible with some existing scripts.
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