Hi Rick,

I will chime in here since I am the labmate trying to integrate some files outputed from FSL with later steps from the AFNI_proc.py script (note I am running a script following the commands that is outputed by the proc.py script-not running AFNI_pro.cpy). I am guessing the crashing is due to typos and how I am changing the AFNI_proc.py script.

For example, it is crashing on the blur estimation step from AFNI_proc.py. Specifically, it crashs on the restrict to uncensored TRs, per run. The error I get is: 'if: Badly formed number.'

Below is the script I adapted from the AFNI_proc.py script:

foreach run ( 01 02 03 04 )
set trs = (`1d_tool.py -infile ${subfolder}/${subject}/${subject}.${results}/X.xmat_FNIRT.1D -show_trs_uncensored encoded -show_trs_run ${run}`)
if ( ${trs} == "" ) continue
3dFWHMx -detrend -mask ${subfolder}/${subject}/${subject}.${results}/full_mask.${subject}_RPI.nii \
${subfolder}/${subject}/${subject}.${results}/all_runs_FNIRT.${subject}.nii"[${trs}]" >> ${subfolder}/${subject}/${subject}.${results}/blur.epits_FNIRT.1D
end

I am guessing the error is due to how I am defining the variables here to run in my script...Any thoughts on what could be leading to the error?

Thanks,

Danny