</pre><hr>Prestats<br><pre>

/usr/local/fsl/bin/fslmaths /Users/chris/demo/event/eventfmri prefiltered_func_data -odt float
Total original volumes = 200
Deleting 1 volume(s) - BE WARNED for future analysis!

/usr/local/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 1 199

/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 99 1

/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 99 -rmsrel -rmsabs

/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png 

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png 

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png 

/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv mask_mask mask

/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1182.150269 

/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 118.2150269 -Tmin -bin mask -odt char

/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
876.384705 

/usr/local/fsl/bin/fslmaths mask -dilF mask

/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/local/fsl/bin/susan prefiltered_func_data_thresh 657.28852875 3.39702760085 3 1 1 mean_func 657.28852875 prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 11.4105140619 prefiltered_func_data_intnorm

/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 16.6666666667 -1 prefiltered_func_data_tempfilt

/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/local/fsl/bin/fslhd -x filtered_func_data | sed 's/  dt = .*/  dt = '3.0'/g' > grot

cat grot | /usr/local/fsl/bin/fslcreatehd - filtered_func_data

/bin/rm grot

/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*
