Dear FSL experts,
I am trying to analyze resting state fMRI data using Feat GUI. I have the following questions regarding the commands that FEAT is using (bellow are the commands from the report that FEAT generated-Preprocessing: Stage 2
1. why feat uses this command? /usr/pubsw/packages/fsl/5.0.7/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1219.962769

2. How feat cacluate the threshold in the following command? /usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_bet -thr 121.9962769 -Tmin -bin mask -odt char

3. Why feat uses this command? /usr/pubsw/packages/fsl/5.0.7/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
742.292480

4. How the thresholds were st up in Susan tool in the cmmand /usr/pubsw/packages/fsl/5.0.7/bin/susan prefiltered_func_data_thresh 556.71936 2.12314225053 3 1 1 mean_func 556.71936 prefiltered_func_data_smooth

Thank you for your help
Jon




Preprocessing:Stage 2

/usr/pubsw/packages/fsl/5.0.7/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final

/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/pubsw/packages/fsl/5.0.7/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/pubsw/packages/fsl/5.0.7/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/pubsw/packages/fsl/5.0.7/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/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/usr/pubsw/packages/fsl/5.0.7/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/pubsw/packages/fsl/5.0.7/bin/immv mask_mask mask

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/usr/pubsw/packages/fsl/5.0.7/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1219.962769

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_bet -thr 121.9962769 -Tmin -bin mask -odt char

/usr/pubsw/packages/fsl/5.0.7/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
742.292480

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths mask -dilF mask

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/pubsw/packages/fsl/5.0.7/bin/susan prefiltered_func_data_thresh 556.71936 2.12314225053 3 1 1 mean_func 556.71936 prefiltered_func_data_smooth

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_smooth -mul 13.4717786714 prefiltered_func_data_intnorm

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_intnorm -bptf 14.9253731343 -1 -add tempMean prefiltered_func_data_tempfilt

/usr/pubsw/packages/fsl/5.0.7/bin/imrm tempMean

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/pubsw/packages/fsl/5.0.7/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*