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feat2_pre
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</pre><hr>Preprocessing:Stage 1<br><pre>
/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz"
Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
Option -y ( standard dof ) selected with argument "12"
Option -z ( standard search ) selected with argument "90"
</pre><hr>Registration<br><pre>
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg
/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
Running FAST segmentation FLIRT pre-alignment Running BBR 0.436200 0.999899 -0.001807 0.014099 0.000000 0.001680 0.999958 0.009056 0.000000 -0.014115 -0.009032 0.999860 0.000000 2.273952 0.940215 1.394828 1.000000
/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/packages/fsl-5.0.10/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/packages/fsl-5.0.10/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
/bin/rm example_func2highres1.png
</pre><hr>Preprocessing:Stage 2<br><pre>
/usr/local/packages/fsl-5.0.10/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/local/packages/fsl-5.0.10/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/packages/fsl-5.0.10/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/packages/fsl-5.0.10/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/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func
/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet
/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 744.585571
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char
/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
594.438538
/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt
/usr/local/packages/fsl-5.0.10/bin/imrm tempMean
/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*