</pre><hr>Higher-level input files preparation<br><pre>

/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_sg6VTo -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_CCQ8Nj -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_n8Tu84 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_uAY1E4 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_aTP8xU -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_9LzFQy -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_YXkCQq -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_3v5K5s -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_SU0hUv -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_fK670N -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_Qub1Xl -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_7IOwRV -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_pKLUOO -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_s3UicZ -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_w1PjHx -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_l9OYsl -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_chbynU -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_d5TQWv -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_vTBWTH -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_X0zFrq -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_7TcvjH -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_iODKgP -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_4zeLfM -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_ulC7W7 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_Zr2Sq6 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_MxX4rD -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_Cc8UXH -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_oUR3Pu -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_wkD8e3 -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_eyMw5h -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_D110ew -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_qWIFuD -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_GEwtTa -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_X6aNPt -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_csK37z -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_VLzwAk -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_WqDWhC -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_Kye8d3 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_MTnPv6 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_DCMkNL -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_NFGrgG -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_0VIFwU -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_uScJEc -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_2P4N4l -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_q72k0X -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_mNN0pi -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_vRb6gN -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_EN95wC -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_w1WHSd -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_C5fGFc -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_XkxtF8 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_k1RCO9 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_zrh01l -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_7QMq9y -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_KpTp2V -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_5RPRjr -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_5RLEAk -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_X7FVqq -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_9JVEND -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_CFXB4R -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_syp5WL -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_HvncXf -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_vz7yJH -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_Q9fhtt -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_NOZecq -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_3koVU0 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_kbl4RT -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_FqqwVo -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_8XjbpJ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_jz37c5 -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_epYLTg -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_kMjgzM -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_vfWlCZ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_NWAqUA -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_v2II6n -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_p4UeiV -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_Xd6jG8 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_pBIGfK -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_QcEZdj -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_z15keL -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_7jEfQz -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_rxOz9v -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_A8hORN -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_xYOZxA -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_6Fz77R -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_tQ66Bt -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_X3vQKF -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_j70kfA -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_WeGujQ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_pdx3WG -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_XeqND2 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_JpPKi0 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_04Bgey -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_yZX9sA -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_8VMQyP -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_FYVD0H -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_oA8beG -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_ob4kFD -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_DKfe8I -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_sjAvhm -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_20aITV -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_slLeYe -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_pYWpt0 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_hDWzKU -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_WsE2ej -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_eLGfde -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_xoCCZ3 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_qNDsZv -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_5si97X -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_KZViuX -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_ZXJVYB -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_0ay8Zp -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_3F3ZWG -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_4lD63V -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_ArlJA2 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_uwkdKQ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_ncYrdQ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_c7AVE2 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_HrF36N -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_lnUfd9 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_8VVIt1 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_lRGUxG -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_hdDhSZ -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_v3VFfN -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_wlvcgT -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_f4eFDM -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_5CU8k3 -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_2fffqk -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_InIpSN -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_9QxM9u -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_tYIVZx -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_i307N1 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_ZCXF7Z -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_Wjcjlb -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_1ejKqd -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_eUEzWT -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_MgCmps -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_JW6OqT -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_1dphAU -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_qwfgTf -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_UskPDi -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_dUBIl5 -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_M29p0D -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_YfVqvN -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_Hi9rb7 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_WAD2La -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_cx5ZP9 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_fG822s -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_gCoP75 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_w7Z7uF -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_P7QAzu -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_jwpKIr -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_W7mOIC -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_3FIdmX -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/featregapply /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat

/usr/local/fsl/bin/flirt -ref reg/standard -in example_func -out frgrot_uuX0TH -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in mask -out frgrot_wBXRAY -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/local/fsl/bin/flirt -ref reg/standard -in mean_func -out frgrot_0ZswOw -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_ZN06G1 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope2 -out frgrot_aCgbCv -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope3 -out frgrot_79XI5F -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope4 -out frgrot_rNY4FO -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/cope5 -out frgrot_8aDA7J -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_mHs9bT -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope2 -out frgrot_4aEybD -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope3 -out frgrot_OL0jGz -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope4 -out frgrot_NSEnkz -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in stats/varcope5 -out frgrot_y4gPV5 -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/local/fsl/bin/flirt -ref reg/standard -in reg/highres -out frgrot_xZiadW -applyxfm -init reg/highres2standard.mat -interp sinc -datatype float


/usr/local/fsl/bin/fslmerge -t bg_image  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/reg/highres /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/reg/highres

/usr/local/fsl/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float

/usr/local/fsl/bin/fslmerge -t mask  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/mask /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/mask

mkdir -p inputreg

/usr/local/fsl/bin/fslmaths ../mask -mul 12 -Tmean masksum -odt short

/usr/local/fsl/bin/fslmaths masksum -thr 12 -add masksum masksum

/usr/local/fsl/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 24 masksum_overlay

/usr/local/fsl/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png

/usr/local/fsl/bin/fslmaths masksum -mul 0 maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique

/usr/local/fsl/bin/fslmaths masksum -thr 11 -uthr 11 -bin -mul maskunique maskunique

/usr/local/fsl/bin/overlay 0 0 ../bg_image -a maskunique 0.9 12 maskunique_overlay

/usr/local/fsl/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png

/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif

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

/usr/local/fsl/bin/fslmerge -t mean_func  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/mean_func /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/mean_func

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

/usr/local/fsl/bin/fslmerge -t cope1  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/cope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/cope1

/usr/local/fsl/bin/fslmaths cope1 -mas mask cope1

printf '1.021956 ' >> design.lcon

/usr/local/fsl/bin/fslmerge -t varcope1  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/varcope1 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/varcope1

/usr/local/fsl/bin/fslmaths varcope1 -mas mask varcope1

/usr/local/fsl/bin/fslmerge -t cope2  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/cope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/cope2

/usr/local/fsl/bin/fslmaths cope2 -mas mask cope2

printf '1.013824 ' >> design.lcon

/usr/local/fsl/bin/fslmerge -t varcope2  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/varcope2 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/varcope2

/usr/local/fsl/bin/fslmaths varcope2 -mas mask varcope2

/usr/local/fsl/bin/fslmerge -t cope3  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/cope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/cope3

/usr/local/fsl/bin/fslmaths cope3 -mas mask cope3

printf '1.037187 ' >> design.lcon

/usr/local/fsl/bin/fslmerge -t varcope3  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/varcope3 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/varcope3

/usr/local/fsl/bin/fslmaths varcope3 -mas mask varcope3

/usr/local/fsl/bin/fslmerge -t cope4  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/cope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/cope4

/usr/local/fsl/bin/fslmaths cope4 -mas mask cope4

printf '1.033791 ' >> design.lcon

/usr/local/fsl/bin/fslmerge -t varcope4  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/varcope4 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/varcope4

/usr/local/fsl/bin/fslmaths varcope4 -mas mask varcope4

/usr/local/fsl/bin/fslmerge -t cope5  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/cope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/cope5

/usr/local/fsl/bin/fslmaths cope5 -mas mask cope5

printf '1.037959 ' >> design.lcon

/usr/local/fsl/bin/fslmerge -t varcope5  /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_left.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/ac/ac_right.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/at/at_right.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/cm/cm_right.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/df/df_right.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/dn/dn_right.feat/reg_standard/stats/varcope5 /Users/jbramen/Documents/fsl_course_data/fmri/ptt/eg/eg_right.feat/reg_standard/stats/varcope5

/usr/local/fsl/bin/fslmaths varcope5 -mas mask varcope5
