#######preprocessing for anatomical images#######
#example of 1 subject

3dcalc -prefix Sub1/3D_anat -a Pre_Sub1/Pre_Sub1_t1_mprage_sag_144.nii -expr a

3dWarp -oblique2card -prefix Sub1/card_3d Sub1/3D_anat+orig

3dSkullStrip -prefix card_3d_ns -input Pre/card_3d+orig

#using the align_epi_anat.py to do the alignment work
align_epi_anat.py       -anat Pre/card_3d_ns+orig \
                        -epi Pos/card_3d_ns+orig \
                        -epi_base 0  -prep_off \
                        -anat_has_skull no   \
                        -epi_strip None \
                        -giant_move -cost lpa \
                        -overwrite -suffix _al
cat_matvec card_3d_ns_al_mat.aff12.1D > anat1_mat.1D
1dmatcalc "&read(anat1_mat.1D) &Sqrt &write(anat_sqrt.1D)"
cat_matvec -ONELINE anat_sqrt.1D > anat_sqrt.aff12.1D
cat_matvec -ONELINE anat_sqrt.1D -I > anat_sqrtI.aff12.1D

3dAllineate -1Dmatrix_apply anat_sqrt.aff12.1D -base anat1_ns+orig -source anat1_ns+orig -prefix anat1_ns_mean
3dAllineate -1Dmatrix_apply anat_sqrtI.aff12.1D -base anat1_ns+orig -source anat2_ns+orig -prefix anat2_ns_mean

#combine 2 anatomical images
3dMean -prefix anat_ns_mean anat1_ns_mean+orig anat2_ns_mean+orig

#transform to tlrc coordinate
@auto_tlrc -base TT_N27+tlrc -input anat_ns_mean+orig -no_ss -suffix NONE


#######preprocessing for functional images#######
 #example for 1 run of 1 subject

3dcalc -prefix run1 -a Pre_Sub1_func_31x31x35_110.nii -expr a
3drefit -TR 2 Sub1/run1/run1+orig
3dDespike -prefix dspk run1+orig
3dvolreg -verbose -tshift 0 -prefix c_Pre_r1 -1Dfile 3drpara_Pre_r1.1D -base '../run2/dspk+orig[109]' 'dspk+orig[2..109]'

#aligned to anatomical image
3dWarp -oblique2card -prefix c_plumb_Pre_r1 c_Pre_r1+orig
3dWarp -oblique2card -prefix c_plumb_Pre_r2 c_Pre_r2+orig
3dWarp -oblique2card -prefix c_plumb_Pos_r1 c_Pos_r1+orig
3dWarp -oblique2card -prefix c_plumb_Pos_r2 c_Pos_r2+orig

align_epi_anat.py -anat anat_ns_mean+orig                     \
   -epi c_plumb_Pre_r2+orig -epi_base 0 -volreg_base 2 -epi2anat -master_epi MIN_DXYZ      \
   -anat_has_skull no -overwrite -tlrc_apar anat_ns_mean+tlrc \
   -giant_move -child_epi c_plumb_Pre_r1+orig.HEAD


align_epi_anat.py -anat anat_ns_mean+orig                     \
   -epi c_plumb_Pos_r2+orig -epi_base 0 -volreg_base 2 -epi2anat -master_epi MIN_DXYZ      \
   -anat_has_skull no -overwrite -tlrc_apar anat_ns_mean+tlrc \
   -giant_move -child_epi c_plumb_Pre_r1+orig.HEAD


#resample
3dresample -prefix c_plumb_resample_Pre_r1_tlrc_al -master /mask/grey_frac+tlrc -inset c_plumb_Pre_r1_tlrc_al+tlrc

#bandpass
3dFourier -prefix fc_plumb_Pre_r1_tlrc_al -highpass 0.0078 -ignore 0 -retrend c_plumb_resample_Pre_r1_tlrc_al+tlrc

#normalization
3dTstat -prefix meancplumb fc_plumb_Pre_r1_tlrc_al+tlrc
3dcalc -prefix nfc_plumb_Pre_r1 -a fc_plumb_Pre_r1_tlrc_al+tlrc -b meancplumb+tlrc -expr 'min(200, a/b*100)*step(a)*step(b)'


#######compute mean time course for each stimulus condition#######

3dMean -prefix BMUpr_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[24..30]' 'nfc_plumb_Pre_r1+tlrc[54..60]' 'nfc_plumb_Pre_r1+tlrc[90..96]' 'nfc_plumb_Pre_r2+tlrc[24..30]' 'nfc_plumb_Pre_r2+tlrc[54..60]' 'nfc_plumb_Pre_r2+tlrc[90..96]'~

3dMean -prefix BMUpr_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[24..30]' 'nfc_plumb_Pos_r1+tlrc[54..60]' 'nfc_plumb_Pos_r1+tlrc[90..96]' 'nfc_plumb_Pos_r2+tlrc[24..30]' 'nfc_plumb_Pos_r2+tlrc[54..60]' 'nfc_plumb_Pos_r2+tlrc[90..96]'~

3dMean -prefix BMInv_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[30..36]' 'nfc_plumb_Pre_r1+tlrc[60..66]' 'nfc_plumb_Pre_r1+tlrc[84..90]' 'nfc_plumb_Pre_r2+tlrc[30..36]' 'nfc_plumb_Pre_r2+tlrc[60..66]' 'nfc_plumb_Pre_r2+tlrc[84..90]'~

3dMean -prefix BMInv_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[30..36]' 'nfc_plumb_Pos_r1+tlrc[60..66]' 'nfc_plumb_Pos_r1+tlrc[84..90]' 'nfc_plumb_Pos_r2+tlrc[30..36]' 'nfc_plumb_Pos_r2+tlrc[60..66]' 'nfc_plumb_Pos_r2+tlrc[84..90]'~


3dMean -prefix FaceUpr_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[0..6]' 'nfc_plumb_Pre_r1+tlrc[48..54]' 'nfc_plumb_Pre_r1+tlrc[96..102]' 'nfc_plumb_Pre_r2+tlrc[0..6]' 'nfc_plumb_Pre_r2+tlrc[48..54]' 'nfc_plumb_Pre_r2+tlrc[96..102]'~

3dMean -prefix FaceUpr_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[0..6]' 'nfc_plumb_Pos_r1+tlrc[48..54]' 'nfc_plumb_Pos_r1+tlrc[96..102]' 'nfc_plumb_Pos_r2+tlrc[0..6]' 'nfc_plumb_Pos_r2+tlrc[48..54]' 'nfc_plumb_Pos_r2+tlrc[96..102]'~

3dMean -prefix FaceInv_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[6..12]' 'nfc_plumb_Pre_r1+tlrc[66..72]' 'nfc_plumb_Pre_r1+tlrc[78..84]' 'nfc_plumb_Pre_r2+tlrc[6..12]' 'nfc_plumb_Pre_r2+tlrc[66..72]' 'nfc_plumb_Pre_r2+tlrc[78..84]'~

3dMean -prefix FaceInv_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[6..12]' 'nfc_plumb_Pos_r1+tlrc[66..72]' 'nfc_plumb_Pos_r1+tlrc[78..84]' 'nfc_plumb_Pos_r2+tlrc[6..12]' 'nfc_plumb_Pos_r2+tlrc[66..72]' 'nfc_plumb_Pos_r2+tlrc[78..84]'~


3dMean -prefix HouseUpr_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[12..17]' 'nfc_plumb_Pre_r1+tlrc[42..47]' 'nfc_plumb_Pre_r1+tlrc[102..107]' 'nfc_plumb_Pre_r2+tlrc[12..17]' 'nfc_plumb_Pre_r2+tlrc[42..47]' 'nfc_plumb_Pre_r2+tlrc[102..107]'~

3dMean -prefix HouseUpr_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[12..17]' 'nfc_plumb_Pos_r1+tlrc[42..47]' 'nfc_plumb_Pos_r1+tlrc[102..107]' 'nfc_plumb_Pos_r2+tlrc[12..17]' 'nfc_plumb_Pos_r2+tlrc[42..47]' 'nfc_plumb_Pos_r2+tlrc[102..107]'~

3dMean -prefix HouseInv_MeanTimeCourse_nfc_Pre 'nfc_plumb_Pre_r1+tlrc[18..23]' 'nfc_plumb_Pre_r1+tlrc[36..41]' 'nfc_plumb_Pre_r1+tlrc[72..77]' 'nfc_plumb_Pre_r2+tlrc[18..23]' 'nfc_plumb_Pre_r2+tlrc[36..41]' 'nfc_plumb_Pre_r2+tlrc[72..77]'~

3dMean -prefix HouseInv_MeanTimeCourse_nfc_Pos 'nfc_plumb_Pos_r1+tlrc[18..23]' 'nfc_plumb_Pos_r1+tlrc[36..41]' 'nfc_plumb_Pos_r1+tlrc[72..77]' 'nfc_plumb_Pos_r2+tlrc[18..23]' 'nfc_plumb_Pos_r2+tlrc[36..41]' 'nfc_plumb_Pos_r2+tlrc[72..77]'~



#######GLM#######

#prepare motion parameter
cat 3drpara_Pre_r1.1D 3drpara_Pre_r2.1D 3drpara_Pos_r1.1D 3drpara_Pos_r2.1D > dfile.rall.1D
1d_tool.py -infile dfile.rall.1D -set_nruns 4 -demean -write motion_demean.1D

3dDeconvolve -input nfc_plumb_Pre_r1+tlrc nfc_plumb_Pre_r2+tlrc nfc_plumb_Pos_r1+tlrc nfc_plumb_Pos_r2+tlrc -local_times -polort 2 -num_stimts 12 -mask /mask/grey_frac+tlrc -stim_times 1 FaceUprallruns.1D 'BLOCK(12,1)' -stim_label 1 FaceUpr -stim_times 2 FaceInvallruns.1D 'BLOCK(12,1)' -stim_label 2 FaceInv -stim_times 3 HouseUprallruns.1D 'BLOCK(12,1)' -stim_label 3 HouseUpr -stim_times 4 HouseInvallruns.1D 'BLOCK(12,1)' -stim_label 4 HouseInv -stim_times 5 BMUprallruns.1D 'BLOCK(12,1)' -stim_label 5 BMUpr -stim_times 6 BMInvallruns.1D 'BLOCK(12,1)' -stim_label 6 BMInv -stim_file 7 'motion_demean.1D[0]' -stim_base 7 -stim_label 7 roll_01 -stim_file 8 'motion_demean.1D[1]' -stim_base 8 -stim_label 8 pitch_01 -stim_file 9 'motion_demean.1D[2]' -stim_base 9 -stim_label 9 yaw_01 -stim_file 10 'motion_demean.1D[3]' -stim_base 10 -stim_label 10 dS_01 -stim_file 11 'motion_demean.1D[4]' -stim_base 11 -stim_label 11 dL_01 -stim_file 12 'motion_demean.1D[5]' -stim_base 12 -stim_label 12 dP_01 -gltsym 'SYM: +BMUpr +BMInv -HouseUpr -HouseInv' -glt_label 1 BMUprInvVsHourseUprInv -gltsym 'SYM: +FaceUpr +FaceInv -HouseUpr -HouseInv' -glt_label 2 FaceUprInvVsHourseUprInv -gltsym 'SYM: +BMInv -HouseInv' -glt_label 3 BMInvVsHourseInv -gltsym 'SYM: +FaceUpr -HouseUpr' -glt_label 4 FaceUprVsHourseUpr -jobs 4 -fout -tout -bucket Sub1_nfc_all_runs_pre_pro_loc_uncensored_motionbased.buck