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- #!/bin/tcsh
- # NB: all parameters in this file are set for testing purposes (=
- # brevity, in most case). These are NOT meant to be realistic use
- # cases in practice!
- set here = ${PWD}
- set fatdir = AFNI_demos/FATCAT_DEMO
- set dir2 = test_extra
- set fatdir2 = ${fatdir}/${dir2}
- set mainpref = "$1"
- if ( "${mainpref}" == "" ) then
- set mainpref = RUN_00
- endif
- set otext = ${here}/o.status_failures_ptaylor.txt
- # -------------------------------------------------------------------------
- # Preliminary: check that supplement dir exists
- if ( ! -e ${fatdir2} ) then
- echo "** To run these tests you need a supplementary dir in the"
- echo " FATCAT_DEMO directory, called: ${dir2}"
- exit 1
- endif
- # -------------------------------------------------------------------------
- \mkdir -p ${mainpref}
- # want absolute path to dir of test outputs
- cd ${mainpref}
- set testdir = ${PWD}
- cd -
- printf "" > ${otext}
- cd ${fatdir}
- # -------------------------------------------------------------------------
- # -------------------------------------------------------------------------
- set prog = 3ddot_beta
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -input SOME_ICA_NETS_in_DWI+orig.HEAD \
- -mask mask_DWI+orig.HEAD \
- -doeta2 \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # output file will be: ${opref}_eta2.dat
- # -------------------------------------------------------------------------
- set prog = 1dDW_Grad_o_Mat++
- set opref = ${testdir}/o.${prog}
- set ombat = ${opref}_BMAT.txt
- set ocvec = ${opref}_cvec_n-1.txt
- echo "++ test-run: ${prog}"
- # For 3dDWItoDT
- ${prog} \
- -echo_edu \
- -in_row_vec bvec'[2..32]' \
- -in_bvals bval'[2..32]' \
- -flip_y \
- -out_col_matA ${ombat}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # for the 3dDTtoNoisyDWI; has N-1 (no '0', sigh)
- ${prog} \
- -echo_edu \
- -in_row_vec bvec'[3..32]' \
- -flip_y \
- -out_col_vec ${ocvec}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dDWItoDT
- set opref = ${testdir}/o.${prog}
- # just using '-linear' for speed!
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -prefix ${opref} \
- -mask mask_DWI+orig.HEAD \
- -eigs \
- -scale_out_1000 \
- -sep_dsets \
- -linear \
- -bmatrix_FULL ${dir2}/grad_BMAT.txt \
- AVEB0_DWI.nii.gz
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # produces several dsets: ${odti}_{FA,MD,V1,V2,.....}+orig.HEAD
- # -------------------------------------------------------------------------
- set prog = 3dROIMaker
- set opref = ${testdir}/o.${prog}
- # just using '-linear' for speed!
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -nifti \
- -inset SOME_ICA_NETS_in_DWI+orig.HEAD \
- -thresh 3.0 \
- -volthr 130 \
- -inflate 2 \
- -wm_skel ${dir2}/DT_FA+orig.HEAD \
- -skel_thr 0.2 \
- -skel_stop \
- -mask mask_DWI+orig.HEAD \
- -prefix ${opref} \
- -overwrite
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dDTtoNoisyDWI
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -choose_seed 7 \
- -dt_in ${dir2}/DT_DT+orig.HEAD \
- -mask mask_DWI+orig.HEAD \
- -grads ${dir2}/grad_cvec_n-1.txt \
- -noise_DWI 0.05 \
- -noise_B0 0 \
- -prefix ${opref}.nii.gz
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dEigsToDT
- set opref = ${testdir}/o.${prog}
- set odt2 = ${opref}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -eig_vals "${dir2}/DT_L*" \
- -eig_vecs "${dir2}/DT_V*" \
- -prefix ${odt2}
- # -------------------------------------------------------------------------
- set prog = 3dVecRGB_to_HSL
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -in_vec ${dir2}/DT_V1+orig.HEAD \
- -in_scal ${dir2}/DT_FA+orig.HEAD \
- -mask mask_DWI+orig.HEAD \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dTORTOISEtoHere
- set opref = ${testdir}/o.${prog}
- set odtT = ${opref}_PREP.nii.gz
- echo "++ test-run: ${prog}"
- # first, make a DT copy in the TORTOISE style
- 3dTcat \
- -echo_edu \
- -prefix ${odtT} \
- ${dir2}/DT_DT+orig.HEAD'[0,2,5,1,3,4]'
- ${prog} \
- -echo_edu \
- -dt_tort ${odtT} \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dDWUncert
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- # run in prep for PROB tracking
- ${prog} \
- -echo_edu \
- -inset AVEB0_DWI.nii.gz \
- -mask mask_DWI+orig.HEAD \
- -pt_choose_seed 5 \
- -prefix ${opref} \
- -input ${dir2}/DT \
- -bmatrix_FULL ${dir2}/grad_BMAT.txt \
- -iters 10
-
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dTrackID
- set opref = ${testdir}/o.${prog}
- set otrdet = ${opref}_DET
- set otrpr = ${opref}_PROB
- echo "++ test-run: ${prog}"
- # WB DET tracking
- ${prog} \
- -echo_edu \
- -mode DET \
- -dti_in ${dir2}/DT \
- -netrois mask_DWI+orig.HEAD \
- -logic OR \
- -alg_Thresh_Len 30 \
- -alg_Nseed_X 1 \
- -alg_Nseed_Y 1 \
- -alg_Nseed_Z 1 \
- -prefix ${otrdet}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # network PROB tracking; depends on ROI ICMAP_GMI being created
- ${prog} \
- -echo_edu \
- -mode PROB \
- -choose_seed 5 \
- -no_indipair_out \
- -nifti \
- -dti_in ${dir2}/DT \
- -uncert ${dir2}/o.UNCERT+orig.HEAD \
- -netrois ${dir2}/ROI_ICMAP_GMI+orig.HEAD \
- -mask mask_DWI+orig.HEAD \
- -alg_Thresh_Frac 0.2 \
- -alg_Nseed_Vox 5 \
- -alg_Nmonte 5 \
- -dump_rois AFNI \
- -prefix ${otrpr}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dNetCorr
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -inset REST_in_DWI.nii.gz'[5..50]' \
- -in_rois ${dir2}/ROI_ICMAP_GM+orig.HEAD \
- -prefix ${opref} \
- -fish_z \
- -ts_wb_Z \
- -nifti \
- -ts_out
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dMatch
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -only_dice_thr \
- -inset SOME_ICA_NETS_in_DWI+orig.HEAD \
- -refset MULTISITE_in_DWI+orig.HEAD \
- -mask mask_DWI+orig.HEAD \
- -in_min 1.0 \
- -ref_min 3 \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dRSFC
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -input REST_in_DWI.nii.gz'[5..100]' \
- -prefix ${opref} \
- -mask mask_DWI+orig.HEAD \
- -band 0.01 0.1
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dLombScargle
- set opref = ${testdir}/o.${prog}
- set olsamp = ${opref}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -nifti \
- -inset REST_in_DWI.nii.gz'[5..100]' \
- -prefix ${opref} \
- -mask mask_DWI+orig.HEAD \
- -censor_str '[0..3,5,6..18,22..34,36..47,49,51..60,63..84,86..88,90,92..$]'
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dAmpToRSFC
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -nifti \
- -band 0.01 0.1 \
- -mask mask_DWI+orig.HEAD \
- -in_amp ${dir2}/o.3dLombScargle_amp.nii.gz \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dClusterize
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -mask mask_DWI+orig.HEAD \
- -inset SOME_ICA_NETS_in_DWI+orig.HEAD \
- -ithr 0 \
- -idat 0 \
- -bisided -3 3 \
- -NN 2 \
- -clust_nvox 200 \
- -pref_map ${opref}_MAP.nii.gz \
- -pref_dat ${opref}_DAT.nii.gz \
- > ${opref}_REP.txt
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dReHo
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -mask mask_DWI+orig.HEAD \
- -inset REST_in_DWI.nii.gz'[5..50]' \
- -nneigh 7 \
- -prefix ${opref} \
-
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # check with ROIs (and different kind of neighborhood opts); depends
- # on 3dROIMaker output, above
- ${prog} \
- -echo_edu \
- -mask mask_DWI+orig.HEAD \
- -inset REST_in_DWI.nii.gz'[5..50]' \
- -box_X 2 \
- -box_Y 2 \
- -box_Z 3 \
- -prefix ${opref}_ROI \
- -in_rois ${dir2}/ROI_ICMAP_GM+orig.HEAD
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dSliceNDice
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- # make masks
- 3dcalc \
- -echo_edu \
- -a SOME_ICA_NETS_in_DWI+orig.HEAD'[0]' \
- -b mask_DWI+orig.HEAD \
- -expr 'step(b)*(step(a-3)+step(-3-a))' \
- -prefix ${opref}_preA.nii.gz
- 3dcalc \
- -echo_edu \
- -a SOME_ICA_NETS_in_DWI+orig.HEAD'[1]' \
- -b mask_DWI+orig.HEAD \
- -expr 'step(b)*(step(a-3)+step(-3-a))' \
- -prefix ${opref}_preB.nii.gz
- ${prog} \
- -echo_edu \
- -out_domain all \
- -insetA ${opref}_preA.nii.gz \
- -insetB ${opref}_preB.nii.gz \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dSpaceTimeCorr
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- # make a quick+small mask (sphere around xyz origin), because this
- # prog is computationally intense --> slow
- 3dcalc \
- -echo_edu \
- -a mask_DWI+orig.HEAD \
- -expr 'step(100-(x-0)*(x-0)-(y-0)*(y-0)-(z-0)*(z-0))' \
- -prefix ${opref}_MASK.nii.gz
- ${prog} \
- -echo_edu \
- -insetA REST_in_DWI.nii.gz'[5..15]' \
- -insetB REST_in_DWI.nii.gz'[25..35]' \
- -mask ${opref}_MASK.nii.gz \
- -prefix ${opref}
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- set prog = 3dZipperZapper
- set opref = ${testdir}/o.${prog}
- echo "++ test-run: ${prog}"
- ${prog} \
- -echo_edu \
- -input AVEB0_DWI.nii.gz'[0..10]' \
- -mask mask_DWI+orig.HEAD \
- -prefix ${opref} \
- -do_out_slice_param
-
- if ( ${status} ) printf "${prog}\n" >> ${otext}
- # -------------------------------------------------------------------------
- # -------------------------------------------------------------------------
- # -------------------------------------------------------------------------
- set nfail_status = `cat ${otext} | wc -l`
- echo ""
- echo ""
- echo "---------------------------------------------------------"
- echo " DONE"
- echo ""
- echo ""
- if ( ${nfail_status} ) then
- echo "** Number of progs that failed status: ${nfail_status}"
- cat ${otext}
- else
- echo "++ No programs had failure status :)"
- endif
- echo ""
- echo "---------------------------------------------------------"
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