def test_RetroTS_basic(data, vol_tr, python_interpreter):
seedval = 31416
kwargs_log = {
"append_to_ignored": ["Clock time", "but max simulated alpha="]
}
out_prefix = data.outdir / f"reg.01.a.{vol_tr}"
cmd = """
RetroTS.py
-c {data.ECG_epiRTslt_scan_4}
-r {data.Resp_epiRTslt_scan_4}
-v {vol_tr}
-p 50
-n 30
-prefix {out_prefix}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data,
cmd,
python_interpreter=python_interpreter,
kwargs_1d={"all_close_kwargs": {
"rtol": 0.15
}},
# kwargs_log=kwargs_log,
# add_env_vars=add_env_vars,
)
differ.run(timeout=None)
def test_3dSliceNDice(data, ptaylor_env):
opref = data.outdir / "o.3dSliceNDice"
# make masks first
cmd = f"""
3dcalc
-echo_edu
-a {data.SOME_ICA_NETS_in_DWI}'[0]'
-b {data.mask_DWI}
-expr 'step(b)*(step(a-3)+step(-3-a))'
-prefix {opref}_preA.nii.gz;
3dcalc
-echo_edu
-a {data.SOME_ICA_NETS_in_DWI}'[1]'
-b {data.mask_DWI}
-expr 'step(b)*(step(a-3)+step(-3-a))'
-prefix {opref}_preB.nii.gz;
3dSliceNDice
-echo_edu
-out_domain all
-insetA {opref}_preA.nii.gz
-insetB {opref}_preB.nii.gz
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(
data,
cmd,
)
differ.run(timeout=60)
def test_3dClustSim_basic(data, add_env_vars):
seedval = 31416
kwargs_log = {
"append_to_ignored": ["Clock time", "but max simulated alpha="]
}
outfile_prefix = data.outdir / "clust_sim_out"
cmd = """
3dClustSim
-nxyz 16 8 4
-dxyz 3 3 3
-BALL
-acf 0.7 3 3
-LOTS
-seed {seedval}
-prefix {outfile_prefix}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data,
cmd,
kwargs_1d={"all_close_kwargs": {
"rtol": 0.15
}},
kwargs_log=kwargs_log,
add_env_vars=add_env_vars,
)
differ.run(timeout=60)
def test_RetroTS_bids_custom_slice_order(data, vol_tr, python_interpreter):
seedval = 31416
kwargs_log = {
"append_to_ignored": ["Clock time", "but max simulated alpha="]
}
out_prefix = data.outdir / f"reg.02.a.{vol_tr}"
cmd = """
RetroTS.py
-phys_file {data.epiRTslt_scan_4_bids}
-v {vol_tr}
-n 1
-p 50
-slice_order custom
-slice_offset [1000]
-prefix {out_prefix}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data,
cmd,
python_interpreter=python_interpreter,
kwargs_1d={"all_close_kwargs": {
"rtol": 0.15
}},
# kwargs_log=kwargs_log,
# add_env_vars=add_env_vars,
)
differ.run(timeout=None)
def test_3dAllineate_basic(data, python_interpreter):
outname = "aligned"
if OMP:
outname += "_with_omp"
outfile = data.outdir / (outname + ".nii.gz")
out_1d = outfile.parent / (outfile.stem.split(".")[0] + ".1D")
cmd = """
3dAllineate
-base {data.anat1}
-source {data.epi}'[0]'
-prefix {outfile}
-1Dparam_save {out_1d}
-maxrot 2
-maxshf 1
-nmatch 20
-conv 2
-cost lpc
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data,
cmd,
python_interpreter=python_interpreter,
kwargs_log={
"append_to_ignored": [
"Output dataset",
"++ Wrote -1Dparam_save",
"total CPU time",
]
},
)
differ.run()
def test_3dTproject_basic(data, add_env_vars):
kwargs_log = {"append_to_ignored": ["clock time", "OpenMP"]}
kwargs_scans = {"data_kwargs": {"atol": 0.0001}}
outfile = data.outdir / "out.nii.gz"
cmd = """
3dTproject
-input {data.epi}
-prefix {outfile}
-polort 2
-passband 0.01 0.1
-automask
-dt 2.0
-blur 2.0
-norm
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data,
cmd,
kwargs_log=kwargs_log,
kwargs_scans=kwargs_scans,
add_env_vars=add_env_vars,
)
differ.run()
def test_3dDWUncert(data, ptaylor_env):
opref = data.outdir / "o.3dDWUncert"
cmd = f"""
3dDWUncert
-echo_edu
-inset {data.AVEB0_DWI}
-mask {data.mask_DWI}
-pt_choose_seed 5
-prefix {opref}
-input {data.tests_data_dir / fatdir2}/DT
-bmatrix_FULL {data.grad_BMAT}
-iters 10
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(
data,
cmd,
kwargs_log={
"append_to_ignored": [" min", "Nvox progress proxy count"]
},
)
differ.run(timeout=60)
def test_3dcopy_basic(data):
outfile = data.outdir / "copied.nii.gz"
cmd = """
3dcopy {data.anatomical} {outfile}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dSkullStrip_basic(data, dset_name):
ifile = getattr(data, dset_name)
ofile = data.outdir / "out_ss.nii.gz"
cmd = """3dSkullStrip -prefix {ofile} -input {ifile}"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dCM_basic(data):
cmd = """
3dCM
{data.anat}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dAutomask_basic(data):
outfile_prefix = data.outdir / ("masked_image.nii.gz")
cmd = """
3dAutomask -prefix {outfile_prefix} {data.anat}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dcalc_basic(data):
outfile = data.outdir / "outside_brain.nii.gz"
cmd = """
3dcalc -a {data.anatomical} -b {data.no_skull} -expr 'a*not(b)' -prefix {outfile}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(
data, cmd, kwargs_log={"append_to_ignored": ["Output dataset"]})
differ.run()
def test_3dTcat_basic(data):
outfile = data.outdir / "out.nii.gz"
cmd = """
3dTcat -prefix {outfile} {data.epi}'[150..$]'
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dRSFC(data, ptaylor_env):
opref = data.outdir / "o.3dRSFC"
cmd = f"""
3dRSFC
-echo_edu
-input {data.mini_REST_proc_unfilt}
-prefix {opref}
-band 0.01 0.1
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dEigsToDT(data, ptaylor_env):
opref = data.outdir / "o.3dEigsToDT"
cmd = f"""
3dEigsToDT
-echo_edu
-eig_vals '{data.tests_data_dir / fatdir2}/DT_L*'
-eig_vecs '{data.tests_data_dir / fatdir2}/DT_V*'
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dReHo(data, ptaylor_env):
opref = data.outdir / "o.3dReHo"
cmd = f"""
3dReHo
-echo_edu
-inset {data.mini_REST_proc_unfilt}'[0..45]'
-nneigh 7
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dLombScargle(data, ptaylor_env):
olsamp = data.outdir / "o.3dLombScargle"
cmd = f"""
3dLombScargle
-echo_edu
-nifti
-inset {data.mini_REST_proc_unfilt}
-prefix {olsamp}
-censor_str '[0..3,5,6..18,22..34,36..47,49,51..60,63..84,86..88,90,92..$]'
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dTORTOISEtoHere(data, ptaylor_env):
opref = data.outdir / "o.3dTORTOISEtoHere"
cmd = f"""
3dTORTOISEtoHere
-echo_edu
-dt_tort {data.odtT}
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_1dDW_Grad_o_Mat_plus_plus_colvec(data, ptaylor_env):
outfile = data.outdir / "o.1dDW_Grad_o_Mat++_cvec_n-1.txt"
cmd = f"""
1dDW_Grad_o_Mat++
-echo_edu
-in_row_vec {data.bvec}'[3..32]'
-flip_y
-out_col_vec {outfile}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dZipperZapper(data, ptaylor_env):
opref = data.outdir / "o.3dZipperZapper"
cmd = f"""
3dZipperZapper
-echo_edu
-input {data.AVEB0_DWI}'[0..10]'
-mask {data.mask_minisphere_dwi}
-prefix {opref}
-do_out_slice_param
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dVecRGB_to_HSL(data, ptaylor_env):
opref = data.outdir / "o.3dVecRGB_to_HSL"
cmd = f"""
3dVecRGB_to_HSL
-echo_edu
-in_vec {data.DT_V1}
-in_scal {data.DT_FA}
-mask {data.mask_DWI}
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dAmpToRSFC(data, ptaylor_env):
opref = data.outdir / "o.3dAmpToRSFC"
cmd = f"""
3dAmpToRSFC
-nifti
-band 0.01 0.1
-mask {data.mask_DWI}
-in_amp {data.OLSAMP}
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3ddot_beta(data, ptaylor_env):
opref = data.outdir / "o.3ddot_beta"
cmd = f"""
3ddot_beta
-echo_edu
-input {data.SOME_ICA_NETS_in_DWI}
-mask {data.mask_DWI}
-doeta2
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dmaskdump_basic(data):
outfile_path = data.outdir / ("Vrel_tstats.txt")
cmd = """
3dmaskdump
-noijk
-mask {data.mask} {data.epi}
> {outfile_path}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dmaskave_basic(data):
outfile_prefix = data.outdir / ("anat_roi_resam.nii.gz")
out_1d = data.outdir / ("epi_avg.1D")
cmd = """
3dmaskave
-mask {data.mask}
-quiet {data.epi}
> {out_1d}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dNetCorr(data, ptaylor_env):
opref = data.outdir / "o.3dNetCorr"
cmd = f"""
3dNetCorr
-echo_edu
-inset {data.REST_in_DWI}'[5..50]'
-in_rois {data.ROI_ICMAP_GM}
-prefix {opref}
-fish_z
-ts_wb_Z
-nifti
-ts_out
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run(timeout=60)
def test_1dDW_Grad_o_Mat__plus____plus___basic(data):
outfile = data.outdir / "GRADS_30.dat"
cmd = """
1dDW_Grad_o_Mat++
-in_row_vec {data.bvec}'[2..32]'
-flip_y
-out_col_vec {outfile}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dTstat_basic(data, statistic):
outfile = data.outdir / "stat.nii.gz"
cmd = """
3dTstat
-prefix {outfile}
-{statistic}
{data.epi}
"""
cmd = " ".join(cmd.format(**locals()).split())
# If this is known to cause difficulties, reduce the rtol
kwargs_scans = {"data_kwargs": {}, "header_kwargs": {}}
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd, kwargs_scans=kwargs_scans)
differ.run(timeout=60)
def test_1d_tool(data):
outfile = data.outdir / "1d_tool_output.1d"
cmd = """
1d_tool.py
-set_run_lengths 150 150 150
-index_to_run_tr 324
> {outfile}
"""
cmd = " ".join(cmd.format(**locals()).split())
# Run command and test all outputs match
differ = tools.OutputDiffer(data, cmd)
differ.run()
def test_3dMatch(data, ptaylor_env):
opref = data.outdir / "o.3dMatch"
cmd = f"""
3dMatch
-echo_edu
-only_dice_thr
-inset {data.SOME_ICA_NETS_in_DWI}
-refset {data.MULTISITE_in_DWI}
-mask {data.mask_DWI}
-in_min 1.0
-ref_min 3
-prefix {opref}
"""
cmd = " ".join(cmd.split())
differ = tools.OutputDiffer(data, cmd)
differ.run()