rapidtide 3.0a13__py3-none-any.whl → 3.0a14__py3-none-any.whl

rapidtide/tests/test_fullrunhappy_v4.py

@@ -25,22 +25,30 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v4(debug=False, displayplots=False):
+def test_fullrunhappy_v4(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run happy
     inputargs = [
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
-        os.path.join(get_test_temp_path(), "happyout4"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout4"),
         "--estweights",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--projmask",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_smallmask.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_smallmask.nii.gz"),
         "--mklthreads",
         "-1",
         "--model",
         "model_revised",
         "--motionfile",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--aliasedcorrelation",
     ]
     happy_workflow.happy_main(happy_parser.process_args(inputargs=inputargs))
@@ -48,4 +56,4 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v4(debug=True, displayplots=True)
+    test_fullrunhappy_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunhappy_v5.py

@@ -25,16 +25,24 @@ import rapidtide.workflows.happy_parser as happy_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunhappy_v4(debug=False, displayplots=False):
+def test_fullrunhappy_v4(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run happy
     inputargs = [
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.nii.gz"),
-        os.path.join(get_examples_path(), "sub-HAPPYTEST.json"),
-        os.path.join(get_test_temp_path(), "happyout5"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.nii.gz"),
+        os.path.join(exampleroot, "sub-HAPPYTEST.json"),
+        os.path.join(testtemproot, "happyout5"),
         "--model",
         "model_revised",
         "--motionfile",
-        os.path.join(get_examples_path(), "sub-HAPPYTEST_mcf.par"),
+        os.path.join(exampleroot, "sub-HAPPYTEST_mcf.par"),
         "--nomotderiv",
         "--nomotorthogonalize",
         "--motfiltorder",
@@ -53,4 +61,4 @@ def test_fullrunhappy_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunhappy_v4(debug=True, displayplots=True)
+    test_fullrunhappy_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v1.py

@@ -26,11 +26,19 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v1(debug=False, displayplots=False):
+def test_fullrunrapidtide_v1(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -46,11 +54,11 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "4.0",
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
-    rapidtide_quality.qualitycheck(os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1"))
+    rapidtide_quality.qualitycheck(os.path.join(testtemproot, "sub-RAPIDTIDETEST1"))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_fixval"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_fixval"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -70,8 +78,8 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_fixmap"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_fixmap"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -85,11 +93,11 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "3",
         "--nodenoise",
         "--initialdelay",
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_desc-maxtime_map.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST1_desc-maxtime_map.nii.gz"),
     ]
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v1(debug=True, displayplots=True)
+    test_fullrunrapidtide_v1(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v2.py

@@ -25,27 +25,35 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v2(debug=False, displayplots=False):
+def test_fullrunrapidtide_v2(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST2"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST2"),
         "--tincludemask",
-        os.path.join(get_examples_path(), "tmask3.txt"),
+        os.path.join(exampleroot, "tmask3.txt"),
         "--corrmask",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz"),
         "--globalmeaninclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--globalmeanexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--refineinclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--refineexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--offsetinclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_brainmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_brainmask.nii.gz"),
         "--offsetexclude",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_nullmask.nii.gz"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_nullmask.nii.gz"),
         "--spatialfilt",
         "-1",
         "--savelags",
@@ -74,7 +82,7 @@ def test_fullrunrapidtide_v2(debug=False, displayplots=False):
         "--refineprenorm",
         "var",
         "--motionfile",
-        os.path.join(get_examples_path(), "fakemotion.par"),
+        os.path.join(exampleroot, "fakemotion.par"),
     ]
     if debug:
         print(inputargs)
@@ -83,4 +91,4 @@ def test_fullrunrapidtide_v2(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v2(debug=True, displayplots=True)
+    test_fullrunrapidtide_v2(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v3.py

@@ -25,13 +25,21 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v3(debug=False, displayplots=False):
+def test_fullrunrapidtide_v3(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST3"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST3"),
         "--corrmask",
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_restrictedmask.nii.gz:1"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_restrictedmask.nii.gz:1"),
         "--maxpasses",
         "2",
         "--numnull",
@@ -60,7 +68,7 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
         "R",
         "--regressor",
         os.path.join(
-            get_examples_path(),
+            exampleroot,
             "sub-RAPIDTIDETEST_desc-oversampledmovingregressor_timeseries.json:pass3",
         ),
     ]
@@ -71,4 +79,4 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v3(debug=True, displayplots=True)
+    test_fullrunrapidtide_v3(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v4.py

@@ -25,18 +25,25 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v4(debug=False, displayplots=False):
+def test_fullrunrapidtide_v4(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-NIRSRAPIDTIDETEST.txt"),
-        os.path.join(get_test_temp_path(), "sub-NIRSRAPIDTIDETEST4"),
+        os.path.join(exampleroot, "sub-NIRSRAPIDTIDETEST.txt"),
+        os.path.join(testtemproot, "sub-NIRSRAPIDTIDETEST4"),
         "--globalmeaninclude",
-        os.path.join(get_examples_path(), "sub-NIRSRAPIDTIDETEST_mask.txt"),
+        os.path.join(exampleroot, "sub-NIRSRAPIDTIDETEST_mask.txt"),
         "--nirs",
         "--datatstep",
         "0.2560",
-        "--globalmaskmethod",
-        "variance",
+        "--dataiszeromean",
         "--norefinedelay",
         "--despecklepasses",
         "0",
@@ -59,4 +66,4 @@ def test_fullrunrapidtide_v4(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v4(debug=True, displayplots=True)
+    test_fullrunrapidtide_v4(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v5.py

@@ -25,11 +25,19 @@ import rapidtide.workflows.rapidtide_parser as rapidtide_parser
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v5(debug=False, displayplots=False):
+def test_fullrunrapidtide_v5(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST_cifti.ptseries.nii"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST5"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST_cifti.ptseries.nii"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST5"),
         "--nprocs",
         "-1",
         "--passes",
@@ -46,4 +54,4 @@ def test_fullrunrapidtide_v5(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v5(debug=True, displayplots=True)
+    test_fullrunrapidtide_v5(debug=True, local=True, displayplots=True)

rapidtide/tests/test_fullrunrapidtide_v6.py

@@ -28,11 +28,19 @@ import rapidtide.workflows.retroregress as rapidtide_retroregress
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
-def test_fullrunrapidtide_v6(debug=False, displayplots=False):
+def test_fullrunrapidtide_v6(debug=False, local=False, displayplots=False):
+    # set input and output directories
+    if local:
+        exampleroot = "../data/examples/src"
+        testtemproot = "./tmp"
+    else:
+        exampleroot = get_examples_path()
+        testtemproot = get_test_temp_path()
+
     # run rapidtide
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--spatialfilt",
         "2",
         "--simcalcrange",
@@ -54,10 +62,10 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
     rapidtide_workflow.rapidtide_main(rapidtide_parser.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "2deriv"),
+        os.path.join(testtemproot, "2deriv"),
         "--nprocs",
         "-1",
         "--regressderivs",
@@ -69,10 +77,10 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
     rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "1deriv_refined_corrected"),
+        os.path.join(testtemproot, "1deriv_refined_corrected"),
         "--nprocs",
         "1",
         "--regressderivs",
@@ -85,10 +93,10 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
     rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
-        os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
-        os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST6"),
+        os.path.join(exampleroot, "sub-RAPIDTIDETEST.nii.gz"),
+        os.path.join(testtemproot, "sub-RAPIDTIDETEST6"),
         "--alternateoutput",
-        os.path.join(get_test_temp_path(), "concordance"),
+        os.path.join(testtemproot, "concordance"),
         "--nprocs",
         "-1",
         "--regressderivs",
@@ -118,8 +126,8 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         "lfofilterR",
     ]:
         print(f"Testing map={map}")
-        filename1 = os.path.join(get_test_temp_path(), f"sub-RAPIDTIDETEST6_desc-{map}_map.nii.gz")
-        filename2 = os.path.join(get_test_temp_path(), f"concordance_desc-{map}_map.nii.gz")
+        filename1 = os.path.join(testtemproot, f"sub-RAPIDTIDETEST6_desc-{map}_map.nii.gz")
+        filename2 = os.path.join(testtemproot, f"concordance_desc-{map}_map.nii.gz")
         assert tide_io.checkniftifilematch(
             filename1,
             filename2,
@@ -132,4 +140,4 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_fullrunrapidtide_v6(debug=True, displayplots=True)
+    test_fullrunrapidtide_v6(debug=True, local=True, displayplots=True)

rapidtide/tests/test_refinedelay.py

@@ -195,7 +195,9 @@ def eval_refinedelay(
 
     delayoffset = filteredregressderivratios * 0.0
     for i in range(filteredregressderivratios.shape[0]):
-        delayoffset[i] = tide_refinedelay.ratiotodelay(filteredregressderivratios[i])
+        delayoffset[i], closestoffset = tide_refinedelay.ratiotodelay(
+            filteredregressderivratios[i]
+        )
 
     # do the tests
     msethresh = 0.1

rapidtide/workflows/atlasaverage.py

@@ -135,6 +135,15 @@ def _get_parser():
         ),
         default=None,
     )
+    parser.add_argument(
+        "--regionlabelfile",
+        type=lambda x: pf.is_valid_file(parser, x),
+        help=(
+            "The name of of a text file containing the labels of the regions, one per line.  The first line is "
+            "the label integer value 1, etc."
+        ),
+        default=None,
+    )
     parser.add_argument(
         "--includemask",
         dest="includespec",
@@ -224,11 +233,9 @@ def atlasaverage(args):
         sys.exit()
 
     print("reshaping")
-    xsize = thedims[1]
-    ysize = thedims[2]
-    numslices = thedims[3]
-    numtimepoints = thedims[4]
-    numvoxels = int(xsize) * int(ysize) * int(numslices)
+    xdim, ydim, numslices, numtimepoints = tide_io.parseniftidims(thedims)
+    xsize, ysize, slicethickness, tr = tide_io.parseniftisizes(thesizes)
+    numvoxels = int(xdim) * int(ydim) * int(numslices)
 
     templatevoxels = np.reshape(template_data, numvoxels).astype(int)
     inputvoxels = np.reshape(input_data, (numvoxels, numtimepoints))
@@ -273,7 +280,7 @@ def atlasaverage(args):
         themask = themask * includemask.reshape((numvoxels))
         if args.debug:
             tide_io.savetonifti(
-                includemask.reshape((xsize, ysize, numslices)),
+                includemask.reshape((xdim, ydim, numslices)),
                 template_hdr,
                 f"{args.outputroot}_includemask",
             )
@@ -281,7 +288,7 @@ def atlasaverage(args):
         themask = themask * (1 - excludemask.reshape((numvoxels)))
         if args.debug:
             tide_io.savetonifti(
-                excludemask.reshape((xsize, ysize, numslices)),
+                excludemask.reshape((xdim, ydim, numslices)),
                 template_hdr,
                 f"{args.outputroot}_excludemask",
             )
@@ -289,11 +296,21 @@ def atlasaverage(args):
         themask = themask * extramask.reshape((numvoxels))
         if args.debug:
             tide_io.savetonifti(
-                extramask.reshape((xsize, ysize, numslices)),
+                extramask.reshape((xdim, ydim, numslices)),
                 template_hdr,
                 f"{args.outputroot}_extramask",
             )
 
+    # get the region names
+    if args.regionlabelfile is None:
+        regionlabels = []
+        numregions = np.max(templatevoxels)
+        numdigits = int(np.log10(numregions)) + 1
+        for regnum in range(1, numregions + 1):
+            regionlabels.append(f"region_{str(regnum).zfill(numdigits)}")
+    else:
+        regionlabels = tide_io.readlabels(args.regionlabelfile)
+
     # decide what regions we will summarize
     if args.regionlistfile is None:
         numregions = np.max(templatevoxels)
@@ -301,6 +318,11 @@ def atlasaverage(args):
     else:
         regionlist = tide_io.readvec(args.regionlistfile).astype(int)
         numregions = len(regionlist)
+        newlabels = []
+        for theregion in range(numregions):
+            newlabels.append(regionlabels[theregion])
+        regionlabels = newlabels
+
     timecourses = np.zeros((numregions, numtimepoints), dtype="float")
     print(f"{numregions=}, {regionlist=}")
 
@@ -348,7 +370,13 @@ def atlasaverage(args):
                 )
         if args.debug:
             print("timecourses shape:", timecourses.shape)
-        tide_io.writenpvecs(timecourses, args.outputroot)
+        tide_io.writebidstsv(
+            args.outputroot,
+            timecourses,
+            1.0 / tr,
+            columns=regionlabels,
+            yaxislabel="delay offset",
+        )
     else:
         print("processing 3D input file")
         outputvoxels = inputvoxels * 0.0
@@ -416,19 +444,19 @@ def atlasaverage(args):
                 segmentedatlasvoxels += scratchvoxels
         template_hdr["dim"][4] = 1
         tide_io.savetonifti(
-            outputvoxels.reshape((xsize, ysize, numslices)),
+            outputvoxels.reshape((xdim, ydim, numslices)),
             template_hdr,
             args.outputroot,
         )
         tide_io.savetonifti(
-            segmentedatlasvoxels.reshape((xsize, ysize, numslices)),
+            segmentedatlasvoxels.reshape((xdim, ydim, numslices)),
             template_hdr,
             args.outputroot + "_percentiles",
         )
 
         if args.includename is not None or args.excludename is not None:
             tide_io.savetonifti(
-                (templatevoxels * themask).reshape((xsize, ysize, numslices)),
+                (templatevoxels * themask).reshape((xdim, ydim, numslices)),
                 template_hdr,
                 f"{args.outputroot}_maskedatlas",
             )