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

rapidtide/workflows/delayvar.py

@@ -27,6 +27,7 @@ from pathlib import Path
 import numpy as np
 from scipy.stats import pearsonr
 from sklearn.decomposition import PCA
+from tf_keras.src.dtensor.integration_test_utils import train_step
 
 import rapidtide.filter as tide_filt
 import rapidtide.io as tide_io
@@ -61,7 +62,8 @@ DEFAULT_DELAYOFFSETSPATIALFILT = -1
 DEFAULT_WINDOWSIZE = 30.0
 DEFAULT_SYSTEMICFITTYPE = "pca"
 DEFAULT_PCACOMPONENTS = 1
-DEFAULT_TRAINWIDTH = 0.0
+DEFAULT_LAGMIN = 0.0
+DEFAULT_LAGMAX = 0.0
 DEFAULT_TRAINSTEP = 0.5
 
 
@@ -146,19 +148,19 @@ def _get_parser():
         default=True,
     )
     parser.add_argument(
-        "--trainwidth",
-        dest="trainwidth",
-        action="store",
+        "--trainrange",
+        dest="lag_extrema",
+        action=pf.IndicateSpecifiedAction,
+        nargs=2,
         type=float,
-        metavar="WIDTH",
+        metavar=("LAGMIN", "LAGMAX"),
         help=(
-            "Train the ratio offset function over this range of central delays (in seconds).  The derivative "
+            "Set the range of delay offset center frequencies to span LAGMIN to LAGMAX. The derivative "
             "ratio calculation only works over a narrow range, so if the static offset is large, "
             "you need to train the ratio calculation with a central delay close to that value. "
-            "Set negative to select the width automatically. "
-            f"Default is {DEFAULT_TRAINWIDTH}"
+            f"LAGMAX.  Default is {DEFAULT_LAGMIN} to {DEFAULT_LAGMAX} seconds. "
         ),
-        default=DEFAULT_TRAINWIDTH,
+        default=(DEFAULT_LAGMIN, DEFAULT_LAGMAX),
     )
     parser.add_argument(
         "--trainstep",
@@ -209,6 +211,13 @@ def _get_parser():
         help="Use NCOMP components for PCA fit of delay offset.",
         default=DEFAULT_PCACOMPONENTS,
     )
+    parser.add_argument(
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help=("Be wicked chatty."),
+        default=False,
+    )
     parser.add_argument(
         "--debug",
         dest="debug",
@@ -259,6 +268,9 @@ def delayvar(args):
     # get the pid of the parent process
     args.pid = os.getpid()
 
+    args.lagmin = args.lag_extrema[0]
+    args.lagmax = args.lag_extrema[1]
+
     # specify the output name
     if args.alternateoutput is None:
         outputname = args.datafileroot
@@ -502,6 +514,16 @@ def delayvar(args):
     # windowed delay deviation estimation
     lagstouse_valid = lagtimes_valid
 
+    # find the robust range of the static delays
+    (
+        pct02,
+        pct98,
+    ) = tide_stats.getfracvals(lagstouse_valid, [0.02, 0.98], debug=args.debug)
+    if args.lagmin == -999:
+        args.lagmin = np.round(pct02 / args.trainstep, 0) * args.trainstep
+    if args.lagmax == -999:
+        args.lagmax = np.round(pct98 / args.trainstep, 0) * args.trainstep
+
     print("\n\nWindowed delay estimation")
     TimingLGR.info("Windowed delay estimation start")
     LGR.info("\n\nWindowed delay estimation")
@@ -537,7 +559,7 @@ def delayvar(args):
             thehpf.apply(genlagsamplerate, reference_y),
             padtime=thepadtime,
         )
-        genlagtc.save(f"{outputname}_desc-lagtcgenerator_timeseries")
+        genlagtc.save(f"{outputname}_desc-hpflagtcgenerator_timeseries")
 
     # and filter the data if necessary
     if args.hpf:
@@ -582,7 +604,7 @@ def delayvar(args):
         numwins,
     )
     internalwinfmrishape = (numvalidspatiallocs, wintrs)
-    if args.debug or args.focaldebug:
+    if args.debug:
         print(f"window space shape = {internalwinspaceshape}")
         print(f"internalwindowfmrishape shape = {internalwinfmrishape}")
 
@@ -591,6 +613,7 @@ def delayvar(args):
     windowedmedfiltregressderivratios = np.zeros(internalwinspaceshape, dtype=float)
     windowedfilteredregressderivratios = np.zeros(internalwinspaceshape, dtype=float)
     windoweddelayoffset = np.zeros(internalwinspaceshape, dtype=float)
+    windowedclosestoffset = np.zeros(internalwinspaceshape, dtype=float)
     if usesharedmem:
         if args.debug:
             print("allocating shared memory")
@@ -626,17 +649,30 @@ def delayvar(args):
     if args.debug:
         print(f"wintrs={wintrs}, winskip={winskip}, numtrs={numtrs}, numwins={numwins}")
     thewindowprocoptions = therunoptions
+    if args.verbose:
+        thewindowprocoptions["showprogressbar"] = True
+    else:
+        thewindowprocoptions["showprogressbar"] = False
     if args.focaldebug:
         thewindowprocoptions["saveminimumsLFOfiltfiles"] = True
         winoutputlevel = "max"
     else:
         thewindowprocoptions["saveminimumsLFOfiltfiles"] = False
         winoutputlevel = "min"
+
+    # Now get the derivative ratios the individual windows
+    print("Finding derivative ratios:")
     for thewin in range(numwins):
-        print(f"Processing window {thewin + 1} of {numwins}")
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
         starttr = thewin * winskip
         endtr = starttr + wintrs
         winlabel = f"_win-{str(thewin + 1).zfill(3)}"
+        if args.verbose:
+            thisLGR = LGR
+            thisTimingLGR = TimingLGR
+        else:
+            thisLGR = None
+            thisTimingLGR = None
 
         windowedregressderivratios[:, thewin], windowedregressrvalues[:, thewin] = (
             tide_refinedelay.getderivratios(
@@ -657,8 +693,8 @@ def delayvar(args):
                 winmovingsignal,
                 winlagtc,
                 winfiltereddata,
-                LGR,
-                TimingLGR,
+                thisLGR,
+                thisTimingLGR,
                 thewindowprocoptions,
                 regressderivs=1,
                 starttr=starttr,
@@ -666,7 +702,33 @@ def delayvar(args):
                 debug=args.debug,
             )
         )
+        if args.focaldebug:
+            theheader = copy.deepcopy(fmri_header)
+            theheader["dim"][4] = wintrs
+            theheader["toffset"] = winwidth / 2.0
+            maplist = [
+                (
+                    winlagtc,
+                    "windowedlagtcs",
+                    "bold",
+                    None,
+                    f"Lagtcs in each {winspace} second window",
+                ),
+            ]
+            tide_io.savemaplist(
+                outputname + winlabel,
+                maplist,
+                validvoxels,
+                (xsize, ysize, numslices, wintrs),
+                theheader,
+                bidsbasedict,
+                debug=args.debug,
+            )
 
+    # Filter the derivative ratios
+    print("Filtering derivative ratios:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
         (
             windowedmedfiltregressderivratios[:, thewin],
             windowedfilteredregressderivratios[:, thewin],
@@ -681,34 +743,62 @@ def delayvar(args):
             fileiscifti=False,
             textio=False,
             rt_floattype=rt_floattype,
+            verbose=args.verbose,
             debug=args.debug,
         )
 
+    # Train the ratio offsets
+    print("Training ratio offsets:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
+        starttr = thewin * winskip
+        endtr = starttr + wintrs
+        winlabel = f"_win-{str(thewin + 1).zfill(3)}"
         # find the mapping of glm ratios to delays
         tide_refinedelay.trainratiotooffset(
             genlagtc,
             initial_fmri_x[starttr:endtr],
             outputname + winlabel,
             winoutputlevel,
-            trainwidth=args.trainwidth,
-            trainstep=args.trainstep,
+            trainlagmin=args.lagmin,
+            trainlagmax=args.lagmax,
+            trainlagstep=args.trainstep,
             mindelay=args.mindelay,
             maxdelay=args.maxdelay,
             numpoints=args.numpoints,
-            debug=args.debug,
+            verbose=args.verbose,
+            debug=args.focaldebug,
         )
         TimingLGR.info("Refinement calibration end")
 
-        # now calculate the delay offsets
+    # now calculate the delay offsets
+    print("Calculating delay offsets:")
+    for thewin in range(numwins):
+        print(f"\tProcessing window {thewin + 1} of {numwins}")
+        winlabel = f"_win-{str(thewin + 1).zfill(3)}"
         TimingLGR.info("Calculating delay offsets")
-        if args.focaldebug:
+        if args.debug:
             print(
                 f"calculating delayoffsets for {windowedfilteredregressderivratios.shape[0]} voxels"
             )
         for i in range(windowedfilteredregressderivratios.shape[0]):
-            windoweddelayoffset[i, thewin] = tide_refinedelay.ratiotodelay(
-                windowedfilteredregressderivratios[i, thewin]
+            (windoweddelayoffset[i, thewin], windowedclosestoffset[i, thewin]) = (
+                tide_refinedelay.ratiotodelay(
+                    windowedfilteredregressderivratios[i, thewin],
+                    offset=lagstouse_valid[i],
+                    debug=args.focaldebug,
+                )
             )
+        namesuffix = "_desc-delayoffset_hist"
+        tide_stats.makeandsavehistogram(
+            windoweddelayoffset[:, thewin],
+            therunoptions["histlen"],
+            1,
+            outputname + winlabel + namesuffix,
+            displaytitle="Histogram of delay offsets calculated from GLM",
+            dictvarname="delayoffsethist",
+            thedict=None,
+        )
 
     # now see if there are common timecourses in the delay offsets
     themean = np.mean(windoweddelayoffset, axis=1)
@@ -749,7 +839,7 @@ def delayvar(args):
         # unscale the PCA cleaned data
         for vox in range(0, windoweddelayoffset.shape[0]):
             reduceddata[vox, :] = reduceddata[vox, :] * thevar[vox] + themean[vox]
-        if args.focaldebug:
+        if args.debug:
             print("complex processing: reduceddata.shape =", scaledvoxels.shape)
         # pcadata = np.mean(reduceddata, axis=0)
         pcadata = thefit.components_[0]
@@ -850,22 +940,13 @@ def delayvar(args):
             nprocs_regressionfilt=args.nprocs,
             regressderivs=1,
             showprogressbar=args.showprogressbar,
-            debug=args.focaldebug,
+            debug=args.debug,
         )
 
-    namesuffix = f"_desc-delayoffsetwin{thewin}_hist"
-    tide_stats.makeandsavehistogram(
-        windoweddelayoffset[:, thewin],
-        therunoptions["histlen"],
-        1,
-        outputname + namesuffix,
-        displaytitle="Histogram of delay offsets calculated from GLM",
-        dictvarname="delayoffsethist",
-        thedict=None,
-    )
     theheader = copy.deepcopy(fmri_header)
     theheader["dim"][4] = numwins
     theheader["pixdim"][4] = winspace
+    theheader["toffset"] = winwidth / 2.0
     maplist = [
         (
             windoweddelayoffset,
@@ -874,6 +955,13 @@ def delayvar(args):
             None,
             f"Delay offsets in each {winspace} second window",
         ),
+        (
+            windowedclosestoffset,
+            "windowedclosestoffset",
+            "info",
+            None,
+            f"Closest delay offsets in each {winspace} second window",
+        ),
         (
             np.square(windowedregressrvalues),
             "windowedregressr2values",

rapidtide/workflows/rapidtide.py

@@ -607,14 +607,16 @@ def rapidtide_main(argparsingfunc):
     fmri_data = nim_data.reshape((numspatiallocs, timepoints))[:, validstart : validend + 1]
 
     # detect zero mean data
-    optiondict["dataiszeromean"] = checkforzeromean(fmri_data)
+    if not optiondict["dataiszeromean"]:
+        # check anyway
+        optiondict["dataiszeromean"] = checkforzeromean(fmri_data)
+
     if optiondict["dataiszeromean"]:
         LGR.warning(
             "WARNING: dataset is zero mean - forcing variance masking and no refine prenormalization. "
             "Consider specifying a global mean and correlation mask."
         )
         optiondict["refineprenorm"] = "None"
-        optiondict["globalmaskmethod"] = "variance"
 
     # reformat the brain mask, if it exists
     if brainmask is None:
@@ -716,18 +718,18 @@ def rapidtide_main(argparsingfunc):
         corrmask[np.where(datarange == 0)] = 0.0
     else:
         # check to see if the data has been demeaned
-        meanim = np.mean(fmri_data, axis=1)
-        stdim = np.std(fmri_data, axis=1)
-        if fileiscifti:
+        if fileiscifti or optiondict["textio"]:
             corrmask = np.uint(nim_data[:, 0] * 0 + 1)
         else:
-            if (np.mean(stdim) < np.mean(meanim)) and not optiondict["nirs"]:
+            if optiondict["dataiszeromean"]:
                 LGR.verbose("generating correlation mask from mean image")
                 corrmask = np.uint16(tide_mask.makeepimask(nim).dataobj.reshape(numspatiallocs))
             else:
                 LGR.verbose("generating correlation mask from std image")
                 corrmask = np.uint16(
-                    tide_stats.makemask(stdim, threshpct=optiondict["corrmaskthreshpct"])
+                    tide_stats.makemask(
+                        np.std(fmri_data, axis=1), threshpct=optiondict["corrmaskthreshpct"]
+                    )
                 )
     if internalbrainmask is not None:
         corrmask = internalbrainmask
@@ -3429,7 +3431,9 @@ def rapidtide_main(argparsingfunc):
                         f"calculating delayoffsets for {filteredregressderivratios.shape[0]} voxels"
                     )
                 for i in range(filteredregressderivratios.shape[0]):
-                    delayoffset[i] = tide_refinedelay.ratiotodelay(filteredregressderivratios[i])
+                    delayoffset[i], closestoffset = tide_refinedelay.ratiotodelay(
+                        filteredregressderivratios[i]
+                    )
             else:
                 medfiltregressderivratios = np.zeros_like(regressderivratios)
                 filteredregressderivratios = np.zeros_like(regressderivratios)

rapidtide/workflows/rapidtide_parser.py

@@ -70,7 +70,6 @@ DEFAULT_MAXPASSES = 15
 DEFAULT_REFINE_TYPE = "pca"
 DEFAULT_INTERPTYPE = "univariate"
 DEFAULT_WINDOW_TYPE = "hamming"
-DEFAULT_GLOBALMASK_METHOD = "mean"
 DEFAULT_GLOBALSIGNAL_METHOD = "sum"
 DEFAULT_CORRWEIGHTING = "phat"
 DEFAULT_CORRTYPE = "linear"
@@ -240,7 +239,7 @@ def _get_parser():
         action="store_true",
         help=(
             "This is a NIRS analysis - this is a macro that "
-            "sets nothresh, refineprenorm=var, ampthresh=0.7, and "
+            "sets nothresh, dataiszeromean=True, refineprenorm=var, ampthresh=0.7, and "
             "lagminthresh=0.1. "
         ),
         default=False,
@@ -382,6 +381,17 @@ def _get_parser():
         ),
         default=False,
     )
+    preproc.add_argument(
+        "--dataiszeromean",
+        dest="dataiszeromean",
+        action="store_true",
+        help=(
+            "Assume that the fMRI data is zero mean (this will be the case if you used AFNI for preprocessing).  "
+            "This affects how masks are generated.  Rapidtide will attempt to detect this, but set explicitly "
+            "if you know this is the case."
+        ),
+        default=False,
+    )
 
     # Add filter options
     pf.addfilteropts(parser, filtertarget="data and regressors", details=True)
@@ -444,19 +454,6 @@ def _get_parser():
         ),
         default=False,
     )
-    preproc.add_argument(
-        "--globalmaskmethod",
-        dest="globalmaskmethod",
-        action="store",
-        type=str,
-        choices=["mean", "variance"],
-        help=(
-            "Select whether to use timecourse mean or variance to "
-            "mask voxels prior to generating global mean. "
-            f'Default is "{DEFAULT_GLOBALMASK_METHOD}".'
-        ),
-        default=DEFAULT_GLOBALMASK_METHOD,
-    )
     preproc.add_argument(
         "--globalmeaninclude",
         dest="globalmeanincludespec",
@@ -2211,6 +2208,7 @@ def process_args(inputargs=None):
         LGR.warning('Using "nirs" macro. Overriding any affected arguments.')
         args["nothresh"] = True
         pf.setifnotset(args, "preservefiltering", False)
+        args["dataiszeromean"] = True
         args["refineprenorm"] = "var"
         args["ampthresh"] = 0.7
         args["ampthreshfromsig"] = False

rapidtide/workflows/regressfrommaps.py

@@ -121,6 +121,7 @@ def regressfrommaps(
         fitmask,
         lagtimes,
         lagtc,
+        LGR=LGR,
         nprocs=nprocs_makelaggedtcs,
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
@@ -187,6 +188,7 @@ def regressfrommaps(
         nprocs=nprocs_regressionfilt,
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
+        verbose=(LGR is not None),
         mp_chunksize=mp_chunksize,
         rt_floatset=rt_floatset,
         rt_floattype=rt_floattype,

rapidtide/workflows/retrolagtcs.py

@@ -257,6 +257,7 @@ def retrolagtcs(args):
         procmask_valid,
         lagtimes_valid,
         lagtc,
+        LGR=LGR,
         nprocs=args.nprocs,
         showprogressbar=args.showprogressbar,
     )

rapidtide/workflows/retroregress.py

@@ -295,7 +295,29 @@ def retroregress(args):
         print(f"illegal output level {args['outputlevel']}")
         sys.exit()
 
+    # save the raw and formatted command lines
+    argstowrite = sys.argv
     thecommandline = " ".join(sys.argv[1:])
+    tide_io.writevec([thecommandline], f"{outputname}_retrocommandline.txt")
+    formattedcommandline = []
+    for thetoken in argstowrite[0:3]:
+        formattedcommandline.append(thetoken)
+    for thetoken in argstowrite[3:]:
+        if thetoken[0:2] == "--":
+            formattedcommandline.append(thetoken)
+        else:
+            formattedcommandline[-1] += " " + thetoken
+    for i in range(len(formattedcommandline)):
+        if i > 0:
+            prefix = "    "
+        else:
+            prefix = ""
+        if i < len(formattedcommandline) - 1:
+            suffix = " \\"
+        else:
+            suffix = ""
+        formattedcommandline[i] = prefix + formattedcommandline[i] + suffix
+    tide_io.writevec(formattedcommandline, f"{outputname}_retroformattedcommandline.txt")
 
     if args.nprocs < 1:
         args.nprocs = tide_multiproc.maxcpus()
@@ -659,7 +681,9 @@ def retroregress(args):
             if args.debug:
                 print(f"calculating delayoffsets for {filteredregressderivratios.shape[0]} voxels")
             for i in range(filteredregressderivratios.shape[0]):
-                delayoffset[i] = tide_refinedelay.ratiotodelay(filteredregressderivratios[i])
+                delayoffset[i], closestoffset = tide_refinedelay.ratiotodelay(
+                    filteredregressderivratios[i]
+                )
                 """delayoffset[i] = tide_refinedelay.coffstodelay(
                     np.asarray([filteredregressderivratios[i]]),
                     mindelay=args.mindelay,

{rapidtide-3.0a13.dist-info → rapidtide-3.0a14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0a13
+Version: 3.0a14
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>

{rapidtide-3.0a13.dist-info → rapidtide-3.0a14.dist-info}/RECORD

@@ -7,7 +7,7 @@ cloud/rapidtide-HCPYA,sha256=kqW8ENbOQhvVqZGz-HqiVbrbzHy4cfyy1rk8ejpJor0,963
 cloud/rapidtide-cloud-test,sha256=SATOwGo4QYLvt-6hE0e3wyK9JjuDU5XzfLrfMoybvcY,466
 cloud/simple-cp-test,sha256=5ef8wmLfcKdny59BV6_DnAPj7O_mi0rOHdFZVN2iiLA,421
 rapidtide/Colortables.py,sha256=Qok5h6-U6sVl0zhITI8D0Uxtp3zmyQv4OCiU-6sNTnM,5814
-rapidtide/DerivativeDelay.py,sha256=ODMwsY3of7rfH0IIqKgCxntTQGeNNSNoGMjKpIluHTg,7200
+rapidtide/DerivativeDelay.py,sha256=OtLUFE3wfGz9y5GuVszUtYYqPXxTzYW2UP_leNRS6ac,7253
 rapidtide/OrthoImageItem.py,sha256=uN-fMX4vVB00-AFoUnfOXXq1qjLXruzOqYttNJYpIpM,21669
 rapidtide/RapidtideDataset.py,sha256=BEGznVDvLzL1Cd9TtuwicCYXcVug8hX1t-6qnEjMEDg,52239
 rapidtide/RegressorRefiner.py,sha256=Cp5hGsEO_KYiTxbtZCLBTsgi5gjKd3xoP_A3TaQtF_E,17232
@@ -26,15 +26,15 @@ rapidtide/fit.py,sha256=GA7v2fuQnSztsUCFdqEbAzdXRyLUXI-aQw_E31WvsOs,68081
 rapidtide/happy_supportfuncs.py,sha256=z9VTliXvZoQEjU6FSaPk6etYUB7KSFCQbdzMIAVx6ik,47937
 rapidtide/helper_classes.py,sha256=jMS1SIU8YFZrZ10s3kOwbT0139CtTG3DLkJoyuDiiNQ,51401
 rapidtide/io.py,sha256=tEw1E1Gsxu-_A1spMz1wU98d9R5xZof06qiGvYr2sEQ,74789
-rapidtide/linfitfiltpass.py,sha256=mzG-sOVtBR0nx3M8nknNUm9yRv2dqPukIqQXW8D3sLc,16095
-rapidtide/makelaggedtcs.py,sha256=GsJ3svPSRJIHzJ9F5ZpT0eW3k6rIUCGXgq4o-sK4R-E,3889
+rapidtide/linfitfiltpass.py,sha256=fXUhCvT9Yd1qmwokHxpK_UBeUA55-FlDkhG10JHGl7o,16142
+rapidtide/makelaggedtcs.py,sha256=FFqnCuTYRBhcpFgJVffvOaiz7j5FjDtwYZ6Pip2U7AE,3998
 rapidtide/maskutil.py,sha256=noqFZzAvyAy0ZzEa1nmEIGzWA0zaPoNSIP3ck1cFKcE,6089
 rapidtide/miscmath.py,sha256=Wj3GXNkXbvGlsdxYGUMTZ3H5a3a1uhfTWZV73XtUYx4,14044
-rapidtide/multiproc.py,sha256=Ri40ebUkxofKwqIKuZ0_FuQvp4uWFPE8yWMOau3TJ78,6238
+rapidtide/multiproc.py,sha256=dMFUZHhtRkNCKQhNdqvO1Eq285DGMdQW13UxyszfuDA,6068
 rapidtide/patchmatch.py,sha256=ZhGuJSwd_UBBJERuABLWzE-HvHLtMgP_Ep4-jq3q1rI,20643
 rapidtide/peakeval.py,sha256=4wboYOtGX1q9p2LmAX_eXcw1YsDWhzlGd-hMVQaso9Y,5198
 rapidtide/qualitycheck.py,sha256=VL4vA4IRoTPZ4fJHwKrYXsJDmsEs4qUV9xvxjvKpchA,11917
-rapidtide/refinedelay.py,sha256=ZHINjXS352WDwFMW79m4YHC_mto8m8-bVOO08EQXEtM,13053
+rapidtide/refinedelay.py,sha256=shx6KyPawJc_hYtfm17Jmk162Zg5AfToyzYEs8FJIWc,16436
 rapidtide/refineregressor.py,sha256=50CXj57k5gccTqfn6tugLM1UxSvr_ImPDch9YwMkL5o,22950
 rapidtide/resample.py,sha256=RA9Rf9Z0jl1nhz4aV5LOlJCm_PVannuBdYZNe3jwECU,30592
 rapidtide/simfuncfit.py,sha256=ypGBraJCk5ParOc-ll9-iVDQHh9OYXqGd3SaN9AoU5Y,11837
@@ -63,7 +63,7 @@ rapidtide/data/examples/src/testboth,sha256=ITAqA3XOC9duFRoBtZgGL9pLnh7Po43i8qjU
 rapidtide/data/examples/src/testcifti,sha256=Nw4UMzkh1oFdW4FuAznuOR9hAr2KJuPF86gZnqqJylU,265
 rapidtide/data/examples/src/testcomplex,sha256=PFY_d30eqYBx5K8cPP_WxsP2YPlYuawo8u1hDhYT-_U,2271
 rapidtide/data/examples/src/testdecomp,sha256=xxxr510aOBjtpJy4aQNAFTyEFZD6QdHp6-Aa_esYalY,269
-rapidtide/data/examples/src/testdelayvar,sha256=x2-miMKk3AAYPC16C4gelWrLyc3p5oDA6m884NzRVAE,301
+rapidtide/data/examples/src/testdelayvar,sha256=tMn1k8IfvBL7MKhgGC6EGcSkChtXWKp1bENOGG4SagI,330
 rapidtide/data/examples/src/testfileorfloat,sha256=9r4mz7pBV_8iFZya9kmtfbnTRS3-94Cx9Q63Ni3mkZs,815
 rapidtide/data/examples/src/testfingerprint,sha256=RlAIC1lMDWMGzZKxY24DJRuaUEL0BenSFBey0gL5dqU,402
 rapidtide/data/examples/src/testfmri,sha256=7gdvJYU2ee0rz4k2PG52JQs-17-T5HyixdLEMeqlzEI,237
@@ -223,17 +223,17 @@ rapidtide/tests/test_doresample.py,sha256=ILQxH6UXtHZ9OwgTpbZE_bek_QKYGmmA6D70r6
 rapidtide/tests/test_fastresampler.py,sha256=xOTyaVPanCnSOd2Lp4RdUF06zhxm7J_bubMCiAtaIbE,3861
 rapidtide/tests/test_filter.py,sha256=_xhk3rbYFtuKgrDdgrrrlITtmQhOUUi5EhFcnxVUioA,10891
 rapidtide/tests/test_findmaxlag.py,sha256=x9mKQ8TmWW4jq8CrlfrX8zwO3n4pYa7aPgF3F1e0aPc,11551
-rapidtide/tests/test_fullrunhappy_v1.py,sha256=BdmYf8dydEccfKTryLTjCHSRNhiWjj29DK3g0BxVz40,1477
-rapidtide/tests/test_fullrunhappy_v2.py,sha256=jp0-cVPkYQQn3iRmFsoIJ9BLHu85uWMgUu1K9FHHJ1U,1942
-rapidtide/tests/test_fullrunhappy_v3.py,sha256=sEWV-Qf_13gJ9BnUmgIu-JtMAh1Jp0Qn8EhTEBU4YmU,1743
-rapidtide/tests/test_fullrunhappy_v4.py,sha256=YL6FWWAL2eeNg-EdaOhdq6r4-84lF_f36hQoGYBl0f4,1753
-rapidtide/tests/test_fullrunhappy_v5.py,sha256=1otOjGN7PADurvB3PUqHq_FxCpd5vr3Q1KD8FrPGXlU,1721
-rapidtide/tests/test_fullrunrapidtide_v1.py,sha256=_NNdHUXIPQW9pFC9NmqaXvauytvv0LqmBOn3UjZvbNQ,2872
-rapidtide/tests/test_fullrunrapidtide_v2.py,sha256=RsMCrq-A4WzVzQxFnyvuotKCT4ipfyepM1RxGBpmMys,2881
-rapidtide/tests/test_fullrunrapidtide_v3.py,sha256=D-CG9SUyr-XTUVXnKZWCEfCVAlHKBOZXMlnCjoXXueQ,2227
-rapidtide/tests/test_fullrunrapidtide_v4.py,sha256=NO1oFSCl2POYluFNGqiYWVk5G2RSSX6hC-jH_RqdvRA,1913
-rapidtide/tests/test_fullrunrapidtide_v5.py,sha256=oXYITl2fKyZR-vT4JLod17Mx0Z68IXissu7yUEiHQPI,1544
-rapidtide/tests/test_fullrunrapidtide_v6.py,sha256=bBiIf6IS6k09KU7U-Q7n2EsDktM-29GWI2bX6uv8Cck,4239
+rapidtide/tests/test_fullrunhappy_v1.py,sha256=C1AFVFM07pNnsRU8z_aKFHdfYTL9kSGBQ7HO5EiQ8TE,1704
+rapidtide/tests/test_fullrunhappy_v2.py,sha256=lrb6hLpbl4b0xWtZTnVHS2JdOSgQlBx1Bi3B5gZ7nFY,2145
+rapidtide/tests/test_fullrunhappy_v3.py,sha256=qmmV-_bjsInZ7Tl8NSVhE8H7DXFARbYqGegGfd9_a7E,1946
+rapidtide/tests/test_fullrunhappy_v4.py,sha256=U3s4j7Cm_S1WcsVbm3LtITHJYlo8SsuVZHwnKPab4WA,1956
+rapidtide/tests/test_fullrunhappy_v5.py,sha256=exckNLj0s-th3KilJ6D_OOWm8--7FSE4u8vkbQ8SjV8,1940
+rapidtide/tests/test_fullrunrapidtide_v1.py,sha256=5FH36vaS786pyZlZvNzrsm9wM_flug8zKRvOujdA-GY,3059
+rapidtide/tests/test_fullrunrapidtide_v2.py,sha256=NNrcveMUMOBqSrNCKvd-L_WBynrtw1MUZf6YsGUh08M,3044
+rapidtide/tests/test_fullrunrapidtide_v3.py,sha256=JARWkh9xgb1xR6hXIY4mlEZ76hTPb3fDIFVwDBDL1Bc,2446
+rapidtide/tests/test_fullrunrapidtide_v4.py,sha256=S_mblVZsrF05rzsDfU4VUR2ugdfHRMcJZpGt98TtX9M,2118
+rapidtide/tests/test_fullrunrapidtide_v5.py,sha256=Z_D7JhGDqNqAIPKs1C5Aj78liAJlT8Qq-lp0d3sGgzM,1779
+rapidtide/tests/test_fullrunrapidtide_v6.py,sha256=VbudxT-yBG9sA1c-WldRMWNWqqTqHGI7EL_wcBKj3j4,4386
 rapidtide/tests/test_io.py,sha256=7BgGhluNPtLJJpATraGHB-kyDkpkcxH9fGv0vnPnfZI,15806
 rapidtide/tests/test_linfitfiltpass.py,sha256=KQSMKgKbBzF0--sw-yqiTtXvaI9pWoAA0jVvHjbia9g,5554
 rapidtide/tests/test_mi.py,sha256=GHqOVn699yNq0m_ZhCrBORc8sjycrUI67AS1UjhRHlU,2272
@@ -243,7 +243,7 @@ rapidtide/tests/test_nullcorr.py,sha256=6257xJHRSPL7HLKnTy1CHphbXH_Ppl4SSexhCmAr
 rapidtide/tests/test_padvec.py,sha256=UKALfQyS9v87QiThxSu51Md3eXkChTpTfm-C0KdXcR0,6728
 rapidtide/tests/test_phaseanalysis.py,sha256=DMzB19c9rz3c5PSwXO4QYOEqNLR85YZLra4wV33O6uI,2150
 rapidtide/tests/test_rapidtideparser.py,sha256=HBoZdmS5UEGDFvlpueNhYXvVbq-pWrhNDCofkc2Tp98,5555
-rapidtide/tests/test_refinedelay.py,sha256=MTz-ad_hhsMBR6rMKQuQfAxdXY9mVMFJ-Y84uzsdhEs,8539
+rapidtide/tests/test_refinedelay.py,sha256=hqnUqf2RHvcxc9HNyiJ9gg9axtnUmD4GZDX7KuOpGMU,8576
 rapidtide/tests/test_runmisc.py,sha256=rrhn_kAnid2c26WgCGr3Va3SfPo14m_bN2p9MOafUH8,2855
 rapidtide/tests/test_sharedmem.py,sha256=Yp5WuYMdKABfqYKvuayq5253pvOC05V_oUK-povjGV8,2026
 rapidtide/tests/test_simulate.py,sha256=m8oGp8qrxQv-FtxX6P3t_nu8bvSizWSZXIij5rtWB6k,3325
@@ -280,11 +280,11 @@ rapidtide/workflows/__init__.py,sha256=2VWpHoQGC8zOLj88k9EtXOsY4cmKzkVG9Og6wracg
 rapidtide/workflows/adjustoffset.py,sha256=2ddMEY-ojhPf-LnzF1jT-NMUhxvkjL9cCm2sfZUBfx8,8440
 rapidtide/workflows/aligntcs.py,sha256=kvTBZWdpvb8_S7b3DcQojrNWPUwFNFXJ58fixWch98M,5348
 rapidtide/workflows/applydlfilter.py,sha256=2b8DJcseZbQrYpv-LBJQsTGQF4iLCxp_Pljpx3yBINA,6785
-rapidtide/workflows/atlasaverage.py,sha256=BErlsUJZl9beHvGULdeD3EZZmfxl4cPXGFXjJkL739E,16462
+rapidtide/workflows/atlasaverage.py,sha256=-zYbDNRHSS2aXZvKg69foKH3-zd7T88hdYeY7aOuV9Q,17478
 rapidtide/workflows/atlastool.py,sha256=MWNSyxa6W0AzUWV5T8-nD-kDpOSUWrr_VvTnEh1YOfY,16076
 rapidtide/workflows/calctexticc.py,sha256=zBchAkNcH1Qd3uL6IDonxSnn8_b5t_pX1S40ZGaZRx4,10486
 rapidtide/workflows/ccorrica.py,sha256=rzcz8ljU3xeB_5p6nAP2-QhvsaobuRDhM1klw45EPUQ,10504
-rapidtide/workflows/delayvar.py,sha256=YEnSCu7wugFw-vAudTkM4DfPLJZS3MXYK0gDm5vCrUU,37660
+rapidtide/workflows/delayvar.py,sha256=lyjnAcZcO9ynBNNDFtcnUBgjDU0QCAoAgwmKGNwMyns,40767
 rapidtide/workflows/diffrois.py,sha256=B9HVgKtTWnSaD1z4_UcqKPP0oBPpWVcsCDhEB7wdMOo,5451
 rapidtide/workflows/endtidalproc.py,sha256=6dnk9coq8HsR5QLm7Zqo8bL8njcvy5l1l64JaUQ5DDA,4923
 rapidtide/workflows/fdica.py,sha256=MZkCnTtd9VAZNIOI55-ZQqaf_N5e9_4wxMw6EY46rSg,14954
@@ -311,14 +311,14 @@ rapidtide/workflows/plethquality.py,sha256=ZNkMS6cGkM2UG796KwCrhiCC7mzEmFt62Nxy1
 rapidtide/workflows/polyfitim.py,sha256=18pCkdk176_hyWdCgRe-B4AEP0wjHheWdPq25SsKy6w,10184
 rapidtide/workflows/proj2flow.py,sha256=MWtf0eTyQ7MfIbWRup4s6TLuk-vKbYgWkSZC9BOBYcM,7290
 rapidtide/workflows/rankimage.py,sha256=twZsGJaVd0raffzKlI0Tupy4DJxHyhBv8WqIUNEtiNM,3482
-rapidtide/workflows/rapidtide.py,sha256=_kAAMIaOS8kpU0AI9ynWQdZ3eN-R7Ad0TSQo8yfhbxU,174391
+rapidtide/workflows/rapidtide.py,sha256=RQaqe6DYO9uG3mMwERBF0hBPkwx1grXWsUdMdWaVtwE,174440
 rapidtide/workflows/rapidtide2std.py,sha256=wGNwyAPnaI3sCG14ORWmlFQRgXmNn6uVVlPirwk1URg,10413
-rapidtide/workflows/rapidtide_parser.py,sha256=k42DInCaHsIkmulZdryVd0xkVrfK2_pJrfVtAdfNcpI,79435
-rapidtide/workflows/regressfrommaps.py,sha256=UvzvfsXUjtLLVpSvjhww5U1zkFPI-POQ2Wkc1YuEsb0,6246
+rapidtide/workflows/rapidtide_parser.py,sha256=Ybsl6bQe1pQBCKT1IyBpvfXNSdLmkKIDoOGjlG8uMlA,79470
+rapidtide/workflows/regressfrommaps.py,sha256=Xz5SQCbasBPzJtXBa7q0-U3Lo4zs-a1JZrfHU1kCUZ8,6298
 rapidtide/workflows/resamplenifti.py,sha256=48vf0JT0C4gjPty_R0RDMRd6opilUQ3stevzAvdKInc,4717
 rapidtide/workflows/resampletc.py,sha256=OZJOHnQAaN371pFt_qb8hY8JQ12WggHK6ZP7Q84rvOk,3959
-rapidtide/workflows/retrolagtcs.py,sha256=bniS1bDLvnvX6gKNCLGvBl26uas0dt5BaXf5An83HdQ,10830
-rapidtide/workflows/retroregress.py,sha256=tM0O0MYKiFP72QlpBp3Ex6cHEjOaUq4rAaAcMjYzids,42466
+rapidtide/workflows/retrolagtcs.py,sha256=b810u7kTzmIM2OubOz_hILlB01ATYQ3s0wPbFROthHc,10847
+rapidtide/workflows/retroregress.py,sha256=DFqEiGz6u7mXIgrPP2Np8KVJ-hjL-I6zLPrMKz61uv0,43382
 rapidtide/workflows/roisummarize.py,sha256=hFYkkYV7fL3gNpAu6Diu1KhOUwLm0cNjWX7V2UNhy4M,6710
 rapidtide/workflows/runqualitycheck.py,sha256=zFjyhfh_9A5U5GIFIIkITuYa8XlwiEM_1dYg7IJgF6w,2434
 rapidtide/workflows/showarbcorr.py,sha256=D6Te4fKQaKZC5GFGNlhFkq--NypJ6msApXjqIuGlGMs,13606
@@ -337,9 +337,9 @@ rapidtide/workflows/tcfrom3col.py,sha256=6tV2lGEtXpI4dn_8kcTCVzZxpJzmopuDwpXvOIE
 rapidtide/workflows/tidepool.py,sha256=1nYPa_-Z-nYZR-fZNo_8dY9LoO_vl7kwiRC_reM2044,86395
 rapidtide/workflows/utils.py,sha256=k2m2F1-tWxhcUYvk5geO1yl-c5bKcDX7Jv7ohvJZaOk,5379
 rapidtide/workflows/variabilityizer.py,sha256=yQFDTBcGehxW44R_FQHeeKrTpeYrrh96xcW1uWbPtYo,3167
-rapidtide-3.0a13.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-rapidtide-3.0a13.dist-info/METADATA,sha256=v9yyxgws4tP-Q2TDofxJi8ZKbTAuBz2m4SqLmxWPsac,15646
-rapidtide-3.0a13.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-rapidtide-3.0a13.dist-info/entry_points.txt,sha256=9NVvZpIx9U6lTWlTFF2ev-wuPAHJxcXI_901_EcGRYA,3323
-rapidtide-3.0a13.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
-rapidtide-3.0a13.dist-info/RECORD,,
+rapidtide-3.0a14.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+rapidtide-3.0a14.dist-info/METADATA,sha256=f3r6Gm863KmFDEr_XN684SsUZ8wboLVet1Bu9GQSGCo,15646
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+rapidtide-3.0a14.dist-info/RECORD,,