rapidtide 3.0a11__py3-none-any.whl → 3.0a12__py3-none-any.whl

rapidtide/Refiner.py

@@ -0,0 +1,464 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2024 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+"""
+A class to impmement regressor refinement
+"""
+import copy
+
+import numpy as np
+
+import rapidtide.fit as tide_fit
+import rapidtide.io as tide_io
+import rapidtide.miscmath as tide_math
+import rapidtide.refineregressor as tide_refineregressor
+import rapidtide.resample as tide_resample
+import rapidtide.stats as tide_stats
+import rapidtide.util as tide_util
+from rapidtide.tests.utils import mse
+
+
+class Refiner:
+
+    refinemaskvoxels = None
+
+    def __init__(
+        self,
+        internalvalidfmrishape,
+        internalvalidpaddedfmrishape,
+        pid,
+        outputname,
+        initial_fmri_x,
+        paddedinitial_fmri_x,
+        os_fmri_x,
+        sharedmem=False,
+        offsettime=0.0,
+        ampthresh=0.3,
+        lagminthresh=0.25,
+        lagmaxthresh=3.0,
+        sigmathresh=1000.0,
+        cleanrefined=False,
+        bipolar=False,
+        fixdelay=False,
+        includemask=None,
+        excludemask=None,
+        LGR=None,
+        nprocs=1,
+        detrendorder=1,
+        alwaysmultiproc=False,
+        showprogressbar=True,
+        chunksize=50000,
+        padtrs=10,
+        refineprenorm="var",
+        refineweighting=None,
+        refinetype="pca",
+        pcacomponents=0.8,
+        dodispersioncalc=False,
+        dispersioncalc_lower=-5.0,
+        dispersioncalc_upper=5.0,
+        dispersioncalc_step=0.5,
+        windowfunc="hamming",
+        passes=3,
+        maxpasses=15,
+        convergencethresh=None,
+        interptype="univariate",
+        usetmask=False,
+        tmask_y=None,
+        tmaskos_y=None,
+        fastresamplerpadtime=45.0,
+        debug=False,
+        rt_floattype="float64",
+        rt_floatset=np.float64,
+    ):
+        self.internalvalidfmrishape = internalvalidfmrishape
+        self.internalvalidpaddedfmrishape = internalvalidpaddedfmrishape
+        self.sharedmem = sharedmem
+        self.outputname = outputname
+        self.initial_fmri_x = initial_fmri_x
+        self.paddedinitial_fmri_x = paddedinitial_fmri_x
+        self.os_fmri_x = os_fmri_x
+
+        self.offsettime = offsettime
+        self.ampthresh = ampthresh
+        self.lagminthresh = lagminthresh
+        self.lagmaxthresh = lagmaxthresh
+        self.sigmathresh = sigmathresh
+        self.cleanrefined = cleanrefined
+        self.bipolar = bipolar
+        self.fixdelay = fixdelay
+        self.LGR = LGR
+        self.nprocs = nprocs
+        self.detrendorder = detrendorder
+        self.alwaysmultiproc = alwaysmultiproc
+        self.showprogressbar = showprogressbar
+        self.chunksize = chunksize
+        self.padtrs = padtrs
+        self.refineprenorm = refineprenorm
+        self.refineweighting = refineweighting
+        self.refinetype = refinetype
+        self.pcacomponents = pcacomponents
+        self.dodispersioncalc = dodispersioncalc
+        self.dispersioncalc_lower = dispersioncalc_lower
+        self.dispersioncalc_upper = dispersioncalc_upper
+        self.dispersioncalc_step = dispersioncalc_step
+        self.windowfunc = windowfunc
+        self.passes = passes
+        self.maxpasses = maxpasses
+        self.convergencethresh = convergencethresh
+        self.interptype = interptype
+        self.usetmask = usetmask
+        self.tmask_y = tmask_y
+        self.tmaskos_y = tmaskos_y
+        self.fastresamplerpadtime = fastresamplerpadtime
+        self.debug = debug
+        self.rt_floattype = rt_floattype
+        self.rt_floatset = rt_floatset
+
+        self.setmasks(includemask, excludemask)
+        self.totalrefinementbytes = self._allocatemem(pid)
+
+    def setmasks(self, includemask, excludemask):
+        self.includemask = includemask
+        self.excludemask = excludemask
+
+    def _allocatemem(self, pid):
+        if self.sharedmem:
+            self.shiftedtcs, self.shiftedtcs_shm = tide_util.allocshared(
+                self.internalvalidfmrishape, self.rt_floatset, name=f"shiftedtcs_{pid}"
+            )
+            self.weights, self.weights_shm = tide_util.allocshared(
+                self.internalvalidfmrishape, self.rt_floatset, name=f"weights_{pid}"
+            )
+            self.paddedshiftedtcs, self.paddedshiftedtcs_shm = tide_util.allocshared(
+                self.internalvalidpaddedfmrishape,
+                self.rt_floatset,
+                name=f"paddedshiftedtcs_{pid}",
+            )
+            self.paddedweights, self.paddedweights_shm = tide_util.allocshared(
+                self.internalvalidpaddedfmrishape,
+                self.rt_floatset,
+                name=f"paddedweights_{pid}",
+            )
+            ramlocation = "in shared memory"
+        else:
+            self.shiftedtcs = np.zeros(self.internalvalidfmrishape, dtype=self.rt_floattype)
+            self.weights = np.zeros(self.internalvalidfmrishape, dtype=self.rt_floattype)
+            self.paddedshiftedtcs = np.zeros(
+                self.internalvalidpaddedfmrishape, dtype=self.rt_floattype
+            )
+            self.paddedweights = np.zeros(
+                self.internalvalidpaddedfmrishape, dtype=self.rt_floattype
+            )
+            ramlocation = "locally"
+        totalrefinementbytes = (
+            self.shiftedtcs.nbytes
+            + self.weights.nbytes
+            + self.paddedshiftedtcs.nbytes
+            + self.paddedweights.nbytes
+        )
+        thesize, theunit = tide_util.format_bytes(totalrefinementbytes)
+        print(f"allocated {thesize:.3f} {theunit} {ramlocation} for refinement")
+        tide_util.logmem("after refinement array allocation")
+        return totalrefinementbytes
+
+    def cleanup(self):
+        del self.paddedshiftedtcs
+        del self.paddedweights
+        del self.shiftedtcs
+        del self.weights
+        if self.sharedmem:
+            tide_util.cleanup_shm(self.paddedshiftedtcs_shm)
+            tide_util.cleanup_shm(self.paddedweights_shm)
+            tide_util.cleanup_shm(self.shiftedtcs_shm)
+            tide_util.cleanup_shm(self.weights_shm)
+
+    def makemask(self, lagstrengths, lagtimes, lagsigma, fitmask):
+        # create the refinement mask
+        (
+            self.refinemaskvoxels,
+            self.refinemask,
+            self.locationfails,
+            self.ampfails,
+            self.lagfails,
+            self.sigmafails,
+            self.numinmask,
+        ) = tide_refineregressor.makerefinemask(
+            lagstrengths,
+            lagtimes,
+            lagsigma,
+            fitmask,
+            offsettime=self.offsettime,
+            ampthresh=self.ampthresh,
+            lagminthresh=self.lagminthresh,
+            lagmaxthresh=self.lagmaxthresh,
+            sigmathresh=self.sigmathresh,
+            cleanrefined=self.cleanrefined,
+            bipolar=self.bipolar,
+            includemask=self.includemask,
+            excludemask=self.excludemask,
+            fixdelay=self.fixdelay,
+            debug=self.debug,
+        )
+
+        if self.numinmask == 0:
+            self.LGR.critical("No voxels in refine mask - adjust thresholds or external masks")
+            return False
+        else:
+            return True
+
+    def getrefinemask(self):
+        return self.refinemask
+
+    def getpaddedshiftedtcs(self):
+        return self.paddedshiftedtcs
+
+    def alignvoxels(self, fmri_data_valid, fmritr, lagtimes):
+        # align timecourses to prepare for refinement
+        self.LGR.info("aligning timecourses")
+        voxelsprocessed_rra = tide_refineregressor.alignvoxels(
+            fmri_data_valid,
+            fmritr,
+            self.shiftedtcs,
+            self.weights,
+            self.paddedshiftedtcs,
+            self.paddedweights,
+            lagtimes,
+            self.refinemask,
+            nprocs=self.nprocs,
+            detrendorder=self.detrendorder,
+            offsettime=self.offsettime,
+            alwaysmultiproc=self.alwaysmultiproc,
+            showprogressbar=self.showprogressbar,
+            chunksize=self.chunksize,
+            padtrs=self.padtrs,
+            debug=self.debug,
+            rt_floatset=self.rt_floatset,
+            rt_floattype=self.rt_floattype,
+        )
+        return voxelsprocessed_rra
+        # self.LGR.info(f"align complete: {voxelsprocessed_rra=}")
+
+    def prenormalize(self, lagtimes, lagstrengths, R2):
+        tide_refineregressor.prenorm(
+            self.paddedshiftedtcs,
+            self.refinemask,
+            lagtimes,
+            self.lagmaxthresh,
+            lagstrengths,
+            R2,
+            self.refineprenorm,
+            self.refineweighting,
+        )
+
+    def refine(
+        self,
+        theprefilter,
+        fmritr,
+        thepass,
+        lagstrengths,
+        lagtimes,
+        previousnormoutputdata,
+        corrmasksize,
+    ):
+        (
+            voxelsprocessed_rr,
+            self.paddedoutputdata,
+        ) = tide_refineregressor.dorefine(
+            self.paddedshiftedtcs,
+            self.refinemask,
+            self.weights,
+            theprefilter,
+            fmritr,
+            thepass,
+            lagstrengths,
+            lagtimes,
+            self.refinetype,
+            1.0 / fmritr,
+            self.outputname,
+            detrendorder=self.detrendorder,
+            pcacomponents=self.pcacomponents,
+            dodispersioncalc=self.dodispersioncalc,
+            dispersioncalc_lower=self.dispersioncalc_lower,
+            dispersioncalc_upper=self.dispersioncalc_upper,
+            dispersioncalc_step=self.dispersioncalc_step,
+            windowfunc=self.windowfunc,
+            cleanrefined=self.cleanrefined,
+            bipolar=self.bipolar,
+            debug=self.debug,
+            rt_floatset=self.rt_floatset,
+            rt_floattype=self.rt_floattype,
+        )
+        outputdict = {}
+        outputdict["refinemasksize_pass" + str(thepass)] = voxelsprocessed_rr
+        outputdict["refinemaskpct_pass" + str(thepass)] = 100.0 * voxelsprocessed_rr / corrmasksize
+        outputdict["refinelocationfails_pass" + str(thepass)] = self.locationfails
+        outputdict["refineampfails_pass" + str(thepass)] = self.ampfails
+        outputdict["refinelagfails_pass" + str(thepass)] = self.lagfails
+        outputdict["refinesigmafails_pass" + str(thepass)] = self.sigmafails
+
+        fmrifreq = 1.0 / fmritr
+        if voxelsprocessed_rr > 0:
+            paddednormoutputdata = tide_math.stdnormalize(
+                theprefilter.apply(fmrifreq, self.paddedoutputdata)
+            )
+            outputdata = self.paddedoutputdata[self.padtrs : -self.padtrs]
+            normoutputdata = tide_math.stdnormalize(theprefilter.apply(fmrifreq, outputdata))
+            normunfilteredoutputdata = tide_math.stdnormalize(outputdata)
+            tide_io.writebidstsv(
+                f"{self.outputname}_desc-refinedmovingregressor_timeseries",
+                normunfilteredoutputdata,
+                fmrifreq,
+                columns=["unfiltered_pass" + str(thepass)],
+                extraheaderinfo={
+                    "Description": "The raw and filtered probe regressor produced by the refinement procedure, at the time resolution of the data"
+                },
+                append=(thepass > 1),
+            )
+            tide_io.writebidstsv(
+                f"{self.outputname}_desc-refinedmovingregressor_timeseries",
+                normoutputdata,
+                fmrifreq,
+                columns=["filtered_pass" + str(thepass)],
+                extraheaderinfo={
+                    "Description": "The raw and filtered probe regressor produced by the refinement procedure, at the time resolution of the data"
+                },
+                append=True,
+            )
+
+        # check for convergence
+        regressormse = mse(normoutputdata, previousnormoutputdata)
+        outputdict["regressormse_pass" + str(thepass).zfill(2)] = regressormse
+        self.LGR.info(f"regressor difference at end of pass {thepass:d} is {regressormse:.6f}")
+        if self.convergencethresh is not None:
+            if thepass >= self.maxpasses:
+                self.LGR.info("refinement ended (maxpasses reached)")
+                stoprefining = True
+                refinestopreason = "maxpassesreached"
+            elif regressormse < self.convergencethresh:
+                self.LGR.info("refinement ended (refinement has converged")
+                stoprefining = True
+                refinestopreason = "convergence"
+            else:
+                stoprefining = False
+        elif thepass >= self.passes:
+            stoprefining = True
+            refinestopreason = "passesreached"
+        else:
+            stoprefining = False
+            refinestopreason = None
+        outputdict["refinestopreason"] = refinestopreason
+
+        if self.detrendorder > 0:
+            resampnonosref_y = tide_fit.detrend(
+                tide_resample.doresample(
+                    self.paddedinitial_fmri_x,
+                    paddednormoutputdata,
+                    self.initial_fmri_x,
+                    method=self.interptype,
+                ),
+                order=self.detrendorder,
+                demean=True,
+            )
+            resampref_y = tide_fit.detrend(
+                tide_resample.doresample(
+                    self.paddedinitial_fmri_x,
+                    paddednormoutputdata,
+                    self.os_fmri_x,
+                    method=self.interptype,
+                ),
+                order=self.detrendorder,
+                demean=True,
+            )
+        else:
+            resampnonosref_y = tide_resample.doresample(
+                self.paddedinitial_fmri_x,
+                paddednormoutputdata,
+                self.initial_fmri_x,
+                method=self.interptype,
+            )
+            resampref_y = tide_resample.doresample(
+                self.paddedinitial_fmri_x,
+                paddednormoutputdata,
+                self.os_fmri_x,
+                method=self.interptype,
+            )
+        if self.usetmask:
+            resampnonosref_y *= self.tmask_y
+            thefit, R2val = tide_fit.mlregress(self.tmask_y, resampnonosref_y)
+            resampnonosref_y -= thefit[0, 1] * self.tmask_y
+            resampref_y *= self.tmaskos_y
+            thefit, R2val = tide_fit.mlregress(self.tmaskos_y, resampref_y)
+            resampref_y -= thefit[0, 1] * self.tmaskos_y
+
+        # reinitialize genlagtc for resampling
+        previousnormoutputdata = np.zeros_like(normoutputdata)
+        genlagtc = tide_resample.FastResampler(
+            self.paddedinitial_fmri_x,
+            paddednormoutputdata,
+            padtime=self.fastresamplerpadtime,
+        )
+        genlagtc.save(f"{self.outputname}_desc-lagtcgenerator_timeseries")
+        if self.debug:
+            genlagtc.info()
+        (
+            outputdict[f"kurtosis_reference_pass{thepass + 1}"],
+            outputdict[f"kurtosisz_reference_pass{thepass + 1}"],
+            outputdict[f"kurtosisp_reference_pass{thepass + 1}"],
+        ) = tide_stats.kurtosisstats(resampref_y)
+        (
+            outputdict[f"skewness_reference_pass{thepass + 1}"],
+            outputdict[f"skewnessz_reference_pass{thepass + 1}"],
+            outputdict[f"skewnessp_reference_pass{thepass + 1}"],
+        ) = tide_stats.skewnessstats(resampref_y)
+        if not stoprefining:
+            tide_io.writebidstsv(
+                f"{self.outputname}_desc-movingregressor_timeseries",
+                tide_math.stdnormalize(resampnonosref_y),
+                1.0 / fmritr,
+                columns=["pass" + str(thepass + 1)],
+                extraheaderinfo={
+                    "Description": "The probe regressor used in each pass, at the time resolution of the data"
+                },
+                append=True,
+            )
+            oversampfreq = 1.0 / (self.os_fmri_x[1] - self.os_fmri_x[0])
+            tide_io.writebidstsv(
+                f"{self.outputname}_desc-oversampledmovingregressor_timeseries",
+                tide_math.stdnormalize(resampref_y),
+                oversampfreq,
+                columns=["pass" + str(thepass + 1)],
+                extraheaderinfo={
+                    "Description": "The probe regressor used in each pass, at the time resolution used for calculating the similarity function"
+                },
+                append=True,
+            )
+        else:
+            self.LGR.warning(f"refinement failed - terminating at end of pass {thepass}")
+            stoprefining = True
+            refinestopreason = "emptymask"
+
+        return (
+            voxelsprocessed_rr,
+            outputdict,
+            previousnormoutputdata,
+            resampref_y,
+            resampnonosref_y,
+            stoprefining,
+            refinestopreason,
+            genlagtc,
+        )

rapidtide/data/examples/src/testfmri

@@ -1,132 +1,10 @@
 #!/bin/bash
 
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --glmderivs 1 \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_norefine
-
 rapidtide \
     --spatialfilt -1 \
     --nprocs -1 \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
+    --outputlevel max \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_defaultfilt
-
-rapidtide \
-    --spatialfilt 5 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_5mmfilt
-
-rapidtide \
-    --spatialfilt 0 \
-    --nprocs -1 \
-    --searchrange -5 20 \
-    --simcalcrange 50 -1 \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nospatialfilt
-
-#rapidtide \
-#    --spatialfilt 5 \
-#    --nprocs -1 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    --refinedelay \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_corr
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 50 \
-#    --despecklepasses 50 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_spec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --passes 4 \
-#    --despecklepasses 5 \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingspec
-#
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --denoising \
-#    --simcalcrange 50 -1 \
-#    --outputlevel max \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_denoisingnospec
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--padtype constant \
-    #--outputlevel max \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_constantpad
-
-#rapidtide \
-#    --spatialfilt 2 \
-#    --nprocs -1 \
-#    --passes 3 \
-#    --simcalcrange 50 -1 \
-#    --memprofile \
-#    sub-RAPIDTIDETEST.nii.gz \
-#    ../dst/sub-RAPIDTIDETEST_memprofile
-
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_excludemask
-#
-#rapidtide \
-    #--spatialfilt 2 \
-    #--nprocs -1 \
-    #--passes 3 \
-    #--simcalcrange 50 -1 \
-    #--tincludemask tmask3.txt \
-    #--texcludemask tmask3_exclude.txt \
-    #sub-RAPIDTIDETEST.nii.gz \
-    #../dst/sub-RAPIDTIDETEST_bothmasks
-
-#for FILT in 1 2 4 8 16
-#do
-#    rapidtide \
-#        --spatialfilt ${FILT} \
-#        --nprocs -1 \
-#        --passes 3 \
-#        --simcalcrange 50 -1 \
-#        --outputlevel min \
-#        sub-RAPIDTIDETEST.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_${FILT}
-#done
-#
-#for MAP in maxtime maxcorr
-#do
-#    fslmerge -t ../dst/all_${MAP} \
-#        ../dst/sub-RAPIDTIDETEST_1_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_2_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_4_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_8_desc-${MAP}_map.nii.gz \
-#        ../dst/sub-RAPIDTIDETEST_16_desc-${MAP}_map.nii.gz 
-#done
+    ../dst/sub-RAPIDTIDETEST

rapidtide/data/examples/src/testinitdelay

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_defaultfilt
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --regressor ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-movingregressor_timeseries.json:pass3 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_defaultfilt_desc-maxtimerefined_map.nii.gz \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_startfromlast

rapidtide/data/examples/src/testnewrefine

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineglmderivs 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel max \
+    --refineglmderivs 2 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv
+
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to1 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 1 \
+    --outputlevel max
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_2deriv \
+    --alternateoutput ../dst/retrotest_2to1 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 1 \
+    --outputlevel max
+
+retroglm \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_1deriv \
+    --alternateoutput ../dst/retrotest_1to2 \
+    --nprocs -1 \
+    --glmderivs 0 \
+    --refineglmderivs 2 \
+    --outputlevel max

rapidtide/data/examples/src/testrefineonly

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --passes 1 \
+    --nodelayfit \
+    --focaldebug \
+    --dofinalrefine \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_firstpass
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --nodelayfit \
+    --regressor ../dst/sub-RAPIDTIDETEST_firstpass_desc-refinedmovingregressor_timeseries.json:filtered_pass1 \
+    --initialdelay ../dst/sub-RAPIDTIDETEST_firstpass_desc-maxtimerefined_map.nii.gz \
+    --dofinalrefine \
+    --passes 1 \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_secondpass