rapidtide 3.0.7__py3-none-any.whl → 3.0.7.1__py3-none-any.whl

rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-06-16T13:13:35-0400",
+ "date": "2025-06-16T15:12:43-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "9e8ae750c70431c04a50473c749c451e996d490f",
- "version": "3.0.7"
+ "full-revisionid": "6dead8e554dd0464bdfc65de24889374508f920d",
+ "version": "3.0.7.1"
 }
 '''  # END VERSION_JSON
 

rapidtide/data/examples/src/testfmri

@@ -6,6 +6,7 @@ rapidtide \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
     --outputlevel more \
+    --sLFOfiltmask \
     --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
     --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
@@ -20,7 +21,6 @@ rapidtide \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
     --outputlevel more \
-    --nosLFOfiltmask \
     --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
     --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \

rapidtide/workflows/rapidtide.py

@@ -629,7 +629,6 @@ def rapidtide_main(argparsingfunc):
         )
     else:
         internaloffsetexcludemask_valid = None
-
     tide_util.logmem("after selecting valid voxels")
 
     # move fmri_data_valid into shared memory
@@ -742,7 +741,7 @@ def rapidtide_main(argparsingfunc):
                 theheader["dim"][4] = 1
                 theheader["pixdim"][4] = 1.0
         maplist = [
-            (confoundr2, "confoundfilterR2", "map", None, "R2 of the motion/confound regression")
+            (confoundr2, "confoundfilterR2", "map", None, "R2 of the motion/confound regression"),
         ]
         tide_io.savemaplist(
             outputname,
@@ -2656,9 +2655,10 @@ def rapidtide_main(argparsingfunc):
     optiondict["currentstage"] = "presLFOfit"
     tide_io.writedicttojson(optiondict, f"{outputname}_desc-runoptions_info.json")
     if optiondict["dolinfitfilt"] or optiondict["docvrmap"] or optiondict["refinedelay"]:
-        sLFOfiltmask = fitmask + 0.0
-        if optiondict["nosLFOfiltmask"]:
-            sLFOfiltmask = sLFOfiltmask * 0.0 + 1.0
+        if optiondict["sLFOfiltmask"]:
+            sLFOfiltmask = fitmask + 0.0
+        else:
+            sLFOfiltmask = fitmask * 0.0 + 1.0
         if optiondict["dolinfitfilt"]:
             if optiondict["refinedelay"]:
                 TimingLGR.info("Setting up for delay refinement and sLFO filtering")
@@ -3549,7 +3549,13 @@ def rapidtide_main(argparsingfunc):
     if theinputdata.filetype != "nifti":
         unfiltmeanvalue = meanvalue
     maplist = [
-        (unfiltmeanvalue, "unfiltmean", "map", None, "Voxelwise mean of fmri data before smoothing"),
+        (
+            unfiltmeanvalue,
+            "unfiltmean",
+            "map",
+            None,
+            "Voxelwise mean of fmri data before smoothing",
+        ),
         (meanvalue, "mean", "map", None, "Voxelwise mean of fmri data"),
         (stddevvalue, "std", "map", None, "Voxelwise standard deviation of fmri data"),
         (covvalue, "CoV", "map", None, "Voxelwise coefficient of variation of fmri data"),

rapidtide/workflows/rapidtide_parser.py

@@ -1463,10 +1463,10 @@ def _get_parser():
         default=False,
     )
     experimental.add_argument(
-        "--nosLFOfiltmask",
-        dest="nosLFOfiltmask",
+        "--sLFOfiltmask",
+        dest="sLFOfiltmask",
         action="store_true",
-        help=("Don't spatially limit sLFO filter to fit voxels."),
+        help=("Limit sLFO filter to fit voxels."),
         default=False,
     )
     experimental.add_argument(

rapidtide/workflows/retroregress.py

@@ -219,6 +219,13 @@ def _get_parser():
         help=("Output lots of helpful information on a limited subset of operations."),
         default=False,
     )
+    parser.add_argument(
+        "--sLFOfiltmask",
+        dest="sLFOfiltmask",
+        action="store_true",
+        help=("Limit sLFO filter to fit voxels."),
+        default=False,
+    )
     experimental = parser.add_argument_group(
         "Experimental options (not fully tested, or not tested at all, may not work).  Beware!"
     )
@@ -515,6 +522,10 @@ def retroregress(args):
     lagtimes_valid = lagtimes_spacebytime[validvoxels]
     corrmask_valid = corrmask_spacebytime[validvoxels]
     procmask_valid = procmask_spacebytime[validvoxels]
+    if args.sLFOfiltmask:
+        sLFOfiltmask_valid = corrmask_spacebytime[validvoxels] + 0.0
+    else:
+        sLFOfiltmask_valid = corrmask_spacebytime[validvoxels] * 0.0 + 1.0
     if args.debug:
         print(f"{fmri_data_valid.shape=}")
 
@@ -638,7 +649,7 @@ def retroregress(args):
             validvoxels,
             initial_fmri_x,
             lagtimes_valid,
-            corrmask_valid,
+            sLFOfiltmask_valid,
             genlagtc,
             mode,
             outputname,
@@ -770,7 +781,7 @@ def retroregress(args):
         validvoxels,
         initial_fmri_x,
         lagstouse_valid,
-        corrmask_valid,
+        sLFOfiltmask_valid,
         genlagtc,
         mode,
         outputname,
@@ -1032,6 +1043,13 @@ def retroregress(args):
                     "corrfitREAD",
                     "mask",
                     None,
+                    "Correlation mask read for calculation",
+                ),
+                (
+                    sLFOfiltmask_valid,
+                    "corrfitUSED",
+                    "mask",
+                    None,
                     "Correlation mask used for calculation",
                 ),
                 (
@@ -1255,7 +1273,7 @@ def retroregress(args):
                     validvoxels,
                     initial_fmri_x,
                     lagstouse_valid,
-                    corrmask_valid,
+                    sLFOfiltmask_valid,
                     genlagtc,
                     mode,
                     outputname,

{rapidtide-3.0.7.dist-info → rapidtide-3.0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.7
+Version: 3.0.7.1
 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-3.0.7.dist-info → rapidtide-3.0.7.1.dist-info}/RECORD

@@ -11,7 +11,7 @@ rapidtide/OrthoImageItem.py,sha256=w70QNZUelMI7wTWYaqOfkJEb38PdsxgSf0NLdyjlcNs,2
 rapidtide/RapidtideDataset.py,sha256=mHK6dL1cFSSM5jYw6rkzb57lWVVz-TGX-xMeV8IqF-M,53013
 rapidtide/RegressorRefiner.py,sha256=dPG9Vy2nlqxv2Mx9vrYtgYTsNGcVIwWknawDrNdpZxQ,17232
 rapidtide/__init__.py,sha256=cECnPfGNIWXETiummGLjKcNXLROSDiFlLp-RpZSavwc,97
-rapidtide/_version.py,sha256=HDQ6uc9dBVVhrf7M2MUpG-xKl7d0UA0eisj2QL7_Kd4,497
+rapidtide/_version.py,sha256=nGOK9Y4kAlCPPzJq-zQNTe4jFVy3RCsh5YI-vm-Avnw,499
 rapidtide/calccoherence.py,sha256=-_vglu0MZB85Aodw6GpYhBApFBt5eslppfxF4rXM6Xg,3409
 rapidtide/calcnullsimfunc.py,sha256=34osvoQ_tWk3VeFk7g3TYsmpPVRMIkEX31KYvx5Ox_A,5032
 rapidtide/calcsimfunc.py,sha256=xCPYns-XOnLWjwujbP7a7EwGEzhEwOHMf04RpFlL3SI,4713
@@ -65,7 +65,7 @@ rapidtide/data/examples/src/testdecomp,sha256=xxxr510aOBjtpJy4aQNAFTyEFZD6QdHp6-
 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=FatnYBPAPCIC6MVWwfhs7bJkQnkB-DlNXIkb28-8Asw,972
+rapidtide/data/examples/src/testfmri,sha256=esoO2phGnKgFPS31VRsCibVNOONsgmkNCJGpPTxRgpo,970
 rapidtide/data/examples/src/testfmridocker,sha256=jjL7bK29rrcog6uO9BtvcyAU3Sv8_5cbw2nqKoiZ95o,1193
 rapidtide/data/examples/src/testfrozen,sha256=K3qUWDRKPPiCXRgIFuPdwUUjUTzf4QBW8UUhR75NzDM,283
 rapidtide/data/examples/src/testfuncs,sha256=zjq9u7mXMf0UlbUgePyS1mj7QHclicmw6NY0g31SqeY,1551
@@ -322,14 +322,14 @@ rapidtide/workflows/plethquality.py,sha256=kTO74C5aSBmomzt59zs1VeiO_C5SPTxvyZZ0v
 rapidtide/workflows/polyfitim.py,sha256=bVKBrrFa0WjWZju4Lkrr8_9mFWALqCxkpCX28540GQA,10184
 rapidtide/workflows/proj2flow.py,sha256=SbkYTRZ_SViVfiM0QJjo20RrICtbsQpEd2i9o9XDgPU,7290
 rapidtide/workflows/rankimage.py,sha256=9opJb3OikO69wtN8zgF3XJxgoHy1-erzZiDKs8pDM6U,3482
-rapidtide/workflows/rapidtide.py,sha256=aoRCiZNOqxpIW6dRjh__DGovy5qMZDbvdz8bw11jZvg,154228
+rapidtide/workflows/rapidtide.py,sha256=g2EJzfAOo-mTw6233kHa4m1NpB71mIqaEHpd_QBw1Pc,154310
 rapidtide/workflows/rapidtide2std.py,sha256=coxEnRAof6NNpeXjjECPazx5Wotf4l1SJCnaVEvmHQY,10483
-rapidtide/workflows/rapidtide_parser.py,sha256=lua4DzNd9Vi7egAbba8z068zbWW5EKuwqxHQyaa-Kps,78457
+rapidtide/workflows/rapidtide_parser.py,sha256=hnzEyD_SYAZ2puzmuceg9ezWB14UwUofCrd86R-L16k,78437
 rapidtide/workflows/regressfrommaps.py,sha256=GTpqnOkyA1A3Ki0oZ0ugSJrjrYa2gbtIGeKPpF49IxU,5319
 rapidtide/workflows/resamplenifti.py,sha256=GJE7f8bzMRY3QYiMYZOD8bDnga4ah97sp-ZL3yaaIFA,4717
 rapidtide/workflows/resampletc.py,sha256=B4YIKn3qpDaM9dIhYjGwPl-2LtaEhm9fnMBzfBgAUSs,3959
 rapidtide/workflows/retrolagtcs.py,sha256=ep1Ve1GS9NqqE6Pw9kxeWyw78sEg-M1IV-KuSnivd7Y,10847
-rapidtide/workflows/retroregress.py,sha256=sd7L_ri8av1euINcpKLgokrPGQo7QKQDguf0OWL8xD0,52631
+rapidtide/workflows/retroregress.py,sha256=rCtUbrU8AQJvo8_9mx99ty9CQD4RdvFYCAcDFbcnWJk,53239
 rapidtide/workflows/roisummarize.py,sha256=gnGcWOXRgRm6USgilj9K9Q3Mt5oUNCaincvJj1_ayPs,6710
 rapidtide/workflows/runqualitycheck.py,sha256=JIA2olhDk66HHSbLvsFrZieQq56YCIpbWpFzz0_ShHM,2434
 rapidtide/workflows/showarbcorr.py,sha256=FYgc_L8E0IqUeB4XpFZIFXHMuzWYLxQykwyfYTVZ0G8,14115
@@ -348,9 +348,9 @@ rapidtide/workflows/tcfrom3col.py,sha256=kV3V-qZ7A7LkD96aHVXabvohA8udsflHXnzsQIw
 rapidtide/workflows/tidepool.py,sha256=Cac0zhS2ZT6myY_H2A0dAIox8ZoFyf42iB3flSb0qbw,86612
 rapidtide/workflows/utils.py,sha256=urIN-042oUCRDusVUSjBelVN3Te2JP3svY3ckq-yBMU,5379
 rapidtide/workflows/variabilityizer.py,sha256=h7Hhrxn84MclRfbAvKIZJoNzlcKO-8d9lZ6y6YFStk8,3167
-rapidtide-3.0.7.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-rapidtide-3.0.7.dist-info/METADATA,sha256=oa7HDGqrA2y0sAEhBZR0aeUPcm2u7lHdVmWYXb6D7nE,15688
-rapidtide-3.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rapidtide-3.0.7.dist-info/entry_points.txt,sha256=9NVvZpIx9U6lTWlTFF2ev-wuPAHJxcXI_901_EcGRYA,3323
-rapidtide-3.0.7.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
-rapidtide-3.0.7.dist-info/RECORD,,
+rapidtide-3.0.7.1.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+rapidtide-3.0.7.1.dist-info/METADATA,sha256=nFeUGcVYOj4-7nzYgVFTVdvvdZ5vCIRIbLnc__fwWVs,15690
+rapidtide-3.0.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rapidtide-3.0.7.1.dist-info/entry_points.txt,sha256=9NVvZpIx9U6lTWlTFF2ev-wuPAHJxcXI_901_EcGRYA,3323
+rapidtide-3.0.7.1.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
+rapidtide-3.0.7.1.dist-info/RECORD,,