rapidtide 3.0.7__tar.gz → 3.0.7.1__tar.gz

{rapidtide-3.0.7 → rapidtide-3.0.7.1}/CHANGELOG.md

@@ -1,9 +1,13 @@
 # Release history
 
+## Version 3.0.7.1 (6/16/25)
+* (rapidtide) Disabled sLFO filtering by default.  Use ``sLFOfiltmask`` to turn it on.
+* (retroregress) Synced with sLFO filtering changes to rapidtide.
+
 ## Version 3.0.7 (6/16/25)
 * (rapidtide) Save the full autocorrelation function of the probe regressor at each pass.
 * (rapidtide) Now save a version of the mean fMRI image prior to filtering
-* (rapidtide) Added the abilty to disable masking of sLFO filter. Use ``--nosLFOfiltmask`` to disable.
+* (rapidtide) Added the ability to disable masking of sLFO filter. Use ``--nosLFOfiltmask`` to disable.
 * (happy) Implemented multiprocessing for detrending, phase projection, and phase projection smoothing.
 * (happy) Precache convolution gridding kernel outputs to improve repeatability.
 * (happy) Early implementation of Wright's method for finding vessels.

{rapidtide-3.0.7/rapidtide.egg-info → rapidtide-3.0.7.1}/PKG-INFO

@@ -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 → rapidtide-3.0.7.1}/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-3.0.7 → rapidtide-3.0.7.1}/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-3.0.7 → rapidtide-3.0.7.1}/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-3.0.7 → rapidtide-3.0.7.1}/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-3.0.7 → rapidtide-3.0.7.1}/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 → rapidtide-3.0.7.1/rapidtide.egg-info}/PKG-INFO

@@ -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>