antspymm 1.2.8__py3-none-any.whl → 1.3.3__py3-none-any.whl

antspymm/mm.py

@@ -161,6 +161,23 @@ def version( ):
               'antspymm': pkg_resources.require("antspymm")[0].version
               }
 
+def nrg_filename_to_subjectvisit(s, separator='-'):
+    """
+    Extracts a pattern from the input string.
+    
+    Parameters:
+    - s: The input string from which to extract the pattern.
+    - separator: The separator used in the string (default is '-').
+    
+    Returns:
+    - A string in the format of 'PREFIX-Number-Date'
+    """
+    parts = os.path.basename(s).split(separator)
+    # Assuming the pattern is always in the form of PREFIX-Number-Date-...
+    # and PREFIX is always "PPMI", extract the first three parts
+    extracted = separator.join(parts[:3])
+    return extracted
+
 
 def validate_nrg_file_format(path, separator):
     """
@@ -436,11 +453,11 @@ def docsamson(locmod, studycsv, outputdir, projid, sid, dtid, mysep, t1iid=None,
             imfns.append('nmid' + str(i))
     elif locmod == 'rsfMRI':
         imfns=[]
-        for i in range(3):
+        for i in range(4):
             imfns.append('rsfid' + str(i))
     elif locmod == 'DTI':
         imfns=[]
-        for i in range(3):
+        for i in range(4):
             imfns.append('dtid' + str(i))
 
     # Process each file name
@@ -489,7 +506,7 @@ def get_valid_modalities( long=False, asString=False, qc=False ):
     if long:
         mymod = ["T1w", "NM2DMT", "rsfMRI", "rsfMRI_LR", "rsfMRI_RL", "rsfMRILR", "rsfMRIRL", "DTI", "DTI_LR","DTI_RL",  "DTILR","DTIRL","T2Flair", "dwi", "dwi_ap", "dwi_pa", "func", "func_ap", "func_pa", "perf"]
     elif qc:
-        mymod = [ 'T1w', 'T2Flair', 'NM2DMT','DTIdwi','DTIb0', 'rsfMRI', "perf" ]
+        mymod = [ 'T1w', 'T2Flair', 'NM2DMT', 'DTI', 'DTIdwi','DTIb0', 'rsfMRI', "perf" ]
     else:
         mymod = ["T1w", "NM2DMT", "DTI","T2Flair", "rsfMRI", "perf" ]
     if not asString:
@@ -565,15 +582,15 @@ def generate_mm_dataframe(
         raise ValueError("source_image_directory does not exist")
     if len( rsf_filenames ) > 2:
         raise ValueError("len( rsf_filenames ) > 2")
-    if len( dti_filenames ) > 2:
-        raise ValueError("len( dti_filenames ) > 2")
+    if len( dti_filenames ) > 3:
+        raise ValueError("len( dti_filenames ) > 3")
     if len( nm_filenames ) > 11:
         raise ValueError("len( nm_filenames ) > 11")
     if len( rsf_filenames ) < 2:
         for k in range(len(rsf_filenames),2):
             rsf_filenames.append(None)
-    if len( dti_filenames ) < 2:
-        for k in range(len(dti_filenames),2):
+    if len( dti_filenames ) < 3:
+        for k in range(len(dti_filenames),3):
             dti_filenames.append(None)
     if len( nm_filenames ) < 10:
         for k in range(len(nm_filenames),10):
@@ -649,7 +666,7 @@ def generate_mm_dataframe(
         'perfid']
     mycols0 = corecols + [
         'rsfid1', 'rsfid2',
-        'dtid1', 'dtid2']
+        'dtid1', 'dtid2','dtid3']
     nmext = [
         'nmid1', 'nmid2' 'nmid3', 'nmid4', 'nmid5',
         'nmid6', 'nmid7','nmid8', 'nmid9', 'nmid10', 'nmid11'
@@ -981,25 +998,28 @@ def outlierness_by_modality( qcdf, uid='filename', outlier_columns = ['noise', '
     from PyNomaly import loop
     from sklearn.neighbors import LocalOutlierFactor
     qcdfout = qcdf.copy()
+    pd.set_option('future.no_silent_downcasting', True)
+    qcdfout.replace([np.inf, -np.inf], np.nan, inplace=True)
     if uid not in qcdfout.keys():
-        raise ValueError(uid + " not in dataframe")
+        raise ValueError( str(uid) + " not in dataframe")
     if 'ol_loop' not in qcdfout.keys():
         qcdfout['ol_loop']=math.nan
     if 'ol_lof' not in qcdfout.keys():
         qcdfout['ol_lof']=math.nan
+    didit=False
     for mod in get_valid_modalities( qc=True ):
+        didit=True
         lof = LocalOutlierFactor()
         locsel = qcdfout["modality"] == mod
         rr = qcdfout[locsel][outlier_columns]
-        with pd.option_context('mode.use_inf_as_na', True):
-            for myolcol in outlier_columns:
-                rr[myolcol].fillna(rr[myolcol].mean(), inplace=True)
+        column_means = rr.mean()
+        rr.fillna(column_means, inplace=True)
         if rr.shape[0] > 1:
             if verbose:
-                print(mod)
+                print("calc: " + mod + " outlierness " )
             myneigh = np.min( [24, int(np.round(rr.shape[0]*0.5)) ] )
             temp = antspyt1w.loop_outlierness(rr.astype(float), standardize=True, extent=3, n_neighbors=myneigh, cluster_labels=None)
-            qcdfout.loc[locsel,'ol_loop']=temp
+            qcdfout.loc[locsel,'ol_loop']=temp.astype('float64')
             yhat = lof.fit_predict(rr)
             temp = lof.negative_outlier_factor_*(-1.0)
             temp = temp - temp.min()
@@ -1007,6 +1027,8 @@ def outlierness_by_modality( qcdf, uid='filename', outlier_columns = ['noise', '
             yhat[ yhat == -1] = 1 # these are outliers
             qcdfout.loc[locsel,'ol_lof_decision']=yhat
             qcdfout.loc[locsel,'ol_lof']=temp/temp.max()
+    if verbose:
+        print( didit )
     return qcdfout
 
 
@@ -1084,6 +1106,11 @@ def study_dataframe_from_matched_dataframe( matched_dataframe, rootdir, outputdi
         dtfn2=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn2'].iloc[0]+iext) ))[0]
         if exists( dtfn2 ):
             dtList.append( dtfn2 )
+    if 'dtfn3' in csvrow.keys():
+        dtid=str(int(csvrow['dtid3'].iloc[0]))
+        dtfn3=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn3'].iloc[0]+iext) ))[0]
+        if exists( dtfn3 ):
+            dtList.append( dtfn3 )
     if 'rsffn1' in csvrow.keys():
         rsid=str(int(csvrow['rsfid1'].iloc[0]))
         rsfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn1'].iloc[0]+iext) ))[0]
@@ -1159,6 +1186,8 @@ def highest_quality_repeat(mxdfin, idvar, visitvar, qualityvar):
     if qualityvar not in mxdfin.columns:
         raise ValueError("qualityvar not in dataframe")
 
+    mxdfin[qualityvar] = mxdfin[qualityvar].astype(float)
+
     vizzes = mxdfin[visitvar].unique()
     uids = mxdfin[idvar].unique()
     useit = np.zeros(mxdfin.shape[0], dtype=bool)
@@ -1195,40 +1224,48 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
     """
     import pandas as pd
     import numpy as np
+    qc_dataframe['filename']=qc_dataframe['filename'].astype(str)
+    qc_dataframe['ol_loop']=qc_dataframe['ol_loop'].astype(float)
+    qc_dataframe['ol_lof']=qc_dataframe['ol_lof'].astype(float)
+    qc_dataframe['ol_lof_decision']=qc_dataframe['ol_lof_decision'].astype(float)
     mmdf = best_mmm( qc_dataframe, 'T1w', outlier_column=outlier_column )['filt']
     fldf = best_mmm( qc_dataframe, 'T2Flair', outlier_column=outlier_column )['filt']
     nmdf = best_mmm( qc_dataframe, 'NM2DMT', outlier_column=outlier_column )['filt']
     rsdf = best_mmm( qc_dataframe, 'rsfMRI', outlier_column=outlier_column )['filt']
     dtdf = best_mmm( qc_dataframe, 'DTI', outlier_column=outlier_column )['filt']
-    mmdf['flairid'] = np.nan
-    mmdf['flairfn'] = np.nan
-    mmdf['flairloop'] = np.nan
-    mmdf['flairlof'] = np.nan
-    mmdf['dtid1'] = np.nan
-    mmdf['dtfn1'] = np.nan
-    mmdf['dtloop1'] = np.nan
-    mmdf['dtlof1'] = np.nan
-    mmdf['dtid2'] = np.nan
-    mmdf['dtfn2'] = np.nan
-    mmdf['dtloop2'] = np.nan
-    mmdf['dtlof2'] = np.nan
-    mmdf['rsfid1'] = np.nan
-    mmdf['rsffn1'] = np.nan
-    mmdf['rsfloop1'] = np.nan
-    mmdf['rsflof1'] = np.nan
-    mmdf['rsfid2'] = np.nan
-    mmdf['rsffn2'] = np.nan
-    mmdf['rsfloop2'] = np.nan
-    mmdf['rsflof2'] = np.nan
+    mmdf['flairid'] = None
+    mmdf['flairfn'] = None
+    mmdf['flairloop'] = None
+    mmdf['flairlof'] = None
+    mmdf['dtid1'] = None
+    mmdf['dtfn1'] = None
+    mmdf['dtntimepoints1'] = 0
+    mmdf['dtloop1'] = math.nan
+    mmdf['dtlof1'] = math.nan
+    mmdf['dtid2'] = None
+    mmdf['dtfn2'] = None
+    mmdf['dtntimepoints2'] = 0
+    mmdf['dtloop2'] = math.nan
+    mmdf['dtlof2'] = math.nan
+    mmdf['rsfid1'] = None
+    mmdf['rsffn1'] = None
+    mmdf['rsfntimepoints1'] = 0
+    mmdf['rsfloop1'] = math.nan
+    mmdf['rsflof1'] = math.nan
+    mmdf['rsfid2'] = None
+    mmdf['rsffn2'] = None
+    mmdf['rsfntimepoints2'] = 0
+    mmdf['rsfloop2'] = math.nan
+    mmdf['rsflof2'] = math.nan
     for k in range(1,11):
         myid='nmid'+str(k)
-        mmdf[myid] = np.nan
+        mmdf[myid] = None
         myid='nmfn'+str(k)
-        mmdf[myid] = np.nan
+        mmdf[myid] = None
         myid='nmloop'+str(k)
-        mmdf[myid] = np.nan
+        mmdf[myid] = math.nan
         myid='nmlof'+str(k)
-        mmdf[myid] = np.nan
+        mmdf[myid] = math.nan
     if verbose:
         print( mmdf.shape )
     for k in range(mmdf.shape[0]):
@@ -1237,12 +1274,13 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
                 progger = str( k ) # np.round( k / mmdf.shape[0] * 100 ) )
                 print( progger, end ="...", flush=True)
         if dtdf is not None:
-            locsel = (dtdf["subjectIDdate"] == mmdf["subjectIDdate"].iloc[k]) & (dtdf[outlier_column] < 0.5)
+            locsel = (dtdf["subjectIDdate"] == mmdf["subjectIDdate"].iloc[k])
             if sum(locsel) == 1:
                 mmdf.iloc[k, mmdf.columns.get_loc("dtid1")] = dtdf["imageID"][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("dtfn1")] = dtdf["fn"][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("dtfn1")] = dtdf[unique_identifier][locsel].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("dtloop1")] = dtdf[outlier_column][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("dtlof1")] = dtdf['ol_lof_decision'][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("dtlof1")] = float(dtdf['ol_lof_decision'][locsel].values[0])
+                mmdf.iloc[k, mmdf.columns.get_loc("dtntimepoints1")] = float(dtdf['dimt'][locsel].values[0])
             elif sum(locsel) > 1:
                 locdf = dtdf[locsel]
                 dedupe = locdf[["snr","cnr"]].duplicated()
@@ -1250,21 +1288,24 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
                 if locdf.shape[0] > 1:
                     locdf = locdf.sort_values(outlier_column).iloc[:2]
                 mmdf.iloc[k, mmdf.columns.get_loc("dtid1")] = locdf["imageID"].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("dtfn1")] = locdf["fn"].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("dtfn1")] = locdf[unique_identifier].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("dtloop1")] = locdf[outlier_column].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("dtlof1")] = locdf['ol_lof_decision'][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("dtlof1")] = float(locdf['ol_lof_decision'][locsel].values[0])
+                mmdf.iloc[k, mmdf.columns.get_loc("dtntimepoints1")] = float(dtdf['dimt'][locsel].values[0])
                 if locdf.shape[0] > 1:
                     mmdf.iloc[k, mmdf.columns.get_loc("dtid2")] = locdf["imageID"].values[1]
-                    mmdf.iloc[k, mmdf.columns.get_loc("dtfn2")] = locdf["fn"].values[1]
+                    mmdf.iloc[k, mmdf.columns.get_loc("dtfn2")] = locdf[unique_identifier].values[1]
                     mmdf.iloc[k, mmdf.columns.get_loc("dtloop2")] = locdf[outlier_column].values[1]
-                    mmdf.iloc[k, mmdf.columns.get_loc("dtlof2")] = locdf['ol_lof_decision'][locsel].values[1]
+                    mmdf.iloc[k, mmdf.columns.get_loc("dtlof2")] = float(locdf['ol_lof_decision'][locsel].values[1])
+                    mmdf.iloc[k, mmdf.columns.get_loc("dtntimepoints2")] = float(dtdf['dimt'][locsel].values[1])
         if rsdf is not None:
-            locsel = (rsdf["subjectIDdate"] == mmdf["subjectIDdate"].iloc[k]) & (rsdf[outlier_column] < 0.5)
+            locsel = (rsdf["subjectIDdate"] == mmdf["subjectIDdate"].iloc[k])
             if sum(locsel) == 1:
                 mmdf.iloc[k, mmdf.columns.get_loc("rsfid1")] = rsdf["imageID"][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("rsffn1")] = rsdf["fn"][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("rsffn1")] = rsdf[unique_identifier][locsel].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("rsfloop1")] = rsdf[outlier_column][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("rsflof1")] = rsdf['ol_lof_decision'][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("rsflof1")] = float(rsdf['ol_lof_decision'].values[0])
+                mmdf.iloc[k, mmdf.columns.get_loc("rsfntimepoints1")] = float(rsdf['dimt'][locsel].values[0])
             elif sum(locsel) > 1:
                 locdf = rsdf[locsel]
                 dedupe = locdf[["snr","cnr"]].duplicated()
@@ -1272,22 +1313,24 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
                 if locdf.shape[0] > 1:
                     locdf = locdf.sort_values(outlier_column).iloc[:2]
                 mmdf.iloc[k, mmdf.columns.get_loc("rsfid1")] = locdf["imageID"].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("rsffn1")] = locdf["fn"].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("rsffn1")] = locdf[unique_identifier].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("rsfloop1")] = locdf[outlier_column].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("rsflof1")] = locdf['ol_lof_decision'].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("rsflof1")] = float(locdf['ol_lof_decision'].values[0])
+                mmdf.iloc[k, mmdf.columns.get_loc("rsfntimepoints1")] = float(locdf['dimt'][locsel].values[0])
                 if locdf.shape[0] > 1:
                     mmdf.iloc[k, mmdf.columns.get_loc("rsfid2")] = locdf["imageID"].values[1]
-                    mmdf.iloc[k, mmdf.columns.get_loc("rsffn2")] = locdf["fn"].values[1]
+                    mmdf.iloc[k, mmdf.columns.get_loc("rsffn2")] = locdf[unique_identifier].values[1]
                     mmdf.iloc[k, mmdf.columns.get_loc("rsfloop2")] = locdf[outlier_column].values[1]
-                    mmdf.iloc[k, mmdf.columns.get_loc("rsflof2")] = locdf['ol_lof_decision'].values[1]
+                    mmdf.iloc[k, mmdf.columns.get_loc("rsflof2")] = float(locdf['ol_lof_decision'].values[1])
+                    mmdf.iloc[k, mmdf.columns.get_loc("rsfntimepoints2")] = float(locdf['dimt'][locsel].values[1])
 
         if fldf is not None:
             locsel = fldf['subjectIDdate'] == mmdf['subjectIDdate'].iloc[k]
             if locsel.sum() == 1:
                 mmdf.iloc[k, mmdf.columns.get_loc("flairid")] = fldf['imageID'][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("flairfn")] = fldf['filename'][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("flairfn")] = fldf[unique_identifier][locsel].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("flairloop")] = fldf[outlier_column][locsel].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("flairlof")] = fldf['ol_lof_decision'][locsel].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("flairlof")] = float(fldf['ol_lof_decision'][locsel].values[0])
             elif sum(locsel) > 1:
                 locdf = fldf[locsel]
                 dedupe = locdf[["snr","cnr"]].duplicated()
@@ -1295,9 +1338,9 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
                 if locdf.shape[0] > 1:
                     locdf = locdf.sort_values(outlier_column).iloc[:2]
                 mmdf.iloc[k, mmdf.columns.get_loc("flairid")] = locdf["imageID"].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("flairfn")] = locdf["fn"].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("flairfn")] = locdf[unique_identifier].values[0]
                 mmdf.iloc[k, mmdf.columns.get_loc("flairloop")] = locdf[outlier_column].values[0]
-                mmdf.iloc[k, mmdf.columns.get_loc("flairlof")] = locdf['ol_lof_decision'].values[0]
+                mmdf.iloc[k, mmdf.columns.get_loc("flairlof")] = float(locdf['ol_lof_decision'].values[0])
 
         if nmdf is not None:
             locsel = nmdf['subjectIDdate'] == mmdf['subjectIDdate'].iloc[k]
@@ -1305,16 +1348,40 @@ def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column
                 locdf = nmdf[locsel]
                 for i in range(np.min( [10,locdf.shape[0]])):
                     nmid = "nmid"+str(i+1)
-                    mmdf[nmid].iloc[k] = locdf['imageID'].iloc[i]
+                    mmdf.loc[k,nmid] = locdf['imageID'].iloc[i]
                     nmfn = "nmfn"+str(i+1)
-                    mmdf[nmfn].iloc[k] = locdf['imageID'].iloc[i]
+                    mmdf.loc[k,nmfn] = locdf['imageID'].iloc[i]
                     nmloop = "nmloop"+str(i+1)
-                    mmdf[nmloop].iloc[k] = locdf[outlier_column].iloc[i]
+                    mmdf.loc[k,nmloop] = locdf[outlier_column].iloc[i]
                     nmloop = "nmlof"+str(i+1)
-                    mmdf[nmloop].iloc[k] = locdf['ol_lof_decision'].iloc[i]
+                    mmdf.loc[k,nmloop] = float(locdf['ol_lof_decision'].iloc[i])
 
+    mmdf['rsf_total_timepoints']=mmdf['rsfntimepoints1']+mmdf['rsfntimepoints2']
+    mmdf['dt_total_timepoints']=mmdf['dtntimepoints1']+mmdf['dtntimepoints2']
     return mmdf
 
+
+def add_repeat_column(df, groupby_column):
+    """
+    Adds a 'repeat' column to the DataFrame that counts occurrences of each unique value
+    in the specified 'groupby_column'. The count increments from 1 for each identical entry.
+    
+    Parameters:
+    - df: pandas DataFrame.
+    - groupby_column: The name of the column to group by and count repeats.
+    
+    Returns:
+    - Modified pandas DataFrame with an added 'repeat' column.
+    """
+    # Validate if the groupby_column exists in the DataFrame
+    if groupby_column not in df.columns:
+        raise ValueError(f"Column '{groupby_column}' does not exist in the DataFrame.")
+    
+    # Count the occurrences of each unique value in the specified column and increment from 1
+    df['repeat'] = df.groupby(groupby_column).cumcount() + 1
+    
+    return df
+
 def best_mmm( mmdf, wmod, mysep='-', outlier_column='ol_loop', verbose=False):
     """
     Selects the best repeats per modality.
@@ -1333,6 +1400,8 @@ def best_mmm( mmdf, wmod, mysep='-', outlier_column='ol_loop', verbose=False):
     list: a list containing two metadata dataframes - raw and filt. raw contains all the metadata for the selected modality and filt contains the metadata filtered for highest quality repeats.
 
     """
+#    mmdf = mmdf.astype(str)
+    mmdf[outlier_column]=mmdf[outlier_column].astype(float)
     msel = mmdf['modality'] == wmod
     if wmod == 'rsfMRI':
         msel1 = mmdf['modality'] == 'rsfMRI'
@@ -1345,34 +1414,44 @@ def best_mmm( mmdf, wmod, mysep='-', outlier_column='ol_loop', verbose=False):
         msel2 = mmdf['modality'] == 'DTI_LR'
         msel3 = mmdf['modality'] == 'DTI_RL'
         msel4 = mmdf['modality'] == 'DTIdwi'
-        msel = msel1 | msel2 | msel3 | msel4
+        msel5 = mmdf['modality'] == 'DTIb0'
+        msel = msel1 | msel2 | msel3 | msel4 | msel5
     if sum(msel) == 0:
         return {'raw': None, 'filt': None}
-    uids = list(mmdf['filename'][msel])
-    metasub = mmdf[msel]
+    metasub = mmdf[msel].copy()
 
     if verbose:
         print(f"{wmod} {(metasub.shape[0])} pre")
 
-    metasub['subjectID']=math.nan
-    metasub['date']=math.nan
-    metasub['subjectIDdate']=math.nan
-    metasub['imageID']=math.nan
-    for k in range(len(uids)):
-        temp = uids[k].split( mysep )
-        metasub['subjectID'].iloc[k] = temp[1]
-        metasub['date'].iloc[k] = temp[2]
-        metasub['subjectIDdate'].iloc[k] = temp[1] + mysep + temp[2]
-        metasub['imageID'].iloc[k] = temp[4]
-
-    metasub['negol'] = metasub[outlier_column].max() - metasub[outlier_column]
+    metasub['subjectID']=None
+    metasub['date']=None
+    metasub['subjectIDdate']=None
+    metasub['imageID']=None
+    metasub['negol']=math.nan
+    for k in metasub.index:
+        temp = metasub.loc[k, 'filename'].split( mysep )
+        metasub.loc[k,'subjectID'] = str( temp[1] )
+        metasub.loc[k,'date'] = str( temp[2] )
+        metasub.loc[k,'subjectIDdate'] = str( temp[1] + mysep + temp[2] )
+        metasub.loc[k,'imageID'] = str( temp[4])
+
+
+    if 'ol_' in outlier_column:
+        metasub['negol'] = metasub[outlier_column].max() - metasub[outlier_column]
+    else:
+        metasub['negol'] = metasub[outlier_column]
     if 'date' not in metasub.keys():
-        metasub['date']='NA'
-    metasubq = highest_quality_repeat(metasub, 'filename', 'date', 'negol')
+        metasub['date']=None
+    metasubq = add_repeat_column( metasub, 'subjectIDdate' )
+    metasubq = highest_quality_repeat(metasubq, 'filename', 'date', 'negol')
 
     if verbose:
         print(f"{wmod} {metasubq.shape[0]} post")
 
+#    metasub = metasub.astype(str)
+#    metasubq = metasubq.astype(str)
+    metasub[outlier_column]=metasub[outlier_column].astype(float)
+    metasubq[outlier_column]=metasubq[outlier_column].astype(float)
     return {'raw': metasub, 'filt': metasubq}
 
 def mm_read( x, standardize_intensity=False, modality='' ):
@@ -1783,10 +1862,12 @@ def merge_dwi_data( img_LRdwp, bval_LR, bvec_LR, img_RLdwp, bval_RL, bvec_RL ):
     bvec_RL : array
 
     """
+    import warnings
     insamespace = ants.image_physical_space_consistency( img_LRdwp, img_RLdwp )
     if not insamespace :
-        raise ValueError('not insamespace ... corrected image pair should occupy the same physical space')
-
+        warnings.warn('not insamespace ... corrected image pair should occupy the same physical space; returning only the 1st set and wont join these data.')
+        return img_LRdwp, bval_LR, bvec_LR
+    
     bval_LR = np.concatenate([bval_LR,bval_RL])
     bvec_LR = np.concatenate([bvec_LR,bvec_RL])
     # concatenate the images
@@ -2555,7 +2636,7 @@ def template_figure_with_overlay(scalar_label_df, prefix, outputfilename=None, t
     toviz = temp['overlay']
     return { "underlay": seggm, 'overlay': toviz, 'seg': tcrop  }
 
-def get_data( name=None, force_download=False, version=21, target_extension='.csv' ):
+def get_data( name=None, force_download=False, version=23, target_extension='.csv' ):
     """
     Get ANTsPyMM data filename
 
@@ -2839,6 +2920,34 @@ def super_res_mcimage( image,
     return ants.list_to_ndimage( imageup, mcsr )
 
 
+def segment_timeseries_by_bvalue(bvals):
+    """
+    Segments a time series based on a threshold applied to b-values.
+    
+    This function categorizes indices of the given b-values array into two groups:
+    one for indices where b-values are above a near-zero threshold, and another
+    where b-values are at or below this threshold. The threshold is set to 1e-12.
+    
+    Parameters:
+    - bvals (numpy.ndarray): An array of b-values.
+
+    Returns:
+    - dict: A dictionary with two keys, 'lowermeans' and 'highermeans', each containing
+      the indices of bvals where the b-values are above and at/below the threshold, respectively.
+    """
+    # Define the threshold
+    threshold = 1e-12
+    
+    # Get indices where b-values are greater than the threshold
+    lowermeans = list(np.where(bvals > threshold)[0])
+    
+    # Get indices where b-values are less than or equal to the threshold
+    highermeans = list(np.where(bvals <= threshold)[0])
+    
+    return {
+        'lowermeans': lowermeans,
+        'highermeans': highermeans
+    }
 
 def segment_timeseries_by_meanvalue( image, quantile = 0.995 ):
     """
@@ -3290,7 +3399,7 @@ def dipy_dti_recon(
         space as the image, we will resample directly to the image space.  This
         could lead to problems if the inputs are really incorrect.
 
-    b0_idx : the indices of the B0; if None, use segment_timeseries_by_meanvalue to guess
+    b0_idx : the indices of the B0; if None, use segment_timeseries_by_bvalue
 
     mask_dilation : integer zero or more dilates the brain mask
 
@@ -3321,8 +3430,7 @@ def dipy_dti_recon(
         bvals = bvalsfn.copy()
         bvecs = bvecsfn.copy()
 
-    if b0_idx is None:
-        b0_idx = segment_timeseries_by_meanvalue( image )['highermeans']
+    b0_idx = segment_timeseries_by_bvalue( bvals )['highermeans']
 
     b0 = ants.slice_image( image, axis=3, idx=b0_idx[0] )
     bxtmod='bold'
@@ -3532,6 +3640,9 @@ def joint_dti_recon(
     def fix_dwi_shape( img, bvalfn, bvecfn ):
         if isinstance(bvecfn, str):
             bvals, bvecs = read_bvals_bvecs( bvalfn , bvecfn   )
+        else:
+            bvals = bvalfn
+            bvecs = bvecfn
         if bvecs.shape[0] < img.shape[3]:
             imgout = ants.from_numpy( img[:,:,:,0:bvecs.shape[0]] )
             imgout = ants.copy_image_info( img, imgout )
@@ -4586,7 +4697,7 @@ def get_rsf_outputs( coords ):
         return list( yeo['SystemName'].unique() )
 
 def tra_initializer( fixed, moving, n_simulations=32, max_rotation=30,
-    transform=['rigid'], verbose=False ):
+    transform=['rigid'], compreg=None, verbose=False ):
     """
     multi-start multi-transform registration solution - based on ants.registration
 
@@ -4600,6 +4711,8 @@ def tra_initializer( fixed, moving, n_simulations=32, max_rotation=30,
 
     transform : list of transforms to loop through
 
+    compreg : registration results against which to compare
+
     verbose : boolean
 
     """
@@ -4608,15 +4721,20 @@ def tra_initializer( fixed, moving, n_simulations=32, max_rotation=30,
         output_directory_w = output_directory + "/tra_reg/"
         os.makedirs(output_directory_w,exist_ok=True)
         bestmi = math.inf
+        bestvar = 0.0
         myorig = list(ants.get_origin( fixed ))
         mymax = 0;
         for k in range(len( myorig ) ):
             if abs(myorig[k]) > mymax:
                 mymax = abs(myorig[k])
         maxtrans = mymax * 0.05
-        bestreg=ants.registration( fixed,moving,'Translation',
-            outprefix=output_directory_w+"trans")
-        initx = ants.read_transform( bestreg['fwdtransforms'][0] )
+        if compreg is None:
+            bestreg=ants.registration( fixed,moving,'Translation',
+                outprefix=output_directory_w+"trans")
+            initx = ants.read_transform( bestreg['fwdtransforms'][0] )
+        else :
+            bestreg=compreg
+            initx = ants.read_transform( bestreg['fwdtransforms'][0] )
         for mytx in transform:
             regtx = 'Rigid'
             with tempfile.NamedTemporaryFile(suffix='.h5') as tp:
@@ -4653,6 +4771,9 @@ def tra_initializer( fixed, moving, n_simulations=32, max_rotation=30,
                                 print( "mi @ " + str(k) + " : " + str(mymi), flush=True)
                             bestmi = mymi
                             bestreg = reg
+                            bestvar = myvar
+        if bestvar == 0.0 and compreg is not None:
+            return compreg        
         return bestreg
 
 def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
@@ -4834,7 +4955,7 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
             nm_avg_cropped_new = nm_avg_cropped_new + warpednext
       nm_avg_cropped = nm_avg_cropped_new / len( crop_nm_list )
 
-  slabregUpdated = tra_initializer( nm_avg_cropped, t1c, verbose=verbose  )
+  slabregUpdated = tra_initializer( nm_avg_cropped, t1c, compreg=slabreg,verbose=verbose  )
   tempOrig = ants.apply_transforms( nm_avg_cropped_new, t1c, slabreg['fwdtransforms'] )
   tempUpdate = ants.apply_transforms( nm_avg_cropped_new, t1c, slabregUpdated['fwdtransforms'] )
   miUpdate = ants.image_mutual_information(
@@ -5409,7 +5530,8 @@ def resting_state_fmri_networks( fmri, fmri_template, t1, t1segmentation,
         ptImage=ants.threshold_image( ptImg, pts2bold.loc[i,'ROI'], pts2bold.loc[i,'ROI'] )
     if debug:
       ptImgAll = ptImgAll + ptImage
-    meanROI[:,i] = ants.timeseries_to_matrix( simg, ptImage).mean(axis=1)
+    if ptImage.sum() > 0 :
+        meanROI[:,i] = ants.timeseries_to_matrix( simg, ptImage).mean(axis=1)
 
   if debug:
       ants.image_write( simg, '/tmp/simg.nii.gz' )
@@ -5527,9 +5649,15 @@ def resting_state_fmri_networks( fmri, fmri_template, t1, t1segmentation,
     fname='falffPoint'+kk+anatname
     aname='alffPoint'+kk+anatname
     pname='perafPoint'+kk+anatname
-    outdict[fname]=(outdict['falff'][ptImg==k]).mean()
-    outdict[aname]=(outdict['alff'][ptImg==k]).mean()
-    outdict[pname]=(perafimg[ptImg==k]).mean()
+    localsel = ptImg == k
+    if localsel.sum() > 0 : # check if non-empty
+        outdict[fname]=(outdict['falff'][localsel]).mean()
+        outdict[aname]=(outdict['alff'][localsel]).mean()
+        outdict[pname]=(perafimg[localsel]).mean()
+    else:
+        outdict[fname]=math.nan
+        outdict[aname]=math.nan
+        outdict[pname]=math.nan
 
   rsfNuisance = pd.DataFrame( nuisance )
   if remove_it:
@@ -5562,6 +5690,7 @@ def resting_state_fmri_networks( fmri, fmri_template, t1, t1segmentation,
   outdict['despiking_count_summary'] = despiking_count_summary
   outdict['FD_max'] = corrmo['FD'].max()
   outdict['FD_mean'] = corrmo['FD'].mean()
+  outdict['FD_sd'] = corrmo['FD'].std()
   outdict['bold_evr'] =  antspyt1w.patch_eigenvalue_ratio( und, 512, [16,16,16], evdepth = 0.9, mask = bmask )
   outdict['n_outliers'] = len(hlinds)
   outdict['nc_wm'] = int(nc_wm)
@@ -5638,11 +5767,18 @@ def despike_time_series_afni(image, c1=2.5, c2=4):
     residuals = data - curve
     mad = np.median(np.abs(residuals - np.median(residuals, axis=-1, keepdims=True)), axis=-1, keepdims=True)
     sigma = np.sqrt(np.pi / 2) * mad
+    # Ensure sigma is not zero to avoid division by zero
+    sigma_safe = np.where(sigma == 0, 1e-10, sigma)
+
+    # Optionally, handle NaN or inf values in data, curve, or sigma
+    data = np.nan_to_num(data, nan=0.0, posinf=np.finfo(np.float64).max, neginf=np.finfo(np.float64).min)
+    curve = np.nan_to_num(curve, nan=0.0, posinf=np.finfo(np.float64).max, neginf=np.finfo(np.float64).min)
+    sigma_safe = np.nan_to_num(sigma_safe, nan=1e-10, posinf=np.finfo(np.float64).max, neginf=np.finfo(np.float64).min)
 
     # Despike algorithm
     spike_counts = np.zeros( image.shape[3] )
     for i in range(data.shape[-1]):
-        s = (data[..., i] - curve[..., i]) / sigma[..., 0]
+        s = (data[..., i] - curve[..., i]) / sigma_safe[..., 0]
         ww = s > c1
         s_prime = np.where( ww, c1 + (c2 - c1) * np.tanh((s - c1) / (c2 - c1)), s)
         spike_counts[i] = ww.sum()
@@ -5907,6 +6043,7 @@ def bold_perfusion_minimal(
   outdict['dvars'] = dvars( corrmo['motion_corrected'], gmseg )
   outdict['FD_max'] = rsfNuisance['FD'].max()
   outdict['FD_mean'] = rsfNuisance['FD'].mean()
+  outdict['FD_sd'] = rsfNuisance['FD'].std()
   outdict['outlier_volumes']=hlinds
   outdict['negative_voxels']=negative_voxels
   return convert_np_in_dict( outdict )
@@ -6313,6 +6450,7 @@ Where:
   outdict['high_motion_pct'] = (rsfNuisance['FD'] > FD_threshold ).sum() / rsfNuisance.shape[0]
   outdict['FD_max'] = rsfNuisance['FD'].max()
   outdict['FD_mean'] = rsfNuisance['FD'].mean()
+  outdict['FD_sd'] = rsfNuisance['FD'].std()
   outdict['bold_evr'] =  antspyt1w.patch_eigenvalue_ratio( und, 512, [16,16,16], evdepth = 0.9, mask = bmask )
   outdict['t1reg'] = t1reg
   outdict['outlier_volumes']=hlinds
@@ -6877,11 +7015,14 @@ def mm(
             normalization_dict['MD_norm'] = ants.apply_transforms( group_template, mydti['recon_md'],group_transform+dtirig['fwdtransforms'] )
             normalization_dict['FA_norm'] = ants.apply_transforms( group_template, mydti['recon_fa'],group_transform+dtirig['fwdtransforms'] )
             output_directory = tempfile.mkdtemp()
-            comptx = ants.apply_transforms( group_template, group_template, 
-                group_transform+dtirig['fwdtransforms'], 
-                compose = output_directory + '/xxx' )
-            normalization_dict['DTI_norm'] = transform_and_reorient_dti(
-                group_template, mydti['dti'], comptx, py_based=True, verbose=True )
+            do_dti_norm=False
+            if do_dti_norm:
+                comptx = ants.apply_transforms( group_template, group_template, group_transform+dtirig['fwdtransforms'], compose = output_directory + '/xxx' )
+                tspc=[2.,2.,2.]
+                if srmodel is not None:
+                    tspc=[1.,1.,1.]
+                group_template2mm = ants.resample_image( group_template, tspc  )
+                normalization_dict['DTI_norm'] = transform_and_reorient_dti( group_template2mm, mydti['dti'], comptx, py_based=True, verbose=True )
             import shutil
             shutil.rmtree(output_directory, ignore_errors=True )
         if output_dict['rsf'] is not None:
@@ -7019,6 +7160,8 @@ def write_mm( output_prefix, mm, mm_norm=None, t1wide=None, separator='_', verbo
     if 'flair' in mm:
         if mm['flair'] is not None:
             myop = output_prefix + separator + 'wmh.nii.gz'
+            pngfnb = output_prefix + separator + 'wmh_seg.png'
+            ants.plot( mm['flair']['flair'], mm['flair']['WMH_posterior_probability_map'], axis=2, nslices=21, ncol=7, filename=pngfnb, crop=True )
             if mm['flair']['WMH_probability_map'] is not None:
                 image_write_with_thumbnail( mm['flair']['WMH_probability_map'], myop, thumb=False )
             flwide = dict_to_dataframe( mm['flair'] )
@@ -7066,9 +7209,10 @@ def write_mm( output_prefix, mm, mm_norm=None, t1wide=None, separator='_', verbo
                 mm_wide['dti_high_motion_count'] =  mydti['high_motion_count']
                 mm_wide['dti_FD_mean'] = mydti['framewise_displacement'].mean()
                 mm_wide['dti_FD_max'] = mydti['framewise_displacement'].max()
+                mm_wide['dti_FD_sd'] = mydti['framewise_displacement'].std()
                 fdfn = output_prefix + separator + '_fd.csv'
             else:
-                mm_wide['dti_FD_mean'] = mm_wide['dti_FD_max'] = 'NA'
+                mm_wide['dti_FD_mean'] = mm_wide['dti_FD_max'] = mm_wide['dti_FD_sd'] = 'NA'
 
     if 'perf' in mm:
         if mm['perf'] is not None:
@@ -7708,6 +7852,7 @@ def mm_csv(
     writes output to disk and produces figures
 
     """
+    import traceback
     visualize = True
     verbose = True
     if verbose:
@@ -7965,9 +8110,11 @@ def mm_csv(
                             test_run=test_run,
                             verbose=True )
                     except Exception as e:
+                        error_info = traceback.format_exc()
+                        print(error_info)
                         visualize=False
                         dowrite=False
-                        print(f"An error occurred while processing {overmodX}: {e}")
+                        print(f"antspymmerror occurred while processing {overmodX}: {e}")
                         pass
                     if not test_run:
                         write_mm( output_prefix=mymm, mm=tabPro, mm_norm=normPro, t1wide=None, separator=mysep )
@@ -8021,9 +8168,11 @@ def mm_csv(
                                             test_run=test_run,
                                             verbose=True )
                                     except Exception as e:
+                                        error_info = traceback.format_exc()
+                                        print(error_info)
                                         visualize=False
                                         dowrite=False
-                                        print(f"An error occurred while processing {overmodX}: {e}")
+                                        print(f"antspymmerror occurred while processing {overmodX}: {e}")
                                         pass
                                     if visualize:
                                         maxslice = np.min( [21, hier['brain_n4_dnz'].shape[2] ] )
@@ -8044,9 +8193,11 @@ def mm_csv(
                                         test_run=test_run,
                                         verbose=True )
                                 except Exception as e:
+                                        error_info = traceback.format_exc()
+                                        print(error_info)
                                         visualize=False
                                         dowrite=False
-                                        print(f"An error occurred while processing {overmodX}: {e}")
+                                        print(f"antspymmerror occurred while processing {overmodX}: {e}")
                                         pass
                                 if visualize:
                                     maxslice = np.min( [21, img.shape[2] ] )
@@ -8081,11 +8232,13 @@ def mm_csv(
                                             test_run=test_run,
                                             verbose=True )
                                     except Exception as e:
+                                        error_info = traceback.format_exc()
+                                        print(error_info)
                                         visualize=False
                                         dowrite=False
                                         tabPro={'rsf':None}
                                         normPro={'rsf':None}
-                                        print(f"An error occurred while processing {overmodX}: {e}")
+                                        print(f"antspymmerror occurred while processing {overmodX}: {e}")
                                         pass
                                 if tabPro['rsf'] is not None and visualize:
                                     for tpro in tabPro['rsf']: # FIXMERSF
@@ -8117,10 +8270,12 @@ def mm_csv(
                                         perfusion_m0=perfusion_m0,
                                         verbose=True )
                                 except Exception as e:
+                                        error_info = traceback.format_exc()
+                                        print(error_info)
                                         visualize=False
                                         dowrite=False
                                         tabPro={'perf':None}
-                                        print(f"An error occurred while processing {overmodX}: {e}")
+                                        print(f"antspymmerror occurred while processing {overmodX}: {e}")
                                         pass
                                 if tabPro['perf'] is not None and visualize:
                                     maxslice = np.min( [21, tabPro['perf']['meanBold'].shape[2] ] )
@@ -8137,7 +8292,7 @@ def mm_csv(
                                 bvalfnList = [ bvalfn ]
                                 bvecfnList = [ bvecfn ]
                                 missing_dti_data=False # bval, bvec or images
-                                if len( myimgsr ) > 1:  # find DTI_RL
+                                if len( myimgsr ) == 2:  # find DTI_RL
                                     dtilrfn = myimgsr[myimgcount+1]
                                     if exists( dtilrfn ):
                                         bvalfnRL = re.sub( '.nii.gz', '.bval' , dtilrfn )
@@ -8146,6 +8301,28 @@ def mm_csv(
                                         imgList.append( imgRL )
                                         bvalfnList.append( bvalfnRL )
                                         bvecfnList.append( bvecfnRL )
+                                elif len( myimgsr ) == 3:  # find DTI_RL
+                                    print("DTI trinity")
+                                    dtilrfn = myimgsr[myimgcount+1]
+                                    dtilrfn2 = myimgsr[myimgcount+2]
+                                    if exists( dtilrfn ) and exists( dtilrfn2 ):
+                                        bvalfnRL = re.sub( '.nii.gz', '.bval' , dtilrfn )
+                                        bvecfnRL = re.sub( '.nii.gz', '.bvec' , dtilrfn )
+                                        bvalfnRL2 = re.sub( '.nii.gz', '.bval' , dtilrfn2 )
+                                        bvecfnRL2 = re.sub( '.nii.gz', '.bvec' , dtilrfn2 )
+                                        imgRL = ants.image_read( dtilrfn )
+                                        imgRL2 = ants.image_read( dtilrfn2 )
+                                        bvals, bvecs = read_bvals_bvecs( bvalfnRL , bvecfnRL  )
+                                        print( bvals.max() )
+                                        bvals2, bvecs2 = read_bvals_bvecs( bvalfnRL2 , bvecfnRL2  )
+                                        print( bvals2.max() )
+                                        temp = merge_dwi_data( imgRL, bvals, bvecs, imgRL2, bvals2, bvecs2  )
+                                        imgList.append( temp[0] )
+                                        bvalfnList.append( mymm+mysep+'joined.bval' )
+                                        bvecfnList.append( mymm+mysep+'joined.bvec' )
+                                        write_bvals_bvecs( temp[1], temp[2], mymm+mysep+'joined' )
+                                        bvalsX, bvecsX = read_bvals_bvecs( bvalfnRL2 , bvecfnRL2  )
+                                        print( bvalsX.max() )
                                 # check existence of all files expected ...
                                 for dtiex in bvalfnList+bvecfnList+myimgsr:
                                     if not exists(dtiex):
@@ -8175,20 +8352,22 @@ def mm_csv(
                                             bvals = bvalfnList,
                                             bvecs = bvecfnList,
                                             srmodel=srmodel_DTI_mdl,
-                                            do_tractography=False, #not test_run,
+                                            do_tractography=not test_run,
                                             do_kk=False,
                                             do_normalization=templateTx,
-                                            group_template = ants.resample_image(normalization_template,(2,2,2)),
+                                            group_template = normalization_template,
                                             group_transform = groupTx,
                                             dti_motion_correct = dti_motion_correct,
                                             dti_denoise = dti_denoise,
                                             test_run=test_run,
                                             verbose=True )
                                     except Exception as e:
+                                            error_info = traceback.format_exc()
+                                            print(error_info)
                                             visualize=False
                                             dowrite=False
                                             tabPro={'DTI':None}
-                                            print(f"An error occurred while processing {overmodX}: {e}")
+                                            print(f"antspymmerror occurred while processing {overmodX}: {e}")
                                             pass
                                     mydti = tabPro['DTI']
                                     if visualize and tabPro['DTI'] is not None:
@@ -8835,6 +9014,7 @@ def boot_wmh( flair, t1, t1seg, mmfromconvexhull = 0.0, strict=True,
     wmh_sum_aug = wmh_sum_aug / float( n_simulations )
     wmh_sum_prior_aug = wmh_sum_prior_aug / float( n_simulations )
     return{
+      'flair' : ants.iMath(flair,"Normalize"),
       'WMH_probability_map' : augprob,
       'WMH_posterior_probability_map' : augprob_prior,
       'wmh_mass': wmh_sum_aug,
@@ -9267,6 +9447,7 @@ def blind_image_assessment(
     title=False,
     pull_rank=False,
     resample=None,
+    n_to_skip = 10,
     verbose=False
 ):
     """
@@ -9296,6 +9477,8 @@ def blind_image_assessment(
 
     resample : None, numeric max or min, resamples image to isotropy
 
+    n_to_skip : 10 by default; samples time series every n_to_skip volume
+
     verbose : boolean
 
     """
@@ -9307,6 +9490,7 @@ def blind_image_assessment(
     from pathlib import Path
     import json
     import re
+    from dipy.io.gradients import read_bvals_bvecs
     mystem=''
     if isinstance(image,list):
         isfilename=isinstance( image[0], str)
@@ -9315,6 +9499,7 @@ def blind_image_assessment(
         isfilename=isinstance( image, str)
     outdf = pd.DataFrame()
     mymeta = None
+    MagneticFieldStrength = None
     image_filename=''
     if isfilename:
         image_filename = image
@@ -9322,10 +9507,14 @@ def blind_image_assessment(
             image_filename=image[0]
         json_name = re.sub(".nii.gz",".json",image_filename)
         if exists( json_name ):
-            with open(json_name, 'r') as fcc_file:
-                mymeta = json.load(fcc_file, strict=False)
-                if verbose:
-                    print(json.dumps(mymeta, indent=4))
+            try:
+                with open(json_name, 'r') as fcc_file:
+                    mymeta = json.load(fcc_file)
+                    if verbose:
+                        print(json.dumps(mymeta, indent=4))
+                    fcc_file.close()
+            except:
+                pass
         mystem=Path( image ).stem
         mystem=Path( mystem ).stem
         image_reference = ants.image_read( image )
@@ -9333,6 +9522,7 @@ def blind_image_assessment(
     else:
         image_reference = ants.image_clone( image )
     ntimepoints = 1
+    bvalueMax=None
     if image_reference.dimension == 4:
         ntimepoints = image_reference.shape[3]
         if "DTI" in image_filename:
@@ -9340,11 +9530,16 @@ def blind_image_assessment(
             image_b0, image_dwi = get_average_dwi_b0( image_reference, fast=True )
             image_b0 = ants.iMath( image_b0, 'Normalize' )
             image_dwi = ants.iMath( image_dwi, 'Normalize' )
+            bval_name = re.sub(".nii.gz",".bval",image_filename)
+            bvec_name = re.sub(".nii.gz",".bvec",image_filename)
+            if exists( bval_name ) and exists( bvec_name ):
+                bvals, bvecs = read_bvals_bvecs( bval_name , bvec_name  )
+                bvalueMax = bvals.max()
         else:
             image_b0 = ants.get_average_of_timeseries( image_reference ).iMath("Normalize")
     else:
         image_compare = ants.smooth_image( image_reference, 3, sigma_in_physical_coordinates=False )
-    for jjj in range(ntimepoints):
+    for jjj in range(0,ntimepoints,n_to_skip):
         modality='unknown'
         if "rsfMRI" in image_filename:
             modality='rsfMRI'
@@ -9365,7 +9560,7 @@ def blind_image_assessment(
                     modality='DTIdwi'
             else:
                 image_compare = ants.image_clone( image_b0 )
-        image = ants.iMath( image, 'TruncateIntensity',0.01,0.995)
+        # image = ants.iMath( image, 'TruncateIntensity',0.01,0.995)
         minspc = np.min(ants.get_spacing(image))
         maxspc = np.max(ants.get_spacing(image))
         if resample is not None:
@@ -9397,69 +9592,76 @@ def blind_image_assessment(
         bgmsk = msk*0+1-msk
         mskdil = ants.iMath(msk, "MD", 4 )
         # ants.plot_ortho( image, msk, crop=False )
-        image = ants.crop_image( image, mskdil ).iMath("Normalize")
-        msk = ants.crop_image( msk, mskdil ).iMath("Normalize")
-        bgmsk = ants.crop_image( bgmsk, mskdil ).iMath("Normalize")
-        image_compare = ants.crop_image( image_compare, mskdil ).iMath("Normalize")
         nvox = int( msk.sum() )
-        minshp = np.min( image.shape )
-        npatch = int( np.round(  0.1 * nvox ) )
-        npatch = np.min(  [512,npatch ] )
-        patch_shape = []
-        for k in range( 3 ):
-            p = int( 32.0 / ants.get_spacing( image  )[k] )
-            if p > int( np.round( image.shape[k] * 0.5 ) ):
-                p = int( np.round( image.shape[k] * 0.5 ) )
-            patch_shape.append( p )
-        if verbose:
-            print(image)
-            print( patch_shape )
-            print( npatch )
-        myevr = math.nan # dont want to fail if something odd happens in patch extraction
-        try:
-            myevr = antspyt1w.patch_eigenvalue_ratio( image, npatch, patch_shape,
-                evdepth = 0.9, mask=msk )
-        except:
-            pass
-        if pull_rank:
-            image = ants.rank_intensity(image)
-        imagereflect = ants.reflect_image(image, axis=0)
-        asym_err = ( image - imagereflect ).abs().mean()
-        # estimate noise by center cropping, denoizing and taking magnitude of difference
-        nocrop=False
-        if image.dimension == 3:
-            if image.shape[2] == 1:
-                nocrop=True        
-        if maxspc/minspc > 10:
-            nocrop=True
-        if nocrop:
-            mycc = ants.image_clone( image )
-        else:
-            mycc = antspyt1w.special_crop( image,
-                ants.get_center_of_mass( msk *0 + 1 ), patch_shape )
-        myccd = ants.denoise_image( mycc, p=2,r=2,noise_model='Gaussian' )
-        noizlevel = ( mycc - myccd ).abs().mean()
-#        ants.plot_ortho( image, crop=False, filename=viz_filename, flat=True, xyz_lines=False, orient_labels=False, xyz_pad=0 )
-#        from brisque import BRISQUE
-#        obj = BRISQUE(url=False)
-#        mybrisq = obj.score( np.array( Image.open( viz_filename )) )
         spc = ants.get_spacing( image )
         org = ants.get_origin( image )
-        msk_vol = msk.sum() * np.prod( spc )
-        bgstd = image[ bgmsk == 1 ].std()
-        fgmean = image[ msk == 1 ].mean()
-        bgmean = image[ bgmsk == 1 ].mean()
-        snrref = fgmean / bgstd
-        cnrref = ( fgmean - bgmean ) / bgstd
-        psnrref = antspynet.psnr(  image_compare, image  )
-        ssimref = antspynet.ssim(  image_compare, image  )
-        if nocrop:
-            mymi = math.inf
+        if ( nvox > 0 ):
+            image = ants.crop_image( image, mskdil ).iMath("Normalize")
+            msk = ants.crop_image( msk, mskdil ).iMath("Normalize")
+            bgmsk = ants.crop_image( bgmsk, mskdil ).iMath("Normalize")
+            image_compare = ants.crop_image( image_compare, mskdil ).iMath("Normalize")           
+            npatch = int( np.round(  0.1 * nvox ) )
+            npatch = np.min(  [512,npatch ] )
+            patch_shape = []
+            for k in range( 3 ):
+                p = int( 32.0 / ants.get_spacing( image  )[k] )
+                if p > int( np.round( image.shape[k] * 0.5 ) ):
+                    p = int( np.round( image.shape[k] * 0.5 ) )
+                patch_shape.append( p )
+            if verbose:
+                print(image)
+                print( patch_shape )
+                print( npatch )
+            myevr = math.nan # dont want to fail if something odd happens in patch extraction
+            try:
+                myevr = antspyt1w.patch_eigenvalue_ratio( image, npatch, patch_shape,
+                    evdepth = 0.9, mask=msk )
+            except:
+                pass
+            if pull_rank:
+                image = ants.rank_intensity(image)
+            imagereflect = ants.reflect_image(image, axis=0)
+            asym_err = ( image - imagereflect ).abs().mean()
+            # estimate noise by center cropping, denoizing and taking magnitude of difference
+            nocrop=False
+            if image.dimension == 3:
+                if image.shape[2] == 1:
+                    nocrop=True        
+            if maxspc/minspc > 10:
+                nocrop=True
+            if nocrop:
+                mycc = ants.image_clone( image )
+            else:
+                mycc = antspyt1w.special_crop( image,
+                    ants.get_center_of_mass( msk *0 + 1 ), patch_shape )
+            myccd = ants.denoise_image( mycc, p=2,r=2,noise_model='Gaussian' )
+            noizlevel = ( mycc - myccd ).abs().mean()
+    #        ants.plot_ortho( image, crop=False, filename=viz_filename, flat=True, xyz_lines=False, orient_labels=False, xyz_pad=0 )
+    #        from brisque import BRISQUE
+    #        obj = BRISQUE(url=False)
+    #        mybrisq = obj.score( np.array( Image.open( viz_filename )) )
+            msk_vol = msk.sum() * np.prod( spc )
+            bgstd = image[ bgmsk == 1 ].std()
+            fgmean = image[ msk == 1 ].mean()
+            bgmean = image[ bgmsk == 1 ].mean()
+            snrref = fgmean / bgstd
+            cnrref = ( fgmean - bgmean ) / bgstd
+            psnrref = antspynet.psnr(  image_compare, image  )
+            ssimref = antspynet.ssim(  image_compare, image  )
+            if nocrop:
+                mymi = math.inf
+            else:
+                mymi = ants.image_mutual_information( image_compare, image )
         else:
-            mymi = ants.image_mutual_information( image_compare, image )
-        mriseries='NA'
-        mrimfg='NA'
-        mrimodel='NA'
+            msk_vol = 0
+            myevr = mymi = ssimref = psnrref = cnrref = asym_err = noizlevel = math.nan
+            
+        mriseries=None
+        mrimfg=None
+        mrimodel=None
+        mriSAR=None
+        BandwidthPerPixelPhaseEncode=None
+        PixelBandwidth=None
         if mymeta is not None:
             # mriseries=mymeta['']
             try:
@@ -9470,13 +9672,39 @@ def blind_image_assessment(
                 mrimodel=mymeta['ManufacturersModelName']
             except:
                 pass
+            try:
+                MagneticFieldStrength=mymeta['MagneticFieldStrength']
+            except:
+                pass
+            try:
+                PixelBandwidth=mymeta['PixelBandwidth']
+            except:
+                pass
+            try:
+                BandwidthPerPixelPhaseEncode=mymeta['BandwidthPerPixelPhaseEncode']
+            except:
+                pass
+            try:
+                mriSAR=mymeta['SAR']
+            except:
+                pass
         ttl=mystem + ' '
         ttl=''
         ttl=ttl + "NZ: " + "{:0.4f}".format(noizlevel) + " SNR: " + "{:0.4f}".format(snrref) + " CNR: " + "{:0.4f}".format(cnrref) + " PS: " + "{:0.4f}".format(psnrref)+ " SS: " + "{:0.4f}".format(ssimref) + " EVR: " + "{:0.4f}".format(myevr)+ " MI: " + "{:0.4f}".format(mymi)
-        if viz_filename is not None and ( jjj == 0 or (jjj % 30 == 0) ):
+        if viz_filename is not None and ( jjj == 0 or (jjj % 30 == 0) ) and image.shape[2] < 685:
             viz_filename_use = re.sub( ".png", "_slice"+str(jjj).zfill(4)+".png", viz_filename )
             ants.plot_ortho( image, crop=False, filename=viz_filename_use, flat=True, xyz_lines=False, orient_labels=False, xyz_pad=0,  title=ttl, titlefontsize=12, title_dy=-0.02,textfontcolor='red' )
-        df = pd.DataFrame([[ mystem, noizlevel, snrref, cnrref, psnrref, ssimref, mymi, asym_err, myevr, msk_vol, spc[0], spc[1], spc[2],org[0], org[1], org[2], image.shape[0], image.shape[1], image.shape[2], jjj, modality, mriseries, mrimfg, mrimodel ]], columns=['filename', 'noise', 'snr', 'cnr', 'psnr', 'ssim', 'mi', 'reflection_err', 'EVR', 'msk_vol', 'spc0','spc1','spc2','org0','org1','org2','dimx','dimy','dimz','slice','modality', 'mriseries', 'mrimfg', 'mrimodel' ])
+        df = pd.DataFrame([[ 
+            mystem, 
+            image_reference.dimension, 
+            noizlevel, snrref, cnrref, psnrref, ssimref, mymi, asym_err, myevr, msk_vol, 
+            spc[0], spc[1], spc[2],org[0], org[1], org[2], 
+            image.shape[0], image.shape[1], image.shape[2], ntimepoints, 
+            jjj, modality, mriseries, mrimfg, mrimodel, MagneticFieldStrength, mriSAR, PixelBandwidth, BandwidthPerPixelPhaseEncode, bvalueMax ]], 
+            columns=[
+                'filename', 
+                'dimensionality',
+                'noise', 'snr', 'cnr', 'psnr', 'ssim', 'mi', 'reflection_err', 'EVR', 'msk_vol', 'spc0','spc1','spc2','org0','org1','org2','dimx','dimy','dimz','dimt','slice','modality', 'mriseries', 'mrimfg', 'mrimodel', 'mriMagneticFieldStrength', 'mriSAR', 'mriPixelBandwidth', 'mriPixelBandwidthPE', 'dti_bvalueMax' ])
         outdf = pd.concat( [outdf, df ], axis=0, ignore_index=False )
         if verbose:
             print( outdf )
@@ -9485,6 +9713,29 @@ def blind_image_assessment(
         outdf.to_csv( csvfn )
     return outdf
 
+def remove_unwanted_columns(df):
+    # Identify columns to drop: those named 'X' or starting with 'Unnamed'
+    cols_to_drop = [col for col in df.columns if col == 'X' or col.startswith('Unnamed')]
+    
+    # Drop the identified columns from the DataFrame, if any
+    df_cleaned = df.drop(columns=cols_to_drop, errors='ignore')
+    
+    return df_cleaned
+
+def process_dataframe_generalized(df, group_by_column):
+    # Make sure the group_by_column is excluded from both numeric and other columns calculations
+    numeric_cols = df.select_dtypes(include='number').columns.difference([group_by_column])
+    other_cols = df.columns.difference(numeric_cols).difference([group_by_column])
+    
+    # Define aggregation functions: mean for numeric cols, mode for other cols
+    # Update to handle empty mode results safely
+    agg_dict = {col: 'mean' for col in numeric_cols}
+    agg_dict.update({
+        col: lambda x: pd.Series.mode(x).iloc[0] if not pd.Series.mode(x).empty else None for col in other_cols
+    })    
+    # Group by the specified column, applying different aggregation functions to different columns
+    processed_df = df.groupby(group_by_column, as_index=False).agg(agg_dict)
+    return processed_df
 
 def average_blind_qc_by_modality(qc_full,verbose=False):
     """
@@ -9496,21 +9747,14 @@ def average_blind_qc_by_modality(qc_full,verbose=False):
     Returns:
     pandas dataframe containing the processed qc data.
     """
+    qc_full = remove_unwanted_columns( qc_full )
     # Get unique modalities
     modalities = qc_full['modality'].unique()
     modalities = modalities[modalities != 'unknown']
-    # Get modalities to select
-    m0sel = qc_full['modality'].isin(modalities)
     # Get unique ids
-    uid = qc_full['filename'] + "_" + qc_full['modality'].astype(str)
+    uid = qc_full['filename']
     to_average = uid.unique()
-    # Define column indices
-    contcols = ['noise', 'snr', 'cnr', 'psnr', 'ssim', 'mi','reflection_err', 'EVR', 'msk_vol', 'spc0', 'spc1', 'spc2', 'org0','org1','org2', 'dimx', 'dimy', 'dimz', 'slice']
-    ocols = ['filename','modality', 'mriseries', 'mrimfg', 'mrimodel']
-    # restrict to columns we "know"
-    qc_full = qc_full[ocols+contcols]
-    # Create empty meta dataframe
-    meta = pd.DataFrame(columns=ocols+contcols)
+    meta = pd.DataFrame(columns=qc_full.columns )
     # Process each unique id
     n = len(to_average)
     for k in range(n):
@@ -9522,15 +9766,11 @@ def average_blind_qc_by_modality(qc_full,verbose=False):
         if sum(m1sel) > 1:
             # If more than one entry for id, take the average of continuous columns,
             # maximum of the slice column, and the first entry of the other columns
+            mfsub = process_dataframe_generalized(qc_full[m1sel],'filename')
+        else:
             mfsub = qc_full[m1sel]
-            if mfsub.shape[0] > 1:
-                meta.loc[k, contcols] = mfsub.loc[:, contcols].mean(numeric_only=True)
-                meta.loc[k, 'slice'] = mfsub['slice'].max()
-                meta.loc[k, ocols] = mfsub[ocols].iloc[0]
-        elif sum(m1sel) == 1:
-            # If only one entry for id, just copy the entry
-            mfsub = qc_full[m1sel]
-            meta.loc[k] = mfsub.iloc[0]
+        meta.loc[k] = mfsub.iloc[0]
+    meta['modality'] = meta['modality'].replace(['DTIdwi', 'DTIb0'], 'DTI', regex=True)
     return meta
 
 def wmh( flair, t1, t1seg,
@@ -10163,15 +10403,14 @@ def novelty_detection_quantile(df_train, df_test):
         myqs[mykey] = abs( temp - 0.5 ) / 0.5
     return myqs
 
-
-def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_image, overlay_cmap='bwr', nslices=21, ncol=7, edge_image_dilation = 0, black_bg=True, axes = [0,1,2], fixed_overlay_range=None, crop=True, verbose=False ):
+def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_image, overlay_cmap='bwr', nslices=21, ncol=7, edge_image_dilation = 0, black_bg=True, axes = [0,1,2], fixed_overlay_range=None, crop=5, verbose=False ):
     """
     Create figures based on statistical data and an underlying brain image.
 
     Assumes both ~/.antspyt1w and ~/.antspymm data is available
 
     Parameters:
-    - statistical_df (pandas dataframe): with 2 columns named anat and value
+    - statistical_df (pandas dataframe): with 2 columns named anat and values
         the anat column should have names that meet *partial matching* criterion 
         with respect to regions that are measured in antspymm.   value will be 
         the value to be displayed.   if two examples of a given region exist in 
@@ -10186,12 +10425,13 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
     - black_bg (bool): boolean
     - axes (list): integer list typically [0,1,2] sagittal coronal axial
     - fixed_overlay_range (list): scalar pair will try to keep a constant cbar and will truncate the overlay at these min/max values
-    - crop (bool): crops the image to display by the extent of the overlay
+    - crop (int): crops the image to display by the extent of the overlay; larger values dilate the masks more.
     - verbose (bool): boolean
 
     Returns:
     an image with values mapped to the associated regions
     """
+    import re
 
     # Read the statistical file
     zz = statistical_df 
@@ -10200,19 +10440,21 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
     mydict = pd.read_csv(data_dictionary_path)
     mydict = mydict[~mydict['Measurement'].str.contains("tractography-based connectivity", na=False)]
 
+    statistical_df['anat'] = statistical_df['anat'].str.replace("_", ".", regex=True)
+
     # Load image and process it
     edgeimg = ants.iMath(brain_image,"Normalize")
     if edge_image_dilation > 0:
         edgeimg = ants.iMath( edgeimg, "MD", edge_image_dilation)
 
     # Define lists and data frames
-    postfix = ['bf', 'deep_cit168lab', 'mtl', 'cerebellum', 'dkt_cortex','brainstem']
-    atlas = ['BF', 'CIT168', 'MTL', 'TustisonCobra', 'desikan-killiany-tourville','brainstem']
-    postdesc = ['nbm3CH13', 'CIT168_Reinf_Learn_v1_label_descriptions_pad', 'mtl_description', 'cerebellum', 'dkt','CIT168_T1w_700um_pad_adni_brainstem']
+    postfix = ['bf', 'cit168lab', 'mtl', 'cerebellum', 'dkt_cortex','brainstem','JHU_wm','yeo']
+    atlas = ['BF', 'CIT168', 'MTL', 'TustisonCobra', 'desikan-killiany-tourville','brainstem','JHU_wm','yeo']
+    postdesc = ['nbm3CH13', 'CIT168_Reinf_Learn_v1_label_descriptions_pad', 'mtl_description', 'cerebellum', 'dkt','CIT168_T1w_700um_pad_adni_brainstem','FA_JHU_labels_edited','ppmi_template_500Parcels_Yeo2011_17Networks_2023_homotopic']
     statdf = pd.DataFrame({'img': postfix, 'atlas': atlas, 'csvdescript': postdesc})
     templateprefix = '~/.antspymm/PPMI_template0_'
     # Iterate through columns and create figures
-    col2viz = 'value'
+    col2viz = 'values'
     if True:
         anattoshow = zz['anat'].unique()
         if verbose:
@@ -10224,21 +10466,74 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             if verbose:
                 print(str(k) +  " " + anattoshow[k]  )
             mysub = zz[zz['anat'].str.contains(anattoshow[k])]
+            anatsear=re.sub("dti.fa","",anattoshow[k])
+            anatsear=re.sub("t1.volasym","",anatsear)
+            anatsear=re.sub("t1.thkasym","",anatsear)
+            anatsear=re.sub("t1.areaasym","",anatsear)
+            anatsear=re.sub("t1.vol.","",anatsear)
+            anatsear=re.sub("t1.thk.","",anatsear)
+            anatsear=re.sub("t1.area.","",anatsear)
+            anatsear=re.sub("asymdp.","",anatsear)
+            anatsear=re.sub("asym.","",anatsear)
+            anatsear=re.sub("dti.md.","",anatsear)
+            anatsear=re.sub("dti.fa.","",anatsear)
+            anatsear=re.sub("dti.md","",anatsear)
+            anatsear=re.sub("dti.mean.md.","",anatsear)
+            anatsear=re.sub("dti.mean.fa.","",anatsear)
+            anatsear=re.sub("lravg","",anatsear)
+            atlassearch = mydict['tidynames'].str.contains(anatsear)
+            if atlassearch.sum() > 0:
+                whichatlas = mydict[atlassearch]['Atlas'].iloc[0]
+                oglabelname = mydict[atlassearch]['Label'].iloc[0]
+            else:
+                print(anatsear)
+                oglabelname='unknown'
+                whichatlas=None
+            if verbose:
+                print("oglabelname " + oglabelname )
             vals2viz = mysub[col2viz].agg(['min', 'max'])
             vals2viz = vals2viz[abs(vals2viz).idxmax()]
             myext = None
             if 'dktcortex' in anattoshow[k]:
                 myext = 'dkt_cortex'
             elif 'cit168' in anattoshow[k]:
-                myext = 'deep_cit168lab'
+                myext = 'cit168lab'
             elif 'mtl' in anattoshow[k]:
                 myext = 'mtl'
+                oglabelname=re.sub('mtl', '',anatsear)
             elif 'cerebellum' in anattoshow[k]:
                 myext = 'cerebellum'
+                oglabelname=re.sub('cerebellum', '',anatsear)
+                # oglabelname=oglabelname[2:]
             elif 'brainstem' in anattoshow[k]:
                 myext = 'brainstem'
             elif any(item in anattoshow[k] for item in ['nbm', 'bf']):
                 myext = 'bf'
+                oglabelname=re.sub(r'\.', '_',anatsear)
+            elif whichatlas == 'johns hopkins white matter':
+                myext = 'JHU_wm'
+            elif whichatlas == 'desikan-killiany-tourville':
+                myext = 'dkt_cortex'
+            elif whichatlas == 'CIT168':
+                myext = 'cit168lab'
+            elif whichatlas == 'BF':
+                myext = 'bf'
+                oglabelname=re.sub('bf', '',oglabelname)
+            elif whichatlas == 'yeo_homotopic':
+                myext = 'yeo'
+            if myext is None and verbose:
+                if whichatlas is None:
+                    whichatlas='None'
+                if anattoshow[k] is None:
+                    anattoshow[k]='None'
+                print( "MYEXT " + anattoshow[k] + ' unfound ' + whichatlas )
+            else:
+                if verbose:
+                    print( "MYEXT " + myext )
+
+            if myext == 'cit168lab':
+                oglabelname=re.sub("cit168","",oglabelname)
+            
             for j in postfix:
                 if j == "dkt_cortex":
                     j = 'dktcortex'
@@ -10252,30 +10547,86 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             locfilename =  templateprefix + myext + '.nii.gz'
             if verbose:
                 print( locfilename )
-            myatlas = ants.image_read(locfilename)
-            atlasDescript = pd.read_csv(f"~/.antspyt1w/{correctdescript}.csv")
-            atlasDescript['Description'] = atlasDescript['Description'].str.lower()
-            atlasDescript['Description'] = atlasDescript['Description'].str.replace(" ", "_")
-            atlasDescript['Description'] = atlasDescript['Description'].str.replace("_left_", "_")
-            atlasDescript['Description'] = atlasDescript['Description'].str.replace("_right_", "_")
-            atlasDescript['Description'] = atlasDescript['Description'].str.replace("_left", "")
-            atlasDescript['Description'] = atlasDescript['Description'].str.replace("_right", "")
+            if myext == 'yeo':
+                oglabelname=oglabelname.lower()
+                oglabelname=re.sub("rsfmri_fcnxpro122_","",oglabelname)
+                oglabelname=re.sub("rsfmri_fcnxpro129_","",oglabelname)
+                oglabelname=re.sub("rsfmri_fcnxpro134_","",oglabelname)
+                locfilename = "~/.antspymm/ppmi_template_500Parcels_Yeo2011_17Networks_2023_homotopic.nii.gz"
+                atlasDescript = pd.read_csv(f"~/.antspymm/{correctdescript}.csv")
+                atlasDescript.rename(columns={'SystemName': 'Description'}, inplace=True)
+                atlasDescript.rename(columns={'ROI': 'Label'}, inplace=True)
+                atlasDescript['Description'] = atlasDescript['Description'].str.lower()
+            else:
+                atlasDescript = pd.read_csv(f"~/.antspyt1w/{correctdescript}.csv")
+                atlasDescript['Description'] = atlasDescript['Description'].str.lower()
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace(" ", "_")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("_left_", "_")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("_right_", "_")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("_left", "")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("_right", "")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("left_", "")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("right_", "")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("/",".")
+                if myext == 'JHU_wm':
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("fa-", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("-left-", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("-right-", "")
+                if myext == 'cerebellum':
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("l_", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("r_", "")
+
+            if verbose:
+                print( atlasDescript )
+            oglabelname = oglabelname.lower()
+            oglabelname = re.sub(" ", "_",oglabelname)
+            oglabelname = re.sub("_left_", "_",oglabelname)
+            oglabelname = re.sub("_right_", "_",oglabelname)
+            oglabelname = re.sub("_left", "",oglabelname)
+            oglabelname = re.sub("_right", "",oglabelname)
+            oglabelname = re.sub("t1hier_vol_", "",oglabelname)
+            oglabelname = re.sub("t1hier_area_", "",oglabelname)
+            oglabelname = re.sub("t1hier_thk_", "",oglabelname)
+            oglabelname = re.sub("dktregions", "",oglabelname)
+            oglabelname = re.sub("dktcortex", "",oglabelname)
+            if myext == 'JHU_wm':
+                oglabelname = re.sub("dti_mean_fa.", "",oglabelname)
+                oglabelname = re.sub("dti_mean_md.", "",oglabelname)
+                oglabelname = re.sub(".left.", "",oglabelname)
+                oglabelname = re.sub(".right.", "",oglabelname)
+                oglabelname = re.sub(".lravg.", "",oglabelname)
+                oglabelname = re.sub(".asym.", "",oglabelname)
+
+            if verbose:
+                print("oglabelname " + oglabelname )
+
             if myext == 'cerebellum':
                 atlasDescript['Description'] = atlasDescript['Description'].str.replace("l_", "")
                 atlasDescript['Description'] = atlasDescript['Description'].str.replace("r_", "")
-                whichindex = atlasDescript.index[atlasDescript['Description'] == anattoshow[k]].values[0]
+                whichindex = atlasDescript.index[atlasDescript['Description'] == oglabelname].values[0]
             else:
-                whichindex = atlasDescript.index[atlasDescript['Description'].str.contains(anattoshow[k])]
+                whichindex = atlasDescript.index[atlasDescript['Description'].str.contains(oglabelname)]
 
             if type(whichindex) is np.int64:
                 labelnums = atlasDescript.loc[whichindex, 'Label']
             else:
                 labelnums = list(atlasDescript.loc[whichindex, 'Label'])
+
+            if myext == 'yeo':
+                parts = re.findall(r'\D+', oglabelname)
+                oglabelname = [part.replace('_', '') for part in parts if part.replace('_', '')]
+                filtered_df = atlasDescript[atlasDescript['Description'].isin(oglabelname)]
+                labelnums = filtered_df['Label'].tolist()
+
             if not isinstance(labelnums, list):
                 labelnums=[labelnums]
             addemiszero = ants.threshold_image(addem, 0, 0)
             temp = ants.image_read(locfilename)
             temp = ants.mask_image(temp, temp, level=labelnums, binarize=True)
+            if verbose:
+                print("DEBUG")
+                print(  temp.sum() ) 
+                print( labelnums )
             temp[temp == 1] = (vals2viz)
             temp[addemiszero == 0] = 0
             addem = addem + temp
@@ -10284,8 +10635,8 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             print('Done Adding')
         for axx in axes:
             figfn=output_prefix+f"fig{col2viz}ax{axx}_py.jpg"
-            if crop:
-                cmask = ants.threshold_image( addem,1e-5, 1e9 ).iMath("MD",3) + ants.threshold_image( addem,-1e9, -1e-5 ).iMath("MD",3)
+            if crop > 0:
+                cmask = ants.threshold_image( addem,1e-5, 1e9 ).iMath("MD",crop) + ants.threshold_image( addem,-1e9, -1e-5 ).iMath("MD",crop)
                 addemC = ants.crop_image( addem, cmask )
                 edgeimgC = ants.crop_image( edgeimg, cmask )
             else:
@@ -10305,7 +10656,6 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
         print("DONE brain map figures")
     return addem
 
-
 def filter_df(indf, myprefix):
     """
     Process and filter a pandas DataFrame, removing certain columns, 
@@ -10479,6 +10829,27 @@ def aggregate_antspymm_results(input_csv, subject_col='subjectID', date_col='dat
     df=df.drop(badnames, axis=1)
     return( df )
 
+def find_most_recent_file(file_list):
+    """
+    Finds and returns the most recently modified file from a list of file paths.
+    
+    Parameters:
+    - file_list: A list of strings, where each string is a path to a file.
+    
+    Returns:
+    - The path to the most recently modified file in the list, or None if the list is empty or contains no valid files.
+    """
+    # Filter out items that are not files or do not exist
+    valid_files = [f for f in file_list if os.path.isfile(f)]
+    
+    # Check if the filtered list is not empty
+    if valid_files:
+        # Find the file with the latest modification time
+        most_recent_file = max(valid_files, key=os.path.getmtime)
+        return [most_recent_file]
+    else:
+        return None
+    
 def aggregate_antspymm_results_sdf(
     study_df, 
     project_col='projectID',
@@ -10685,8 +11056,8 @@ def aggregate_antspymm_results_sdf(
                 t1wfn = sorted( glob( modsearch ) )
                 if len( t1wfn ) > 1:
                     nlarge = len(t1wfn)
-                    t1wfn = [ t1wfn[ len(t1wfn)-1 ] ]
-                    warnings.warn("there are " + str( nlarge ) + " number of wide fns with search path " + modsearch + " we take the last of these " + t1wfn[0] )
+                    t1wfn = find_most_recent_file( t1wfn )
+                    warnings.warn("there are " + str( nlarge ) + " number of wide fns with search path " + modsearch + " we take the most recent of these " + t1wfn[0] )
 #                    raise ValueError("there are " + str( len( t1wfn ) ) + " number of wide fns with search path " + modsearch )
                 if len( t1wfn ) == 1:
                     if verbose:
@@ -10802,3 +11173,276 @@ def filter_image_files(image_paths, criteria='largest'):
         raise ValueError("Criteria must be 'smallest', 'largest', or 'brightest'.")
 
     return selected_image_path
+
+
+
+def mm_match_by_qc_scoring(df_a, df_b, match_column, criteria, prefix='matched_', exclude_columns=None):
+    """
+    Match each row in df_a to a row in df_b based on a matching column and criteria for selecting the best match,
+    with options to prefix column names from df_b and exclude certain columns from the final output. Additionally,
+    returns a DataFrame containing rows from df_b that were not matched to any row in df_a.
+
+    Parameters:
+    - df_a: DataFrame A.
+    - df_b: DataFrame B.
+    - match_column: The column name on which rows should match between DataFrame A and B.
+    - criteria: A dictionary where keys are column names and values are 'min' or 'max', indicating whether
+                the column should be minimized or maximized for the best match.
+    - prefix: A string prefix to add to column names from df_b in the final output to avoid duplication.
+    - exclude_columns: A list of column names from df_b to exclude from the final output.
+    
+    Returns:
+    - A tuple of two DataFrames: 
+        1. A new DataFrame combining df_a with matched rows from df_b.
+        2. A DataFrame containing rows from df_b that were not matched to df_a.
+    """
+    from scipy.stats import zscore
+    df_a = df_a.loc[:, ~df_a.columns.str.startswith('Unnamed:')]
+    df_b = df_b.loc[:, ~df_b.columns.str.startswith('Unnamed:')].copy()
+    
+    # Normalize df_b based on criteria
+    for col, crit in criteria.items():
+        if crit == 'max':
+            df_b.loc[df_b.index, f'score_{col}'] = zscore(-df_b[col])
+        elif crit == 'min':
+            df_b.loc[df_b.index, f'score_{col}'] = zscore(df_b[col])
+
+    # Calculate 'best_score' by summing all score columns
+    score_columns = [f'score_{col}' for col in criteria.keys()]
+    df_b['best_score'] = df_b[score_columns].sum(axis=1)
+
+    matched_indices = []  # Track indices of matched rows in df_b
+
+    # Match rows
+    matched_rows = []
+    for _, row_a in df_a.iterrows():
+        matches = df_b[df_b[match_column] == row_a[match_column]]
+        if not matches.empty:
+            best_idx = matches['best_score'].idxmin()
+            best_match = matches.loc[best_idx]
+            matched_indices.append(best_idx)  # Track this index as matched
+            matched_rows.append(best_match)
+        else:
+            matched_rows.append(pd.Series(dtype='float64'))
+
+    # Create a DataFrame from matched rows
+    df_matched = pd.DataFrame(matched_rows).reset_index(drop=True)
+    
+    # Exclude specified columns and add prefix
+    if exclude_columns is not None:
+        df_matched = df_matched.drop(columns=exclude_columns, errors='ignore')
+    df_matched = df_matched.rename(columns=lambda x: f"{prefix}{x}" if x != match_column and x in df_matched.columns else x)
+
+    # Combine df_a with matched rows from df_b
+    result_df = pd.concat([df_a.reset_index(drop=True), df_matched], axis=1)
+    
+    # Extract unmatched rows from df_b
+    unmatched_df_b = df_b.drop(index=matched_indices).reset_index(drop=True)
+
+    return result_df, unmatched_df_b
+
+
+def fix_LR_RL_stuff(df, col1, col2, size_col1, size_col2, id1, id2 ):
+    df_copy = df.copy()
+    # Ensure columns contain strings for substring checks
+    df_copy[col1] = df_copy[col1].astype(str)
+    df_copy[col2] = df_copy[col2].astype(str)
+    df_copy[id1] = df_copy[id1].astype(str)
+    df_copy[id2] = df_copy[id2].astype(str)
+    
+    for index, row in df_copy.iterrows():
+        col1_val = row[col1]
+        col2_val = row[col2]
+        size1 = row[size_col1]
+        size2 = row[size_col2]
+        
+        # Check for 'RL' or 'LR' in each column and compare sizes
+        if ('RL' in col1_val or 'LR' in col1_val) and ('RL' in col2_val or 'LR' in col2_val):
+            continue
+        elif 'RL' not in col1_val and 'LR' not in col1_val and 'RL' not in col2_val and 'LR' not in col2_val:
+            if size1 < size2:
+                df_copy.at[index, col1] = df_copy.at[index, col2]
+                df_copy.at[index, size_col1] = df_copy.at[index, size_col2]
+                df_copy.at[index, id1] = df_copy.at[index, id2]
+                df_copy.at[index, size_col2] = 0
+                df_copy.at[index, col2] = None
+                df_copy.at[index, id2] = None
+            else:
+                df_copy.at[index, col2] = None
+                df_copy.at[index, size_col2] = 0
+                df_copy.at[index, id2] = None
+        elif 'RL' in col1_val or 'LR' in col1_val:
+            if size1 < size2:
+                df_copy.at[index, col1] = df_copy.at[index, col2]
+                df_copy.at[index, id1] = df_copy.at[index, id2]
+                df_copy.at[index, size_col1] = df_copy.at[index, size_col2]
+                df_copy.at[index, size_col2] = 0
+                df_copy.at[index, col2] = None
+                df_copy.at[index, id2] = None
+            else:
+                df_copy.at[index, col2] = None
+                df_copy.at[index, id2] = None
+                df_copy.at[index, size_col2] = 0
+        elif 'RL' in col2_val or 'LR' in col2_val:
+            if size2 < size1:
+                df_copy.at[index, id2] = None
+                df_copy.at[index, col2] = None
+                df_copy.at[index, size_col2] = 0
+            else:
+                df_copy.at[index, col1] = df_copy.at[index, col2]
+                df_copy.at[index, id1] = df_copy.at[index, id2]
+                df_copy.at[index, size_col1] = df_copy.at[index, size_col2]
+                df_copy.at[index, size_col2] = 0
+                df_copy.at[index, col2] = None    
+                df_copy.at[index, id2] = None    
+    return df_copy
+
+
+def renameit(df, old_col_name, new_col_name):
+    """
+    Renames a column in a pandas DataFrame in place. Raises an error if the specified old column name does not exist.
+
+    Parameters:
+    - df: pandas.DataFrame
+        The DataFrame in which the column is to be renamed.
+    - old_col_name: str
+        The current name of the column to be renamed.
+    - new_col_name: str
+        The new name for the column.
+    
+    Raises:
+    - ValueError: If the old column name does not exist in the DataFrame.
+    
+    Returns:
+    None
+    """
+    import warnings
+    # Check if the old column name exists in the DataFrame
+    if old_col_name not in df.columns:
+        warnings.warn(f"The column '{old_col_name}' does not exist in the DataFrame.")
+        return
+    
+    # Proceed with renaming the column if it exists
+    df.rename(columns={old_col_name: new_col_name}, inplace=True)
+
+
+def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, verbose=True ):
+    """
+    Processes a quality control (QC) DataFrame to perform modality-specific matching and filtering based
+    on predefined criteria, optimizing for minimal outliers and noise, and maximal signal-to-noise ratio (SNR),
+    expected value of randomness (EVR), and dimensionality time (dimt).
+
+    This function iteratively matches dataframes derived from the QC dataframe for different imaging modalities,
+    applying a series of filters to select the best matches based on the QC metrics. Matches are made with
+    consideration to minimize outlier loop and noise, while maximizing SNR, EVR, and dimt for each modality.
+
+    Parameters:
+    ----------
+    qc_dataframe : pandas.DataFrame
+        The DataFrame containing QC metrics for different modalities and imaging data.
+    fix_LRRL : bool, optional
+
+    verbose : bool, optional
+        If True, prints the progress and the shape of the DataFrame being processed in each step.
+
+    Process:
+    -------
+    1. Standardizes modalities by merging DTI-related entries.
+    2. Converts specific columns to appropriate data types for processing.
+    3. Performs modality-specific matching and filtering based on the outlier column and criteria for each modality.
+    4. Iteratively processes unmatched data for predefined modalities with specific prefixes to find further matches.
+    
+    Returns:
+    -------
+    pandas.DataFrame
+        The matched and filtered DataFrame after applying all QC scoring and matching operations across specified modalities.
+
+    """
+    qc_dataframe['modality'] = qc_dataframe['modality'].replace(['DTIdwi', 'DTIb0'], 'DTI', regex=True)
+    qc_dataframe['filename']=qc_dataframe['filename'].astype(str)
+    qc_dataframe['ol_loop']=qc_dataframe['ol_loop'].astype(float)
+    qc_dataframe['ol_lof']=qc_dataframe['ol_lof'].astype(float)
+    qc_dataframe['ol_lof_decision']=qc_dataframe['ol_lof_decision'].astype(float)
+    outlier_column='ol_loop'
+    mmdf0 = best_mmm( qc_dataframe, 'T1w', outlier_column=outlier_column )['filt']
+    fldf = best_mmm( qc_dataframe, 'T2Flair', outlier_column=outlier_column )['filt']
+    nmdf = best_mmm( qc_dataframe, 'NM2DMT', outlier_column=outlier_column )['filt']
+    rsdf = best_mmm( qc_dataframe, 'rsfMRI', outlier_column=outlier_column )['filt']
+    dtdf = best_mmm( qc_dataframe, 'DTI', outlier_column=outlier_column )['filt']
+
+    criteria = {'ol_loop': 'min', 'noise': 'min', 'snr': 'max', 'EVR': 'max', 'reflection_err':'min'}
+    xcl = [ 'mrimfg', 'mrimodel','mriMagneticFieldStrength', 'dti_failed', 'rsf_failed', 'subjectID', 'date', 'subjectIDdate','repeat']
+    # Assuming df_a and df_b are already loaded
+    mmdf, undffl = mm_match_by_qc_scoring(mmdf0, fldf, 'subjectIDdate', criteria, 
+                        prefix='T2Flair_', exclude_columns=xcl )
+
+    prefixes = ['NM1_', 'NM2_', 'NM3_', 'NM4_', 'NM5_', 'NM6_']  
+    undfmod = nmdf  # Initialize 'undfmod' with 'nmdf' for the first iteration
+    if verbose:
+        print('start NM')
+        print( undfmod.shape )
+    for prefix in prefixes:
+        if undfmod.shape[0] > 50:
+            mmdf, undfmod = mm_match_by_qc_scoring(mmdf, undfmod, 'subjectIDdate', criteria, prefix=prefix, exclude_columns=xcl)
+            if verbose:
+                print( prefix )
+                print( undfmod.shape )
+
+    criteria = {'ol_loop': 'min', 'noise': 'min', 'snr': 'max', 'EVR': 'max', 'dimt':'max'}
+    # higher bvalues lead to more noise ...
+    criteria = {'ol_loop': 'min', 'noise': 'min',  'dti_bvalueMax':'min',  'dimt':'max'}
+    prefixes = ['DTI1_', 'DTI2_', 'DTI3_']  # List of prefixes for each matching iteration
+    undfmod = dtdf
+    if verbose:
+        print('start DT')
+        print( undfmod.shape )
+    for prefix in prefixes:
+        if undfmod.shape[0] > 50:
+            mmdf, undfmod = mm_match_by_qc_scoring(mmdf, undfmod, 'subjectIDdate', criteria, prefix=prefix, exclude_columns=xcl)
+            if verbose:
+                print( prefix )
+                print( undfmod.shape )
+
+    prefixes = ['rsf1_', 'rsf2_', 'rsf3_']  # List of prefixes for each matching iteration
+    undfmod = rsdf  # Initialize 'undfmod' with 'nmdf' for the first iteration
+    if verbose:
+        print('start rsf')
+        print( undfmod.shape )
+    for prefix in prefixes:
+        if undfmod.shape[0] > 50:
+            mmdf, undfmod = mm_match_by_qc_scoring(mmdf, undfmod, 'subjectIDdate', criteria, prefix=prefix, exclude_columns=xcl)
+            if verbose:
+                print( prefix )
+                print( undfmod.shape )
+    
+    if fix_LRRL:
+        #        mmdf=fix_LR_RL_stuff( mmdf, 'DTI1_filename', 'DTI2_filename', 'DTI1_dimt', 'DTI2_dimt')
+        mmdf=fix_LR_RL_stuff( mmdf, 'rsf1_filename', 'rsf2_filename', 'rsf1_dimt', 'rsf2_dimt', 'rsf1_imageID', 'rsf2_imageID'  )
+    else:
+        import warnings
+        warnings.warn("FIXME: should fix LR and RL situation for the DTI and rsfMRI")
+
+    # now do the necessary replacements
+    
+    renameit( mmdf, 'perf_imageID', 'perfid' )
+    renameit( mmdf, 'perf_filename', 'perffn' )
+    renameit( mmdf, 'T2Flair_imageID', 'flairid' )
+    renameit( mmdf, 'T2Flair_filename', 'flairfn' )
+    renameit( mmdf, 'rsf1_imageID', 'rsfid1' )
+    renameit( mmdf, 'rsf2_imageID', 'rsfid2' )
+    renameit( mmdf, 'rsf1_filename', 'rsffn1' )
+    renameit( mmdf, 'rsf2_filename', 'rsffn2' )
+    renameit( mmdf, 'DTI1_imageID', 'dtid1' )
+    renameit( mmdf, 'DTI2_imageID', 'dtid2' )
+    renameit( mmdf, 'DTI3_imageID', 'dtid3' )
+    renameit( mmdf, 'DTI1_filename', 'dtfn1' )
+    renameit( mmdf, 'DTI2_filename', 'dtfn2' )
+    renameit( mmdf, 'DTI3_filename', 'dtfn3' )
+    for x in range(1,6):
+        temp0="NM"+str(x)+"_imageID"
+        temp1="nmid"+str(x)
+        renameit( mmdf, temp0, temp1 )
+        temp0="NM"+str(x)+"_filename"
+        temp1="nmfn"+str(x)
+        renameit( mmdf, temp0, temp1 )
+    return mmdf