antspymm 1.3.9__py3-none-any.whl → 1.4.1__py3-none-any.whl

antspymm/mm.py

@@ -285,7 +285,7 @@ def get_antsimage_keys(dictionary):
     :param dictionary: A dictionary to inspect
     :return: A list of keys for which the values are ANTsImages
     """
-    return [key for key, value in dictionary.items() if isinstance(value, ants.ANTsImage)]
+    return [key for key, value in dictionary.items() if isinstance(value, ants.core.ants_image.ANTsImage)]
 
 
 def dict_to_dataframe(data_dict, convert_lists=True, convert_arrays=True, convert_images=True, verbose=False):
@@ -328,7 +328,7 @@ def dict_to_dataframe(data_dict, convert_lists=True, convert_arrays=True, conver
                 print( " Key " + key + " is nparray with mean " + str(meanvalue) + " to " + newkey )
             if newkey not in data_dict.keys():
                 processed_data[newkey] = meanvalue
-        elif isinstance(value, ants.ANTsImage) and convert_images:
+        elif isinstance(value, ants.core.ants_image.ANTsImage ) and convert_images:
             meanvalue = value.mean()
             newkey = key+"_mean"
             if newkey not in data_dict.keys():
@@ -1106,40 +1106,83 @@ def study_dataframe_from_matched_dataframe( matched_dataframe, rootdir, outputdi
     dt=get_first_item_as_string( csvrow, 'date'  )  # str(csvrow['date'].iloc[0])
     iid=get_first_item_as_string( csvrow, 'imageID'  ) # str(csvrow['imageID'].iloc[0])
     nrgt1fn=os.path.join( rootdir, pid, sid, dt, 'T1w', iid, str(csvrow['filename'].iloc[0]+iext) )
+    if not exists( nrgt1fn ) and iid == '0':
+        iid='000'
+        nrgt1fn=os.path.join( rootdir, pid, sid, dt, 'T1w', iid, str(csvrow['filename'].iloc[0]+iext) )
     if not exists( nrgt1fn ):
         raise ValueError("T1 " + nrgt1fn + " does not exist in study_dataframe_from_qc_dataframe")
     flList=[]
     dtList=[]
     rsfList=[]
     nmList=[]
+    perfList=[]
     if 'flairfn' in csvrow.keys():
         flid=get_first_item_as_string( csvrow, 'flairid' )
         nrgt2fn=os.path.join( rootdir, pid, sid, dt, 'T2Flair', flid, str(csvrow['flairfn'].iloc[0]+iext) )
+        if not exists( nrgt2fn ) and flid == '0':
+            flid='000'
+            nrgt2fn=os.path.join( rootdir, pid, sid, dt, 'T2Flair', flid, str(csvrow['flairfn'].iloc[0]+iext) )
+        if verbose:
+            print("Trying " + nrgt2fn )
         if exists( nrgt2fn ):
+            if verbose:
+                print("success" )
             flList.append( nrgt2fn )
+    if 'perffn' in csvrow.keys():
+        flid=get_first_item_as_string( csvrow, 'perfid' )
+        nrgt2fn=os.path.join( rootdir, pid, sid, dt, 'perf', flid, str(csvrow['perffn'].iloc[0]+iext) )
+        if not exists( nrgt2fn ) and flid == '0':
+            flid='000'
+            nrgt2fn=os.path.join( rootdir, pid, sid, dt, 'perf', flid, str(csvrow['perffn'].iloc[0]+iext) )
+        if verbose:
+            print("Trying " + nrgt2fn )
+        if exists( nrgt2fn ):
+            if verbose:
+                print("success" )
+            perfList.append( nrgt2fn )
     if 'dtfn1' in csvrow.keys():
         dtid=get_first_item_as_string( csvrow, 'dtid1' )
-        dtfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn1'].iloc[0]+iext) ))[0]
+        dtfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn1'].iloc[0]+iext) ))
+        if len( dtfn1) == 0 :
+            dtid = '000'
+            dtfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn1'].iloc[0]+iext) ))
+        dtfn1=dtfn1[0]
         if exists( dtfn1 ):
             dtList.append( dtfn1 )
     if 'dtfn2' in csvrow.keys():
         dtid=get_first_item_as_string( csvrow, 'dtid2' )
-        dtfn2=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn2'].iloc[0]+iext) ))[0]
+        dtfn2=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn2'].iloc[0]+iext) ))
+        if len( dtfn2) == 0 :
+            dtid = '000'
+            dtfn2=glob.glob(os.path.join( rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn2'].iloc[0]+iext) ))
+        dtfn2=dtfn2[0]
         if exists( dtfn2 ):
             dtList.append( dtfn2 )
     if 'dtfn3' in csvrow.keys():
         dtid=get_first_item_as_string( csvrow, 'dtid3' )
-        dtfn3=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn3'].iloc[0]+iext) ))[0]
+        dtfn3=glob.glob(os.path.join(rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn3'].iloc[0]+iext) ))
+        if len( dtfn3) == 0 :
+            dtid = '000'
+            dtfn3=glob.glob(os.path.join( rootdir, pid, sid, dt, 'DTI*', dtid, str(csvrow['dtfn3'].iloc[0]+iext) ))
+        dtfn3=dtfn3[0]
         if exists( dtfn3 ):
             dtList.append( dtfn3 )
     if 'rsffn1' in csvrow.keys():
         rsid=get_first_item_as_string( csvrow, 'rsfid1' )
-        rsfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn1'].iloc[0]+iext) ))[0]
+        rsfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn1'].iloc[0]+iext) ))
+        if len( rsfn1 ) == 0 :
+            rsid = '000'
+            rsfn1=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn1'].iloc[0]+iext) ))
+        rsfn1=rsfn1[0]
         if exists( rsfn1 ):
             rsfList.append( rsfn1 )
     if 'rsffn2' in csvrow.keys():
         rsid=get_first_item_as_string( csvrow, 'rsfid2' )
         rsfn2=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn2'].iloc[0]+iext) ))[0]
+        if len( rsfn2 ) == 0 :
+            rsid = '000'
+            rsfn2=glob.glob(os.path.join( rootdir, pid, sid, dt, 'rsfMRI*', rsid, str(csvrow['rsffn2'].iloc[0]+iext) ))
+        rsfn2=rsfn2[0]
         if exists( rsfn2 ):
             rsfList.append( rsfn2 )
     for j in range(11):
@@ -1163,6 +1206,8 @@ def study_dataframe_from_matched_dataframe( matched_dataframe, rootdir, outputdi
         print(dtList)
         print("rsfMRI")
         print(rsfList)
+        print("perf")
+        print(perfList)
     studycsv = generate_mm_dataframe(
         pid,
         sid,
@@ -1175,7 +1220,8 @@ def study_dataframe_from_matched_dataframe( matched_dataframe, rootdir, outputdi
         flair_filename=flList,
         dti_filenames=dtList,
         rsf_filenames=rsfList,
-        nm_filenames=nmList)
+        nm_filenames=nmList,
+        perf_filename=perfList)
     return studycsv.dropna(axis=1)
 
 def highest_quality_repeat(mxdfin, idvar, visitvar, qualityvar):
@@ -1233,13 +1279,14 @@ def highest_quality_repeat(mxdfin, idvar, visitvar, qualityvar):
     return mxdfin[useit]
 
 
-def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column='ol_loop',  verbose=False ):
+def match_modalities( qc_dataframe, unique_identifier='filename', outlier_column='ol_loop', mysep='-', verbose=False ):
     """
     Find the best multiple modality dataset at each time point
 
     :param qc_dataframe: quality control data frame with
     :param unique_identifier : the unique NRG filename for each image
     :param outlier_column: outlierness score used to identify the best image (pair) at a given date
+    :param mysep (str, optional): the separator used in the image file names. Defaults to '-'.
     :param verbose: boolean
     :return: filtered matched modality data frame
     """
@@ -1507,8 +1554,8 @@ def mm_read_to_3d( x, slice=None, modality='' ):
     read an image from a filename - and return as 3d or None if that is not possible
     """
     img = ants.image_read( x, reorient=False )
-    if img.dimension < 3:
-        return None
+    if img.dimension <= 3:
+        return img
     elif img.dimension == 4:
         nslices = img.shape[3]
         if slice is None:
@@ -1518,7 +1565,7 @@ def mm_read_to_3d( x, slice=None, modality='' ):
         if sl > nslices:
             sl = nslices-1
         return ants.slice_image( img, axis=3, idx=int(sl) )
-    elif img.dimension == 3:
+    elif img.dimension > 4:
         return img
     return None
 
@@ -2242,11 +2289,14 @@ def dti_reg(
         print("remove_it " + str( remove_it ) )
 
     if b0_idx is None:
-        b0_idx = segment_timeseries_by_meanvalue( image )['highermeans']
+        # b0_idx = segment_timeseries_by_meanvalue( image )['highermeans']
+        b0_idx = segment_timeseries_by_bvalue( bvals )['lowbvals']
+
     # first get a local deformation from slice to local avg space
     # then get a global deformation from avg to ref space
     ab0, adw = get_average_dwi_b0( image )
-    mask = ants.get_mask(adw)
+    # mask is used to roughly locate middle of brain
+    mask = ants.threshold_image( ants.iMath(adw,'Normalize'), 0.1, 1.0 )
     motion_parameters = list()
     motion_corrected = list()
     centerOfMass = mask.get_center_of_mass()
@@ -2657,7 +2707,7 @@ 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=23, target_extension='.csv' ):
+def get_data( name=None, force_download=False, version=24, target_extension='.csv' ):
     """
     Get ANTsPyMM data filename
 
@@ -2953,21 +3003,33 @@ def segment_timeseries_by_bvalue(bvals):
     - bvals (numpy.ndarray): An array of b-values.
 
     Returns:
-    - dict: A dictionary with two keys, 'lowermeans' and 'highermeans', each containing
+    - dict: A dictionary with two keys, 'largerbvals' and 'lowbvals', each containing
       the indices of bvals where the b-values are above and at/below the threshold, respectively.
     """
     # Define the threshold
     threshold = 1e-12
-    
+    def find_min_value(data):
+        if isinstance(data, list):
+            return min(data)
+        elif isinstance(data, np.ndarray):
+            return np.min(data)
+        else:
+            raise TypeError("Input must be either a list or a numpy array")
+
     # 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])
     
+    if len(highermeans) == 0:
+        minval = find_min_value( bvals )
+        lowermeans = list(np.where(bvals > minval )[0])
+        highermeans = list(np.where(bvals <= minval)[0])
+
     return {
-        'lowermeans': lowermeans,
-        'highermeans': highermeans
+        'largerbvals': lowermeans,
+        'lowbvals': highermeans
     }
 
 def segment_timeseries_by_meanvalue( image, quantile = 0.995 ):
@@ -3404,6 +3466,7 @@ def dipy_dti_recon(
     mask_closing = 5,
     fit_method='WLS',
     trim_the_mask=2.0,
+    free_water=False,
     verbose=False ):
     """
     DiPy DTI reconstruction - building on the DiPy basic DTI example
@@ -3430,6 +3493,8 @@ def dipy_dti_recon(
 
     trim_the_mask : float >=0 post-hoc method for trimming the mask
 
+    free_water : boolean
+
     verbose : boolean
 
     Returns
@@ -3445,6 +3510,9 @@ def dipy_dti_recon(
     -------
     >>> import antspymm
     """
+
+    import dipy.reconst.fwdti as fwdti
+
     if isinstance(bvecsfn, str):
         bvals, bvecs = read_bvals_bvecs( bvalsfn , bvecsfn   )
     else: # assume we already read them
@@ -3454,16 +3522,22 @@ def dipy_dti_recon(
     if bvals.max() < 1.0:
         raise ValueError("DTI recon error: maximum bvalues are too small.")
 
-    b0_idx = segment_timeseries_by_bvalue( bvals )['highermeans']
+    b0_idx = segment_timeseries_by_bvalue( bvals )['lowbvals']
 
     b0 = ants.slice_image( image, axis=3, idx=b0_idx[0] )
     bxtmod='bold'
     bxtmod='t2'
     constant_mask=False
+    if verbose:
+        print( np.unique( bvals ), flush=True )
     if mask is not None:
+        if verbose:
+            print("use set bxt in dipy_dti_recon", flush=True)
         constant_mask=True
         mask = ants.resample_image_to_target( mask, b0, interp_type='nearestNeighbor')
     else:
+        if verbose:
+            print("use deep learning bxt in dipy_dti_recon")
         mask = antspynet.brain_extraction( b0, bxtmod ).threshold_image(0.5,1).iMath("GetLargestComponent").morphology("close",2).iMath("FillHoles")
     if mask_closing > 0 and not constant_mask :
         mask = ants.morphology( mask, "close", mask_closing ) # good
@@ -3472,7 +3546,7 @@ def dipy_dti_recon(
     if verbose:
         print("recon dti.TensorModel",flush=True)
 
-    def justthefit( gtab, fit_method, imagein, maskin ):
+    def justthefit( gtab, fit_method, imagein, maskin, free_water=False ):
         if fit_method is None:
             return None, None, None, None
         maskedimage=[]
@@ -3481,7 +3555,10 @@ def dipy_dti_recon(
             maskedimage.append( b0 * maskin )
         maskedimage = ants.list_to_ndimage( imagein, maskedimage )
         maskdata = maskedimage.numpy()
-        tenmodel = dti.TensorModel(gtab,fit_method=fit_method)
+        if free_water:
+            tenmodel = fwdti.FreeWaterTensorModel(gtab)
+        else:
+            tenmodel = dti.TensorModel(gtab,fit_method=fit_method)
         tenfit = tenmodel.fit(maskdata)
         FA = fractional_anisotropy(tenfit.evals)
         FA[np.isnan(FA)] = 1
@@ -3500,14 +3577,16 @@ def dipy_dti_recon(
 
     bvecs = repair_bvecs( bvecs )
     gtab = gradient_table(bvals, bvecs, atol=2.0 )
-    tenfit, FA, MD1, RGB = justthefit( gtab, fit_method, image, maskdil )
+    if free_water:
+        free_water=len( np.unique( bvals ) ) >= 3
+    tenfit, FA, MD1, RGB = justthefit( gtab, fit_method, image, maskdil, free_water=free_water )
     if verbose:
         print("recon dti.TensorModel done",flush=True)
 
     # change the brain mask based on high FA values
     if trim_the_mask > 0 and fit_method is not None:
         mask = trim_dti_mask( FA, mask, trim_the_mask )
-        tenfit, FA, MD1, RGB = justthefit( gtab, fit_method, image, mask )
+        tenfit, FA, MD1, RGB = justthefit( gtab, fit_method, image, mask, free_water=free_water  )
 
     return {
         'tensormodel' : tenfit,
@@ -3591,6 +3670,7 @@ def joint_dti_recon(
     fit_method='WLS',
     impute = False,
     censor = True,
+    free_water = False,
     verbose = False ):
     """
     1. pass in subject data and 1mm JHU atlas/labels
@@ -3645,6 +3725,8 @@ def joint_dti_recon(
 
     censor : boolean
 
+    free_water : boolean
+
     verbose : boolean
 
     Returns
@@ -3754,11 +3836,12 @@ def joint_dti_recon(
     if verbose:
         print("final recon", flush=True)
         print(img_LRdwp)
+
     recon_LR_dewarp = dipy_dti_recon(
             img_LRdwp, bval_LR, bvec_LR,
             mask = brain_mask,
             fit_method=fit_method,
-            mask_dilation=0, verbose=True )
+            mask_dilation=0, free_water=free_water, verbose=True )
     if verbose:
         print("recon done", flush=True)
 
@@ -3822,6 +3905,7 @@ def joint_dti_recon(
         'reg_RL':reg_RL,
         'dtrecon_LR_dewarp':recon_LR_dewarp,
         'dwi_LR_dewarped':img_LRdwp,
+        'bval_unique_count': len(np.unique(bval_LR)),
         'bval_LR':bval_LR,
         'bvec_LR':bvec_LR,
         'bval_RL':bval_RL,
@@ -5054,10 +5138,10 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   nmabovekthresh_mask3 = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
   snvolabovethresh3 = vol_element * nmabovekthresh_mask3.sum()
 
-  k = 4.0
+  k = 1.0
   rrthresh = (rravg + k * rrstd)
-  nmabovekthresh_mask4 = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
-  snvolabovethresh4 = vol_element * nmabovekthresh_mask4.sum()
+  nmabovekthresh_mask1 = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
+  snvolabovethresh1 = vol_element * nmabovekthresh_mask1.sum()
   
   if verbose:
     print( "nm vol @2std above rrmean: " + str( snvolabovethresh ) )
@@ -5065,7 +5149,7 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
     print( "nm intsum @2std above rrmean: " + str( snintsumabovethresh ) )
     print( "nm done" )
 
-  return{
+  return convert_np_in_dict( {
       'NM_avg' : nm_avg,
       'NM_avg_cropped' : nm_avg_cropped,
       'NM_labels': labels2nm,
@@ -5079,11 +5163,11 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
       'NM_avg_substantianigra' : snavg,
       'NM_std_substantianigra' : snstd,
       'NM_volume_substantianigra' : snvol,
+      'NM_volume_substantianigra_1std' : snvolabovethresh1,
       'NM_volume_substantianigra_2std' : snvolabovethresh,
       'NM_intmean_substantianigra_2std' : snintmeanabovethresh,
       'NM_intsum_substantianigra_2std' : snintsumabovethresh,
       'NM_volume_substantianigra_3std' : snvolabovethresh3,
-      'NM_volume_substantianigra_4std' : snvolabovethresh4,
       'NM_avg_refregion' : rravg,
       'NM_std_refregion' : rrstd,
       'NM_min' : nm_avg_cropped.min(),
@@ -5097,7 +5181,7 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
       'NM_substantianigra_z_coordinate' : sn_z,
       'NM_evr' : nm_evr,
       'NM_count': len( list_nm_images )
-       }
+       } )
 
 
 
@@ -9328,7 +9412,9 @@ def quick_viz_mm_nrg(
     dtid, # date
     extract_brain=True,
     slice_factor = 0.55,
-    show_it = None, # output path
+    post = False,
+    original_sourcedir = None,
+    filename = None, # output path
     verbose = True
 ):
     """
@@ -9336,7 +9422,7 @@ def quick_viz_mm_nrg(
 
     Args:
 
-    sourcedir (str): Root folder.
+    sourcedir (str): Root folder for original data (if post=False) or processed data (post=True)
     
     projectid (str): Project name.
     
@@ -9347,73 +9433,114 @@ def quick_viz_mm_nrg(
     extract_brain (bool): If True, the function extracts the brain from the T1w image. Default is True.
     
     slice_factor (float): The slice to be visualized is determined by multiplying the image size by this factor. Default is 0.55.
+
+    post ( bool ) : if True, will visualize example post-processing results.
     
-    show_it (str): Output path. If not None, the visualizations will be saved at this location. Default is None.
+    original_sourcedir (str): Root folder for original data (used if post=True)
+    
+    filename (str): Output path with extension (.png)
     
     verbose (bool): If True, information will be printed while running the function. Default is True.
 
     Returns:
-    vizlist (list): List of image visualizations.
+    None
 
     """
     iid='*'
     import glob as glob
     from os.path import exists
     import ants
-    ex_path = os.path.expanduser( "~/.antspyt1w/" )
-    ex_pathmm = os.path.expanduser( "~/.antspymm/" )
-    templatefn = ex_path + 'CIT168_T1w_700um_pad_adni.nii.gz'
-    if not exists( templatefn ):
-        print( "**missing files** => call get_data from latest antspyt1w and antspymm." )
-        antspyt1w.get_data( force_download=True )
-        get_data( force_download=True )
     temp = sourcedir.split( "/" )
-    splitCount = len( temp )
-    template = mm_read( templatefn ) # Read in template
     subjectrootpath = os.path.join(sourcedir, projectid, sid, dtid)
-    myimgsInput = glob.glob( subjectrootpath+"/*" )
-    myimgsInput.sort( )
     if verbose:
-        print( myimgsInput )
+        print( 'subjectrootpath' )
+        print( subjectrootpath )
     t1_search_path = os.path.join(subjectrootpath, "T1w", "*", "*nii.gz")
     if verbose:
         print(f"t1 search path: {t1_search_path}")
     t1fn = glob.glob(t1_search_path)
-    t1fn.sort()
     if len( t1fn ) < 1:
         raise ValueError('quick_viz_mm_nrg cannot find the T1w @ ' + subjectrootpath )
-    t1fn = t1fn[0]
-    t1 = mm_read( t1fn )
-    nimages = len(myimgsInput)
     vizlist=[]
-    if verbose:
-        print(  " we have : " + str(nimages) + " modalities.  will visualize T1 NM rsfMRI DTIB0 DTIDWI FLAIR")
-    # nrg_modality_list = ["T1w", "NM2DMT", "rsfMRI","rsfMRI_LR","rsfMRI_RL","DTI","DTI_LR", "T2Flair" ],
-    nrg_modality_list = [ 'T1w', 'NM2DMT', 'rsfMRI', 'DWI1', 'DWI2', 'T2Flair' ]
+    undlist=[]
+    nrg_modality_list = [ 'T1w', 'DTI', 'rsfMRI', 'perf', 'T2Flair', 'NM2DMT' ]
+    if post:
+        nrg_modality_list = [ 'T1wHierarchical', 'DTI', 'rsfMRI', 'perf', 'T2Flair', 'NM2DMT' ]
     for nrgNum in [0,1,2,3,4,5]:
+        underlay = None
         overmodX = nrg_modality_list[nrgNum]
-        if overmodX == 'T1w':
+        if  'T1w' in overmodX :
             mod_search_path = os.path.join(subjectrootpath, overmodX, iid, "*nii.gz")
+            if post:
+                mod_search_path = os.path.join(subjectrootpath, overmodX, iid, "*brain_n4_dnz.nii.gz")
+                mod_search_path_ol = os.path.join(subjectrootpath, overmodX, iid, "*thickness_image.nii.gz" )
+                mod_search_path_ol = re.sub( "T1wHierarchical","T1w",mod_search_path_ol)
+                myol = glob.glob(mod_search_path_ol)
+                if len( myol ) > 0:
+                    temper = find_most_recent_file( myol )[0]
+                    underlay = ants.image_read(  temper )
+                    if verbose:
+                        print("T1w overlay " + temper )
+                    underlay = underlay * ants.threshold_image( underlay, 0.2, math.inf )
             myimgsr = glob.glob(mod_search_path)
             if len( myimgsr ) == 0:
                 if verbose:
                     print("No t1 images: " + sid + dtid )
                 return None
-            myimgsr.sort()
-            myimgsr=myimgsr[0]
+            myimgsr=find_most_recent_file( myimgsr )[0]
             vimg=ants.image_read( myimgsr )
-        elif overmodX == 'DWI1':
+        elif  'T2Flair' in overmodX :
+            if verbose:
+                print("search flair")
+            mod_search_path = os.path.join(subjectrootpath, overmodX, iid, "*nii.gz")
+            if post and original_sourcedir is not None:
+                if verbose:
+                    print("post in flair")
+                mysubdir = os.path.join(original_sourcedir, projectid, sid, dtid)
+                mod_search_path_under = os.path.join(mysubdir, overmodX, iid, "*T2Flair*.nii.gz")
+                if verbose:
+                    print("post in flair mod_search_path_under " + mod_search_path_under)
+                mod_search_path = os.path.join(subjectrootpath, overmodX, iid, "*wmh.nii.gz")
+                if verbose:
+                    print("post in flair mod_search_path " + mod_search_path )
+                myimgul = glob.glob(mod_search_path_under)
+                if len( myimgul ) > 0:
+                    myimgul = find_most_recent_file( myimgul )[0]
+                    if verbose:
+                        print("Flair  " + myimgul )
+                    vimg = ants.image_read( myimgul )
+                    myol = glob.glob(mod_search_path)
+                    if len( myol ) == 0:
+                        underlay = myimgsr * 0.0
+                    else:
+                        myol = find_most_recent_file( myol )[0]
+                        if verbose:
+                            print("Flair overlay " + myol )
+                        underlay=ants.image_read( myol )
+                        underlay=underlay*ants.threshold_image(underlay,0.05,math.inf)
+                else:
+                    vimg = noizimg.clone()
+                    underlay = vimg * 0.0
+            if original_sourcedir is None:
+                myimgsr = glob.glob(mod_search_path)
+                if len( myimgsr ) == 0:
+                    vimg = noizimg.clone()
+                else:
+                    myimgsr=find_most_recent_file( myimgsr )[0]
+                    vimg=ants.image_read( myimgsr )
+        elif overmodX == 'DTI':
             mod_search_path = os.path.join(subjectrootpath, 'DTI*', "*", "*nii.gz")
+            if post:
+                mod_search_path = os.path.join(subjectrootpath, 'DTI*', "*", "*fa.nii.gz")
             myimgsr = glob.glob(mod_search_path)
             if len( myimgsr ) > 0:
-                myimgsr.sort()
-                myimgsr=myimgsr[0]
+                myimgsr=find_most_recent_file( myimgsr )[0]
                 vimg=ants.image_read( myimgsr )
             else:
                 if verbose:
                     print("No " + overmodX)
-                vimg = noizimg
-        elif overmodX == 'DWI2':
+                vimg = noizimg.clone()
+        elif overmodX == 'DTI2':
             mod_search_path = os.path.join(subjectrootpath, 'DTI*', "*", "*nii.gz")
             myimgsr = glob.glob(mod_search_path)
             if len( myimgsr ) > 0:
@@ -9423,12 +9550,13 @@ def quick_viz_mm_nrg(
             else:
                 if verbose:
                     print("No " + overmodX)
-                vimg = noizimg
+                vimg = noizimg.clone()
         elif overmodX == 'NM2DMT':
             mod_search_path = os.path.join(subjectrootpath, overmodX, "*", "*nii.gz")
+            if post:
+                mod_search_path = os.path.join(subjectrootpath, overmodX, "*", "*NM_avg.nii.gz" )
             myimgsr = glob.glob(mod_search_path)
             if len( myimgsr ) > 0:
-                myimgsr.sort()
                 myimgsr0=myimgsr[0]
                 vimg=ants.image_read( myimgsr0 )
                 for k in range(1,len(myimgsr)):
@@ -9437,55 +9565,109 @@ def quick_viz_mm_nrg(
             else:
                 if verbose:
                     print("No " + overmodX)
-                vimg = noizimg
+                vimg = noizimg.clone()
         elif overmodX == 'rsfMRI':
             mod_search_path = os.path.join(subjectrootpath, 'rsfMRI*', "*", "*nii.gz")
+            if post:
+                mod_search_path = os.path.join(subjectrootpath, 'rsfMRI*', "*", "*fcnxpro122_meanBold.nii.gz" )
+                mod_search_path_ol = os.path.join(subjectrootpath, 'rsfMRI*', "*", "*fcnxpro122_DefaultMode.nii.gz" )
+                myol = glob.glob(mod_search_path_ol)
+                if len( myol ) > 0:
+                    myol = find_most_recent_file( myol )[0]
+                    underlay = ants.image_read( myol )
+                    if verbose:
+                        print("BOLD overlay " + myol )
+                    underlay = underlay * ants.threshold_image( underlay, 0.1, math.inf )
             myimgsr = glob.glob(mod_search_path)
             if len( myimgsr ) > 0:
-                myimgsr.sort()
-                myimgsr=myimgsr[0]
+                myimgsr=find_most_recent_file( myimgsr )[0]
                 vimg=mm_read_to_3d( myimgsr )
             else:
                 if verbose:
                     print("No " + overmodX)
-                vimg = noizimg
+                vimg = noizimg.clone()
+        elif overmodX == 'perf':
+            mod_search_path = os.path.join(subjectrootpath, 'perf*', "*", "*nii.gz")
+            if post:
+                mod_search_path = os.path.join(subjectrootpath, 'perf*', "*", "*cbf.nii.gz")
+            myimgsr = glob.glob(mod_search_path)
+            if len( myimgsr ) > 0:
+                myimgsr=find_most_recent_file( myimgsr )[0]
+                vimg=mm_read_to_3d( myimgsr )
+            else:
+                if verbose:
+                    print("No " + overmodX)
+                vimg = noizimg.clone()
         else :
+            if verbose:
+                print("Something else here")
             mod_search_path = os.path.join(subjectrootpath, overmodX, "*", "*nii.gz")
             myimgsr = glob.glob(mod_search_path)
+            if post:
+                myimgsr=[]
             if len( myimgsr ) > 0:
-                myimgsr.sort()
-                myimgsr=myimgsr[0]
+                myimgsr=find_most_recent_file( myimgsr )[0]
                 vimg=ants.image_read( myimgsr )
             else:
                 if verbose:
                     print("No " + overmodX)
                 vimg = noizimg
         if True:
-            if extract_brain and overmodX == 'T1w':
+            if extract_brain and overmodX == 'T1w' and post == False:
                 vimg = vimg * antspyt1w.brain_extraction(vimg)
             if verbose:
                 print(f"modality search path: {myimgsr}" + " num: " + str(nrgNum))
-            if len( vimg.shape ) == 4 and ( overmodX == "DWI2"  ):
+            if vimg.dimension == 4 and ( overmodX == "DTI2"  ):
                 ttb0, ttdw=get_average_dwi_b0(vimg)
                 vimg = ttdw
-            elif len( vimg.shape ) == 4 and overmodX == "DWI1":
+            elif vimg.dimension == 4 and overmodX == "DTI":
                 ttb0, ttdw=get_average_dwi_b0(vimg)
                 vimg = ttb0
-            elif len( vimg.shape ) == 4 :
+            elif vimg.dimension == 4 :
                 vimg=ants.get_average_of_timeseries(vimg)
             msk=ants.get_mask(vimg)
-            vimg=ants.crop_image(vimg,msk)
-            if overmodX == 'T1w':
+            if overmodX == 'T2Flair':
+                msk=vimg*0+1
+            if underlay is not None:
+                print( overmodX + " has underlay" )
+            else:
+                underlay = vimg * 0.0
+            if nrgNum == 0:
                 refimg=ants.image_clone( vimg )
                 noizimg = ants.add_noise_to_image( refimg*0, 'additivegaussian', [100,1] )
                 vizlist.append( vimg )
+                undlist.append( underlay )
             else:
-                vimg = ants.resample_image_to_target( vimg, refimg )
                 vimg = ants.iMath( vimg, 'TruncateIntensity',0.01,0.98)
                 vizlist.append( ants.iMath( vimg, 'Normalize' ) * 255 )
+                undlist.append( underlay )
+
+    # mask & crop systematically ...
+    msk = ants.get_mask( refimg )
+    refimg = ants.crop_image( refimg, msk )
+
+    for jj in range(len(vizlist)):
+        vizlist[jj]=ants.resample_image_to_target( vizlist[jj], refimg )
+        undlist[jj]=ants.resample_image_to_target( undlist[jj], refimg )
+        print( 'viz: ' + str( jj ) )
+        print( vizlist[jj] )
+        print( 'und: ' + str( jj ) )
+        print( undlist[jj] )
+
+
+    xyz = [None]*3
+    for i in range(3):
+        if xyz[i] is None:
+            xyz[i] = int(refimg.shape[i] * slice_factor )
+
+    if verbose:
+        print('slice positions')
+        print( xyz )
 
-    listlen = len( vizlist )
-    vizlist = np.asarray( vizlist )
+    ants.plot_ortho_stack( vizlist, overlays=undlist, crop=False, reorient=False, filename=filename, xyz=xyz, orient_labels=False )
+    return
+    # listlen = len( vizlist )
+    # vizlist = np.asarray( vizlist )
     if show_it is not None:
         filenameout=None
         if verbose:
@@ -9497,7 +9679,7 @@ def quick_viz_mm_nrg(
                 filenameout=show_it+'_ax'+str(int(a))+'_sl'+str(n)+'.png'
                 if verbose:
                     print( filenameout )
-            ants.plot_grid(vizlist.reshape(2,3), slices.reshape(2,3), title='MM Subject ' + sid + ' ' + dtid, rfacecolor='white', axes=a, filename=filenameout )
+#            ants.plot_grid(vizlist.reshape(2,3), slices.reshape(2,3), title='MM Subject ' + sid + ' ' + dtid, rfacecolor='white', axes=a, filename=filenameout )
     if verbose:
         print("viz complete.")
     return vizlist
@@ -9608,6 +9790,10 @@ def blind_image_assessment(
         modality='unknown'
         if "rsfMRI" in image_filename:
             modality='rsfMRI'
+        elif "perf" in image_filename:
+            modality='perf'
+        elif "DTI" in image_filename:
+            modality='DTI'
         elif "T1w" in image_filename:
             modality='T1w'
         elif "T2Flair" in image_filename:
@@ -10023,7 +10209,7 @@ def remove_volumes_from_timeseries(time_series, volumes_to_remove):
     :param volumes_to_remove: List of volume indices to remove.
     :return: ANTsImage with specified volumes removed.
     """
-    if not isinstance(time_series, ants.ANTsImage):
+    if not isinstance(time_series, ants.core.ants_image.ANTsImage):
         raise ValueError("time_series must be an ANTsImage.")
 
     if time_series.dimension != 4:
@@ -10033,7 +10219,7 @@ def remove_volumes_from_timeseries(time_series, volumes_to_remove):
     volumes_to_keep = [i for i in range(time_series.shape[3]) if i not in volumes_to_remove]
 
     # Select the volumes to keep
-    filtered_time_series = ants.from_numpy( time_series[..., volumes_to_keep] )
+    filtered_time_series = ants.from_numpy( time_series.numpy()[..., volumes_to_keep] )
 
     return ants.copy_image_info( time_series, filtered_time_series )
 
@@ -10061,7 +10247,7 @@ def impute_timeseries(time_series, volumes_to_impute, method='linear', verbose=F
     :param verbose: boolean
     :return: ANTsImage with specified volumes imputed.
     """
-    if not isinstance(time_series, ants.ANTsImage):
+    if not isinstance(time_series, ants.core.ants_image.ANTsImage):
         raise ValueError("time_series must be an ANTsImage.")
 
     if time_series.dimension != 4:
@@ -10468,7 +10654,136 @@ 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=5, verbose=False ):
+
+
+def shorten_pymm_names(x):
+    """
+    Shortens pmymm names by applying a series of regex substitutions.
+    
+    Parameters:
+    x (str): The input string to be shortened
+    
+    Returns:
+    str: The shortened string
+    """
+    xx = x.lower()
+    xx = re.sub("_", ".", xx)  # Replace underscores with periods
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    # Apply the following regex substitutions in order
+    xx = re.sub("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.","ilf.and.ifo", xx, flags=re.I)
+    xx = re.sub(r"sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.", "ilf.and.ifo", xx, flags=re.I)
+    xx = re.sub(r".cres.stria.terminalis.can.not.be.resolved.with.current.resolution.", "", 
+xx, flags=re.I)
+    xx = re.sub("_", ".", xx)  # Replace underscores with periods
+    xx = re.sub(r"longitudinal.fasciculus", "l.fasc", xx, flags=re.I)
+    xx = re.sub(r"corona.radiata", "cor.rad", xx, flags=re.I)
+    xx = re.sub("central", "cent", xx, flags=re.I)
+    xx = re.sub(r"deep.cit168", "dp.", xx, flags=re.I)
+    xx = re.sub("cit168", "", xx, flags=re.I)
+    xx = re.sub(".include", "", xx, flags=re.I)
+    xx = re.sub("mtg.sn", "", xx, flags=re.I)
+    xx = re.sub("brainstem", ".bst", xx, flags=re.I)
+    xx = re.sub(r"rsfmri.", "rsf.", xx, flags=re.I)
+    xx = re.sub(r"dti.mean.fa.", "dti.fa.", xx, flags=re.I)
+    xx = re.sub("perf.cbf.mean.", "cbf.", xx, flags=re.I)
+    xx = re.sub(".jhu.icbm.labels.1mm", "", xx, flags=re.I)
+    xx = re.sub(".include.optic.radiation.", "", xx, flags=re.I)
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    xx = re.sub("\.\.", ".", xx, flags=re.I)  # Replace double dots with single dot
+    xx = re.sub("cerebellar.peduncle", "cereb.ped", xx, flags=re.I)
+    xx = re.sub(r"anterior.limb.of.internal.capsule", "ant.int.cap", xx, flags=re.I)
+    xx = re.sub(r"posterior.limb.of.internal.capsule", "post.int.cap", xx, flags=re.I)
+    xx = re.sub("t1hier.", "t1.", xx, flags=re.I)
+    xx = re.sub("anterior", "ant", xx, flags=re.I)
+    xx = re.sub("posterior", "post", xx, flags=re.I)
+    xx = re.sub("inferior", "inf", xx, flags=re.I)
+    xx = re.sub("superior", "sup", xx, flags=re.I)
+    xx = re.sub(r"dktcortex", ".ctx", xx, flags=re.I)
+    xx = re.sub(".lravg", "", xx, flags=re.I)
+    xx = re.sub("dti.mean.fa", "dti.fa", xx, flags=re.I)
+    xx = re.sub(r"retrolenticular.part.of.internal", "rent.int.cap", xx, flags=re.I)
+    xx = re.sub(r"iculus.could.be.a.part.of.ant.internal.capsule", "", xx, flags=re.I)  # Twice
+    xx = re.sub(".fronto.occipital.", ".frnt.occ.", xx, flags=re.I)
+    xx = re.sub(r".longitidinal.fasciculus.", ".long.fasc.", xx, flags=re.I)  # Twice
+    xx = re.sub(".external.capsule", ".ext.cap", xx, flags=re.I)
+    xx = re.sub("of.internal.capsule", ".int.cap", xx, flags=re.I)
+    xx = re.sub("fornix.cres.stria.terminalis", "fornix.", xx, flags=re.I)
+    xx = re.sub("capsule", "", xx, flags=re.I)
+    xx = re.sub("and.inf.frnt.occ.fasciculus.", "", xx, flags=re.I)
+    xx = re.sub("crossing.tract.a.part.of.mcp.", "", xx, flags=re.I)
+    return xx[:40]  # Truncate to first 40 characters
+
+
+def shorten_pymm_names2(x, verbose=False ):
+    """
+    Shortens pmymm names by applying a series of regex substitutions.
+
+    Parameters:
+    x (str): The input string to be shortened
+
+    verbose (bool): explain the patterns and replacements and their impact
+
+    Returns:
+    str: The shortened string
+    """
+    # Define substitution patterns as tuples
+    substitutions = [
+        ("_", "."),  
+        ("\.\.", "."),
+        ("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.","ilf.and.ifo"),
+        (r"sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus.", "ilf.and.ifo"),
+        (r".cres.stria.terminalis.can.not.be.resolved.with.current.resolution.", ""),
+        ("_", "."),
+        (r"longitudinal.fasciculus", "l.fasc"),
+        (r"corona.radiata", "cor.rad"),
+        ("central", "cent"),
+        (r"deep.cit168", "dp."),
+        ("cit168", ""),
+        (".include", ""),
+        ("mtg.sn", ""),
+        ("brainstem", ".bst"),
+        (r"rsfmri.", "rsf."),
+        (r"dti.mean.fa.", "dti.fa."),
+        ("perf.cbf.mean.", "cbf."),
+        (".jhu.icbm.labels.1mm", ""),
+        (".include.optic.radiation.", ""),
+        ("\.\.", "."),  # Replace double dots with single dot
+        ("\.\.", "."),  # Replace double dots with single dot
+        ("cerebellar.peduncle", "cereb.ped"),
+        (r"anterior.limb.of.internal.capsule", "ant.int.cap"),
+        (r"posterior.limb.of.internal.capsule", "post.int.cap"),
+        ("t1hier.", "t1."),
+        ("anterior", "ant"),
+        ("posterior", "post"),
+        ("inferior", "inf"),
+        ("superior", "sup"),
+        (r"dktcortex", ".ctx"),
+        (".lravg", ""),
+        ("dti.mean.fa", "dti.fa"),
+        (r"retrolenticular.part.of.internal", "rent.int.cap"),
+        (r"iculus.could.be.a.part.of.ant.internal.capsule", ""),  # Twice
+        (".fronto.occipital.", ".frnt.occ."),
+        (r".longitidinal.fasciculus.", ".long.fasc."),  # Twice
+        (".external.capsule", ".ext.cap"),
+        ("of.internal.capsule", ".int.cap"),
+        ("fornix.cres.stria.terminalis", "fornix."),
+        ("capsule", ""),
+        ("and.inf.frnt.occ.fasciculus.", ""),
+        ("crossing.tract.a.part.of.mcp.", "")
+      ]
+
+    # Apply substitutions in order
+    for pattern, replacement in substitutions:
+        if verbose:
+            print("Pre " + x + " pattern "+pattern + " repl " + replacement )
+        x = re.sub(pattern, replacement, x.lower(), flags=re.IGNORECASE)
+        if verbose:
+            print("Post " + x)
+
+    return x[:40]  # Truncate to first 40 characters
+
+
+def brainmap_figure(statistical_df, data_dictionary, 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=0 ):
     """
     Create figures based on statistical data and an underlying brain image.
 
@@ -10480,7 +10795,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
         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 
         statistical_df, then the largest absolute value will be taken for display.
-    - data_dictionary_path (str): Path to the data dictionary CSV file.
+    - data_dictionary (pandas dataframe): antspymm data dictionary.
     - output_prefix (str): Prefix for the output figure filenames.
     - brain_image (antsImage): the brain image on which results will overlay.
     - overlay_cmap (str): see matplotlib
@@ -10498,12 +10813,18 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
     """
     import re
 
+    def is_bst_region(filename):
+        return filename[-4:] == '.bst'
+
     # Read the statistical file
     zz = statistical_df 
     
     # Read the data dictionary from a CSV file
-    mydict = pd.read_csv(data_dictionary_path)
+    mydict = data_dictionary
     mydict = mydict[~mydict['Measurement'].str.contains("tractography-based connectivity", na=False)]
+    mydict2=mydict.copy()
+    mydict2['tidynames']=mydict2['tidynames'].str.replace(".left","")
+    mydict2['tidynames']=mydict2['tidynames'].str.replace(".right","")
 
     statistical_df['anat'] = statistical_df['anat'].str.replace("_", ".", regex=True)
 
@@ -10516,23 +10837,44 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
     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 = 'values'
     if True:
         anattoshow = zz['anat'].unique()
-        if verbose:
+        if verbose > 0:
             print(col2viz)
             print(anattoshow)
         # Rest of your code for figure creation goes here...
         addem = edgeimg * 0
         for k in range(len(anattoshow)):
-            if verbose:
+            if verbose > 0 :
                 print(str(k) +  " " + anattoshow[k]  )
             mysub = zz[zz['anat'].str.contains(anattoshow[k])]
-            anatsear=re.sub("dti.fa","",anattoshow[k])
+            anatsear=shorten_pymm_names( anattoshow[k] )
+            anatsear=re.sub(r'[()]', '.', anatsear )
+            anatsear=re.sub(r'\.\.', '.', anatsear )
+            anatsear=re.sub("dti.mean.md.snc","md.snc",anatsear)
+            anatsear=re.sub("dti.mean.fa.snc","fa.snc",anatsear)
+            anatsear=re.sub("dti.mean.md.snr","md.snr",anatsear)
+            anatsear=re.sub("dti.mean.fa.snr","fa.snr",anatsear)
+            anatsear=re.sub("dti.mean.md.","",anatsear)
+            anatsear=re.sub("dti.mean.fa.","",anatsear)
+            anatsear=re.sub("dti.md.","",anatsear)
+            anatsear=re.sub("dti.fa.","",anatsear)
+            anatsear=re.sub("dti.md","",anatsear)
+            anatsear=re.sub("dti.fa","",anatsear)
             anatsear=re.sub("cbf.","",anatsear)
+            anatsear=re.sub("rsfmri.fcnxpro122.","",anatsear)
+            anatsear=re.sub("rsfmri.fcnxpro129.","",anatsear)
+            anatsear=re.sub("rsfmri.fcnxpro134.","",anatsear)
+            anatsear=re.sub("t1hier.vollravg","",anatsear)
+            anatsear=re.sub("t1hier.volasym","",anatsear)
+            anatsear=re.sub("t1hier.thkasym","",anatsear)
+            anatsear=re.sub("t1hier.areaasym","",anatsear)
+            anatsear=re.sub("t1hier.vol.","",anatsear)
+            anatsear=re.sub("t1hier.thk.","",anatsear)
+            anatsear=re.sub("t1hier.area.","",anatsear)
             anatsear=re.sub("t1.volasym","",anatsear)
             anatsear=re.sub("t1.thkasym","",anatsear)
             anatsear=re.sub("t1.areaasym","",anatsear)
@@ -10541,30 +10883,68 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             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("asym","",anatsear)
+            anatsear=re.sub("lravg.","",anatsear)
             anatsear=re.sub("lravg","",anatsear)
+            anatsear=re.sub("dktcortex","",anatsear)
+            anatsear=re.sub("dktregions","",anatsear)
+            anatsear=re.sub("_",".",anatsear)
+            anatsear=re.sub("superior","sup",anatsear)
+            anatsear=re.sub("cerebellum","",anatsear)
+            anatsear=re.sub("brainstem","",anatsear)
+            anatsear=re.sub("t.limb.int","t.int",anatsear)
+            anatsear=re.sub("paracentral","paracent",anatsear)
+            anatsear=re.sub("precentral","precent",anatsear)
+            anatsear=re.sub("postcentral","postcent",anatsear)
+            anatsear=re.sub("sup.cerebellar.peduncle","sup.cereb.ped",anatsear)
+            anatsear=re.sub("inferior.cerebellar.peduncle","inf.cereb.ped",anatsear)
+            anatsear=re.sub(".crossing.tract.a.part.of.mcp.","",anatsear)
+            anatsear=re.sub(".column.and.body.of.fornix.","",anatsear)
+            anatsear=re.sub("fronto.occipital.fasciculus.could.be.a.part.of.ant.internal.capsule","frnt.occ",anatsear)
+            anatsear=re.sub("inferior.fronto.occipital.fasciculus.could.be.a.part.of.anterior.internal.capsule","inf.frnt.occ",anatsear)
+            anatsear=re.sub("fornix.cres.stria.terminalis.can.not.be.resolved.with.current.resolution","fornix.column.and.body.of.fornix",anatsear)
+            anatsear=re.sub("external.capsule","ext.cap",anatsear)
+            anatsear=re.sub(".jhu.icbm.labels.1mm","",anatsear)
+            anatsear=re.sub("dp.",".",anatsear)
+            anatsear=re.sub(".mtg.sn.snc.",".snc.",anatsear)
+            anatsear=re.sub(".mtg.sn.snr.",".snr.",anatsear)
+            anatsear=re.sub("mtg.sn.snc.",".snc.",anatsear)
+            anatsear=re.sub("mtg.sn.snr.",".snr.",anatsear)
+            anatsear=re.sub("mtg.sn.snc",".snc.",anatsear)
+            anatsear=re.sub("mtg.sn.snr",".snr.",anatsear)
+            anatsear=re.sub("anterior.","ant.",anatsear)
+            anatsear=re.sub("rsf.","",anatsear)
+            anatsear=re.sub("ant.corona.radiata","ant.cor.rad",anatsear)
+            anatsear=re.sub("sup.corona.radiata","sup.cor.rad",anatsear)
+            anatsear=re.sub("posterior.thalamic.radiation.include.optic.radiation","post.thalamic.radiation",anatsear)
+            anatsear=re.sub("retrolenticular.part.of.internal.capsule","rent.int.cap",anatsear)
+            anatsear=re.sub("post.limb.of.internal.capsule","post.int.cap",anatsear)
+            anatsear=re.sub("ant.limb.of.internal.capsule","ant.int.cap",anatsear)
+            anatsear=re.sub("sagittal.stratum.include.inferior.longitidinal.fasciculus.and.inferior.fronto.occipital.fasciculus","ilf.and.ifo",anatsear)
             atlassearch = mydict['tidynames'].str.contains(anatsear)
-            if verbose:
+            if atlassearch.sum() == 0:
+                atlassearch = mydict2['tidynames'].str.contains(anatsear)
+            if verbose > 0 :
                 print( " anatsear " + anatsear + " atlassearch " )
             if atlassearch.sum() > 0:
                 whichatlas = mydict[atlassearch]['Atlas'].iloc[0]
                 oglabelname = mydict[atlassearch]['Label'].iloc[0]
+                oglabelname=re.sub("_",".",oglabelname)
+                oglabelname=re.sub(r'\.\.','.',oglabelname)
             else:
                 print(anatsear)
                 oglabelname='unknown'
                 whichatlas=None
-            if verbose:
+            if verbose > 0:
                 print("oglabelname " + oglabelname + " whichatlas " + str(whichatlas) )
             vals2viz = mysub[col2viz].agg(['min', 'max'])
             vals2viz = vals2viz[abs(vals2viz).idxmax()]
             myext = None
-            if 'dktcortex' in anattoshow[k] or whichatlas == 'desikan-killiany-tourville' or 'dtkregions' in anattoshow[k]:
+            if anatsear == 'cingulum.hippocampus':
+                myext = 'JHU_wm'
+            elif 'dktcortex' in anattoshow[k] or whichatlas == 'desikan-killiany-tourville' or 'dtkregions' in anattoshow[k]  :
                 myext = 'dkt_cortex'
-            elif 'cit168' in anattoshow[k] or whichatlas == 'CIT168':
+            elif ('cit168' in anattoshow[k] or whichatlas == 'CIT168') and not 'brainstem' in anattoshow[k] and not is_bst_region(anatsear):
                 myext = 'cit168lab'
             elif 'mtl' in anattoshow[k]:
                 myext = 'mtl'
@@ -10573,11 +10953,12 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 myext = 'cerebellum'
                 oglabelname=re.sub('cerebellum', '',anatsear)
                 # oglabelname=oglabelname[2:]
-            elif 'brainstem' in anattoshow[k]:
+            elif 'brainstem' in anattoshow[k] or is_bst_region(anatsear):
                 myext = 'brainstem'
             elif any(item in anattoshow[k] for item in ['nbm', 'bf']):
                 myext = 'bf'
-                oglabelname=re.sub(r'\.', '_',anatsear)
+                oglabelname=re.sub('bf', '',oglabelname)
+#                oglabelname=re.sub(r'\.', '_',anatsear)
             elif whichatlas == 'johns hopkins white matter':
                 myext = 'JHU_wm'
             elif whichatlas == 'desikan-killiany-tourville':
@@ -10589,14 +10970,14 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 oglabelname=re.sub('bf', '',oglabelname)
             elif whichatlas == 'yeo_homotopic':
                 myext = 'yeo'
-            if myext is None and verbose:
+            if myext is None and verbose > 0 :
                 if whichatlas is None:
                     whichatlas='None'
                 if anattoshow[k] is None:
                     anattoshow[k]='None'
                 print( "MYEXT " + anattoshow[k] + ' unfound ' + whichatlas )
             else:
-                if verbose:
+                if verbose > 0 :
                     print( "MYEXT " + myext )
 
             if myext == 'cit168lab':
@@ -10608,18 +10989,21 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 if j == "deep_cit168lab":
                     j = 'deep_cit168'
                 anattoshow[k] = anattoshow[k].replace(j, "")
-            if verbose:
+            if verbose > 0:
                 print( anattoshow[k] + " " + str( vals2viz ) )
-            myatlas = atlas[postfix.index(myext)]
             correctdescript = postdesc[postfix.index(myext)]
             locfilename =  templateprefix + myext + '.nii.gz'
-            if verbose:
+            if verbose > 0:
                 print( locfilename )
             if myext == 'yeo':
                 oglabelname=oglabelname.lower()
                 oglabelname=re.sub("rsfmri_fcnxpro122_","",oglabelname)
                 oglabelname=re.sub("rsfmri_fcnxpro129_","",oglabelname)
                 oglabelname=re.sub("rsfmri_fcnxpro134_","",oglabelname)
+                oglabelname=re.sub("rsfmri.fcnxpro122.","",oglabelname)
+                oglabelname=re.sub("rsfmri.fcnxpro129.","",oglabelname)
+                oglabelname=re.sub("rsfmri.fcnxpro134.","",oglabelname)
+                oglabelname=re.sub("_",".",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)
@@ -10636,15 +11020,25 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                 atlasDescript['Description'] = atlasDescript['Description'].str.replace("left_", "")
                 atlasDescript['Description'] = atlasDescript['Description'].str.replace("right_", "")
                 atlasDescript['Description'] = atlasDescript['Description'].str.replace("/",".")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace("_",".")
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace(r'[()]', '', regex=True)
+                atlasDescript['Description'] = atlasDescript['Description'].str.replace(r'\.\.', '.')
                 if myext == 'JHU_wm':
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("-", ".")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("jhu.icbm.labels.1mm", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("fronto-occipital", "frnt.occ")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("superior", "sup")
                     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_", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("l.", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("r.", "")
+                    atlasDescript['Description'] = atlasDescript['Description'].str.replace("_",".")
 
-            if verbose:
+            if verbose > 0:
                 print( atlasDescript )
             oglabelname = oglabelname.lower()
             oglabelname = re.sub(" ", "_",oglabelname)
@@ -10657,15 +11051,31 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             oglabelname = re.sub("t1hier_thk_", "",oglabelname)
             oglabelname = re.sub("dktregions", "",oglabelname)
             oglabelname = re.sub("dktcortex", "",oglabelname)
+
+            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)
+            oglabelname=re.sub("brainstem","",oglabelname)
             if myext == 'JHU_wm':
                 oglabelname = re.sub("dti_mean_fa.", "",oglabelname)
                 oglabelname = re.sub("dti_mean_md.", "",oglabelname)
+                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)
+                oglabelname = re.sub(".jhu.icbm.labels.1mm", "",oglabelname)
+                oglabelname = re.sub("superior", "sup",oglabelname)
 
-            if verbose:
+            if verbose > 0:
                 print("oglabelname " + oglabelname )
 
             if myext == 'cerebellum':
@@ -10674,7 +11084,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
                     atlasDescript['Description'] = atlasDescript['Description'].str.replace("r_", "")
                     oglabelname=re.sub("ravg","",oglabelname)
                     oglabelname=re.sub("lavg","",oglabelname)
-                    whichindex = atlasDescript.index[atlasDescript['Description'] == oglabelname].values[0]
+                    whichindex = atlasDescript.index[atlasDescript['Description'] == oglabelname].values
                 else:
                     if atlasDescript.empty:
                         print("The DataFrame 'atlasDescript' is empty.")
@@ -10691,6 +11101,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             if myext == 'yeo':
                 parts = re.findall(r'\D+', oglabelname)
                 oglabelname = [part.replace('_', '') for part in parts if part.replace('_', '')]
+                oglabelname = [part.replace('.', '') for part in parts if part.replace('.', '')]
                 filtered_df = atlasDescript[atlasDescript['Description'].isin(oglabelname)]
                 labelnums = filtered_df['Label'].tolist()
 
@@ -10699,7 +11110,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             addemiszero = ants.threshold_image(addem, 0, 0)
             temp = ants.image_read(locfilename)
             temp = ants.mask_image(temp, temp, level=labelnums, binarize=True)
-            if verbose:
+            if verbose > 0:
                 print("DEBUG")
                 print(  temp.sum() ) 
                 print( labelnums )
@@ -10707,7 +11118,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             temp[addemiszero == 0] = 0
             addem = addem + temp
 
-        if verbose:
+        if verbose > 0:
             print('Done Adding')
         for axx in axes:
             figfn=output_prefix+f"fig{col2viz}ax{axx}_py.jpg"
@@ -10726,7 +11137,7 @@ def brainmap_figure(statistical_df, data_dictionary_path, output_prefix, brain_i
             ants.plot(edgeimgC, addemC, axis=axx, nslices=nslices, ncol=ncol,       
                 overlay_cmap=overlay_cmap, resample=False, overlay_alpha=1.0,
                 filename=figfn, cbar=axx==axes[0], crop=True, black_bg=black_bg )
-        if verbose:
+        if verbose > 0:
             print(f"{col2viz} done")
     if verbose:
         print("DONE brain map figures")
@@ -11421,7 +11832,7 @@ def renameit(df, old_col_name, new_col_name):
     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 ):
+def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, mysep='-', 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),
@@ -11436,6 +11847,7 @@ def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, verbose=True ):
     qc_dataframe : pandas.DataFrame
         The DataFrame containing QC metrics for different modalities and imaging data.
     fix_LRRL : bool, optional
+    mysep : string, character such as - or _ the usual antspymm separator argument
 
     verbose : bool, optional
         If True, prints the progress and the shape of the DataFrame being processed in each step.
@@ -11453,17 +11865,19 @@ def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, verbose=True ):
         The matched and filtered DataFrame after applying all QC scoring and matching operations across specified modalities.
 
     """
+    qc_dataframe=remove_unwanted_columns( qc_dataframe )
     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']
+    mmdf0 = best_mmm( qc_dataframe, 'T1w', outlier_column=outlier_column, mysep=mysep )['filt']
+    fldf = best_mmm( qc_dataframe, 'T2Flair', outlier_column=outlier_column, mysep=mysep  )['filt']
+    nmdf = best_mmm( qc_dataframe, 'NM2DMT', outlier_column=outlier_column, mysep=mysep  )['filt']
+    rsdf = best_mmm( qc_dataframe, 'rsfMRI', outlier_column=outlier_column, mysep=mysep  )['filt']
+    dtdf = best_mmm( qc_dataframe, 'DTI', outlier_column=outlier_column, mysep=mysep  )['filt']
+    pfdf = best_mmm( qc_dataframe, 'perf', outlier_column=outlier_column, mysep=mysep  )['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']
@@ -11471,6 +11885,9 @@ def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, verbose=True ):
     mmdf, undffl = mm_match_by_qc_scoring(mmdf0, fldf, 'subjectIDdate', criteria, 
                         prefix='T2Flair_', exclude_columns=xcl )
 
+    mmdf, undfpf = mm_match_by_qc_scoring(mmdf, pfdf, 'subjectIDdate', criteria, 
+                        prefix='perf_', exclude_columns=xcl )
+
     prefixes = ['NM1_', 'NM2_', 'NM3_', 'NM4_', 'NM5_', 'NM6_']  
     undfmod = nmdf  # Initialize 'undfmod' with 'nmdf' for the first iteration
     if undfmod is not None:
@@ -11489,27 +11906,29 @@ def mm_match_by_qc_scoring_all( qc_dataframe, fix_LRRL=True, verbose=True ):
     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 )
+    if undfmod is not None:
+        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 undfmod is not None:
+        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')