Merge pull request #335 from a3sha2/master

acompcor

modules/confound2/confound2.mod

@@ -350,10 +350,18 @@ if (( ${confound2_acompcor[cxt]} == 1 ))
 
 
    acompcor_path=${outdir}/${prefix}_acompcor.1D
+
+   if [[ -f ${confjson[sub]} ]]; then 
+   exec_xcp acompcor_select.py -j ${confjson[sub]} -c ${fmriprepconf[sub]} \
+    -o  ${acompcor_path} 
+
+   else 
     exec_xcp generate_confmat.R \
            -i ${fmriprepconf[sub]} \
            -j aCompCor  \
            -o ${acompcor_path}
+
+   fi
 
  output acompcor  ${prefix}_acompcor.1D
 

modules/prestats/prestats.mod

@@ -230,6 +230,12 @@ while (( ${#rem} > 0 ))
         mask1=${imgprt2}${mskpart}; maskpart2=${mask1#*_*_*_*}
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
 
+        conf2="_desc-confounds_regressors.json"
+        if [[ -f ${imgprt}${conf2} ]]; then 
+           exec_sys cp ${imgprt}${conf2} $out/prestats/${prefix}_fmriconf.json
+           output confjson $out/prestats/${prefix}_fmriconf.json
+        fi
+
          strucn="${img1[sub]%/*/*}";
          strucfile=$(ls -f ${strucn}/anat/*h5 2>/dev/null)
          strucfile1=$(echo $strucfile | cut --delimiter " " --fields 1) 

utils/acompcor_select.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import json
+import pandas as pd 
+from argparse import (ArgumentParser, RawTextHelpFormatter)
+
+
+def get_parser():
+
+    parser = ArgumentParser(
+        formatter_class=RawTextHelpFormatter,
+        description='acompcor selection')
+    parser.add_argument(
+        '-c', '--confmat', action='store', required=True,
+        help='[required]'
+             '\n confmat.')
+    parser.add_argument(
+        '-j', '--confjson', action='store', required=True,
+        help='[required]'
+             '\n conjson.')
+    parser.add_argument(
+        '-o', '--outfile', action='store', required=False,
+        help='output directory')
+    return parser
+
+opts            =   get_parser().parse_args()
+
+
+with open(opts.confjson) as f:
+    data = json.load(f)
+
+WM=[]
+CSF=[]
+for key, value in data.items():
+    if 'a_comp_cor' in key:
+        if value['Mask']=='WM' and value['Retained']==True:
+            WM.append([key,value['VarianceExplained']])
+        if value['Mask']=='CSF' and value['Retained']==True:
+            CSF.append([key,value['VarianceExplained']])
+
+CSFlist=[CSF[0][0],CSF[1][0],CSF[2][0],CSF[3][0],CSF[4][0]]
+WMlist=[WM[0][0],WM[1][0],WM[2][0],WM[3][0],WM[4][0]] 
+
+data2=pd.read_csv(opts.confmat,sep='\t')
+combinelist=CSFlist+WMlist
+acompcor=data2[combinelist]
+acompcor.to_csv(opts.outfile,index=False,sep=' ',header=False)
+
+
+
+
+
+

utils/aslqc.py

@@ -1,16 +1,16 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-# Azeez Adebimpe penn bbl sept 2019
-import nibabel as nib
-import numpy as np
-import pandas as pd 
-import os as os 
-import sys as sys
-import seaborn as sns
-from nibabel.processing import smooth_image
-from scipy.stats import gmean
+#!/usr/bin/env python	
+# -*- coding: utf-8 -*-	
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-	
+# vi: set ft=python sts=4 ts=4 sw=4 et:	
+# Azeez Adebimpe penn bbl sept 2019	
+import nibabel as nib	
+import numpy as np	
+import pandas as pd 	
+import os as os 	
+import sys as sys	
+import seaborn as sns	
+from nibabel.processing import smooth_image	
+from scipy.stats import gmean	
 from argparse import (ArgumentParser, RawTextHelpFormatter)
 
 def get_parser():