Merge pull request #39 from switt4/master

Add correctFieldMapCase4 to support pepolar fieldmaps

etc/correctFieldMapCase4

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+if [ "$#" -lt 1 ]
+then
+    echo "Usage: $0 <in_bids> <subj ID> <session id (optional)>"
+	exit 1
+fi 
+in_bids=$1
+
+exec_path=`dirname $0`
+
+
+subj=$2
+	subj=${subj##sub-} #strip off sub- if it exists, to make consistent
+if [ "$#" -gt 2 ]
+then
+    ses=$3
+	ses=${ses##ses-} #strip off sub- if it exists, to make consistent
+fi
+
+#correct field map json files
+
+if [ -n "$ses" ]
+then
+	$exec_path/correctFieldMapJsonCase4.py $in_bids sub-$subj ses-$ses
+else
+	$exec_path/correctFieldMapJsonCase4.py $in_bids sub-$subj
+fi
+

etc/correctFieldMapJsonCase4.py

@@ -0,0 +1,69 @@
+#! /usr/bin/env python3
+'''
+correct field map json
+'''
+
+import os
+import sys
+import json
+import glob
+import collections
+
+def correctFieldMapJson(bids_dir,sub,ses=None):
+
+    if ses: #ses not None
+        sub_prefix = '{}_{}'.format(sub,ses)
+        sub_path_prefix=os.path.join(sub,ses)
+        sub_root = '{}'.format(sub)
+    else:
+        sub_prefix = '{}'.format(sub)
+        sub_path_prefix = sub_prefix
+        sub_root = '{}'.format(sub)
+
+    sub_dir=os.path.join(bids_dir,sub_path_prefix)
+    sub_root_dir=os.path.join(bids_dir,sub_root) #without session
+
+    for fmri_json_file in glob.glob(os.path.join(sub_dir,'fmap','{}_acq-EPI_dir-*_epi.json'.format(sub_prefix))):
+
+        #debug
+        print(fmri_json_file)
+
+        #load json files
+        with open(fmri_json_file, 'r') as f:
+            fmri_json = json.load(f,object_pairs_hook=collections.OrderedDict)
+
+        # apply to all bold images
+        cwd=os.getcwd()
+        os.chdir(sub_root_dir)
+        if ses:
+            all_bold = glob.glob(os.path.join('{}'.format(ses),'func','{}_*_bold.nii.gz'.format(sub_prefix)))
+        else:
+            all_bold = glob.glob(os.path.join('func','{}_*_bold.nii.gz'.format(sub_prefix)))
+
+        os.chdir(cwd)
+
+        fmri_json["IntendedFor"]=all_bold
+
+        #update json file
+        os.system("chmod a+w {}".format(fmri_json_file))
+        with open(fmri_json_file, 'w') as f:
+            json.dump(fmri_json, f, indent=4, separators=(',', ': '))
+        os.system("chmod a-w {}".format(fmri_json_file))
+
+
+if __name__=="__main__":
+    if len(sys.argv)-1 < 2:
+        print ("Usage: python " + os.path.basename(__file__)+  " 'bids_dir' 'sub' 'ses (optional)'")
+        sys.exit()
+    else:
+        bids_dir = sys.argv[1]
+        sub = sys.argv[2]
+        if len(sys.argv)-1 > 2:
+            ses=sys.argv[3]
+            correctFieldMapJson(bids_dir,sub,ses)
+        else:
+            correctFieldMapJson(bids_dir,sub)
+
+#test
+#Usage: python correctFieldMapJson.py 'bids_dir' 'sub'
+#python correctFieldMapJson.py '/mnt/hgfs/test/correct_fieldmap_json/topsy_7T' 'sub-005'

etc/memp2rage_bids_corrector.py

@@ -12,86 +12,87 @@
 
 
 
-multiecho_dir = sys.argv[1]
-print('multi-echo corrector')
-print(multiecho_dir)
-
-#puts all json and nifti files in the folder into lists
-json_files = sorted(glob.glob(multiecho_dir + "/*echo_*M*RAGE*.json"))
-nifti_files = sorted(glob.glob(multiecho_dir + "/*echo_*M*RAGE*.nii.gz" ))
-print(json_files)
-print(nifti_files)
-for i,k in zip(json_files, nifti_files):
+bids_dir = sys.argv[1]
+for multiecho_dir in glob.glob(f'{bids_dir}/**/anat',recursive=True):
+    print('multi-echo corrector')
+    print(multiecho_dir)
+
+    #puts all json and nifti files in the folder into lists
+    json_files = sorted(glob.glob(multiecho_dir + "/*echo-*_*M*RAGE*.json"))
+    nifti_files = sorted(glob.glob(multiecho_dir + "/*echo-*_*M*RAGE*.nii.gz" ))
+    print(json_files)
+    print(nifti_files)
+    for i,k in zip(json_files, nifti_files):
 
-    #open and load json file    
-    with open(i) as data_file:
-        data = json.load(data_file)
+        #open and load json file    
+        with open(i) as data_file:
+            data = json.load(data_file)
 
-    #in the case of echo-1, the EchoNumber tag does not exist in the json file    
-    if ("EchoNumber" not in data) and ("_echo_" in i):
-        js_addEchoNum = re.sub("_echo_", "_echo-1_", i)
-        js_changeEnding = re.sub("[0-9].json", ".json", js_addEchoNum)
-        print('renaming: '+i+' to '+js_changeEnding)
-        os.rename(i, js_changeEnding)
+        #in the case of echo-1, the EchoNumber tag does not exist in the json file    
+        if ("EchoNumber" not in data) and ("_echo_" in i):
+            js_addEchoNum = re.sub("_echo_", "_echo-1_", i)
+            js_changeEnding = re.sub("[0-9].json", ".json", js_addEchoNum)
+            print('renaming: '+i+' to '+js_changeEnding)
+            os.rename(i, js_changeEnding)
 
-        ni_addEchoNum = re.sub("_echo_", "_echo-1_", k)
-        ni_changeEnding = re.sub("[0-9].nii.gz", ".nii.gz", ni_addEchoNum)
-        print('renaming: '+k+' to '+ni_changeEnding)
-        os.rename(k, ni_changeEnding)
+            ni_addEchoNum = re.sub("_echo_", "_echo-1_", k)
+            ni_changeEnding = re.sub("[0-9].nii.gz", ".nii.gz", ni_addEchoNum)
+            print('renaming: '+k+' to '+ni_changeEnding)
+            os.rename(k, ni_changeEnding)
 
-    #otherwise get EchoNumber value from json file and insert into filename
-    elif "EchoNumber" in data:
-        echonum = data["EchoNumber"]
-
-        js_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_", i)
-        js_changeEnding = re.sub("[0-9].json", ".json", js_addEchoNum)
-        print('renaming: '+i+' to '+js_changeEnding)
-        os.rename(i, js_changeEnding)
+        #otherwise get EchoNumber value from json file and insert into filename
+        elif "EchoNumber" in data:
+            echonum = data["EchoNumber"]
+
+            js_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_", i)
+            js_changeEnding = re.sub("[0-9].json", ".json", js_addEchoNum)
+            print('renaming: '+i+' to '+js_changeEnding)
+            os.rename(i, js_changeEnding)
 
-        ni_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_" , k)
-        ni_changeEnding = re.sub("[0-9].nii.gz", ".nii.gz", ni_addEchoNum)
-        print('renaming: '+k+' to '+ni_changeEnding)
-        os.rename(k, ni_changeEnding)
+            ni_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_" , k)
+            ni_changeEnding = re.sub("[0-9].nii.gz", ".nii.gz", ni_addEchoNum)
+            print('renaming: '+k+' to '+ni_changeEnding)
+            os.rename(k, ni_changeEnding)
 
 
-#combine echos 1 and 2 for memprage
-json_files = sorted(glob.glob(multiecho_dir + "/*echo-1_*MEMPRAGE.json"))
-nifti_files_echo1 = sorted(glob.glob(multiecho_dir + "/*echo-1_*MEMPRAGE.nii.gz"))
-nifti_files_echo2 = sorted(glob.glob(multiecho_dir + "/*echo-2_*MEMPRAGE.nii.gz"))
+    #combine echos 1 and 2 for memprage
+    json_files = sorted(glob.glob(multiecho_dir + "/*echo-1_*MEMPRAGE.json"))
+    nifti_files_echo1 = sorted(glob.glob(multiecho_dir + "/*echo-1_*MEMPRAGE.nii.gz"))
+    nifti_files_echo2 = sorted(glob.glob(multiecho_dir + "/*echo-2_*MEMPRAGE.nii.gz"))
 
-for i,in_json in enumerate(json_files):
-    echo1 = nifti_files_echo1[i]
-    echo2 = nifti_files_echo2[i]
+    for i,in_json in enumerate(json_files):
+        echo1 = nifti_files_echo1[i]
+        echo2 = nifti_files_echo2[i]
 
-    out_json = re.sub('_echo-[0-9]+_','_',in_json)
-    out_json = re.sub('acq-([0-9a-zA-Z]+)4e_','acq-\g<1>AvgEcho12_',out_json)
-    out_json = re.sub('_MEMPRAGE\.','_T1w.',out_json)
-    out_nii = re.sub('\.json','.nii.gz',out_json)
+        out_json = re.sub('_echo-[0-9]+_','_',in_json)
+        out_json = re.sub('acq-([0-9a-zA-Z]+)4e_','acq-\g<1>AvgEcho12_',out_json)
+        out_json = re.sub('_MEMPRAGE\.','_T1w.',out_json)
+        out_nii = re.sub('\.json','.nii.gz',out_json)
 
-   #open and load json file    
-    with open(in_json) as data_file:
-        data = json.load(data_file)
+        #open and load json file    
+        with open(in_json) as data_file:
+            data = json.load(data_file)
 
-    #remove EchoNumber and EchoTime from JSON
-    del data['EchoNumber']
-    del data['EchoTime']
-    data['EchoNumbers'] = [1,2]
+        #remove EchoNumber and EchoTime from JSON
+        del data['EchoNumber']
+        del data['EchoTime']
+        data['EchoNumbers'] = [1,2]
 
-    with open(out_json, 'w') as outfile:
-        json.dump(data, outfile, indent=4)
+        with open(out_json, 'w') as outfile:
+            json.dump(data, outfile, indent=4)
 
-    #average the two niftis
-    echo1_nib = nib.load(echo1)
-    echo2_nib = nib.load(echo2)
+        #average the two niftis
+        echo1_nib = nib.load(echo1)
+        echo2_nib = nib.load(echo2)
 
-    echo1_vol = echo1_nib.get_fdata()
-    echo2_vol = echo2_nib.get_fdata()
+        echo1_vol = echo1_nib.get_fdata()
+        echo2_vol = echo2_nib.get_fdata()
 
-    avg_vol = (echo1_vol + echo2_vol) * 0.5
+        avg_vol = (echo1_vol + echo2_vol) * 0.5
 
-    avg_nib = nib.Nifti1Image(avg_vol, echo1_nib.affine, echo1_nib.header)
+        avg_nib = nib.Nifti1Image(avg_vol, echo1_nib.affine, echo1_nib.header)
 
-    nib.save(avg_nib,out_nii)
+        nib.save(avg_nib,out_nii)
 
 
 

tar2bids

@@ -330,6 +330,7 @@ then
 #check if certain files exist that need further corrections: (the following simply suppresses stderr: 1>/dev/null 2>&1)
 Nfmaps=`ls $output_dir/sub-*/ses-*/fmap/*phasediff.nii.gz 2>/dev/null | wc -l`
 NfmapsCase2=`ls $output_dir/sub-*/ses-*/fmap/*twomagphase1.nii.gz 2>/dev/null | wc -l`
+NfmapsCase4=`ls $output_dir/sub-*/ses-*/fmap/*epi.nii.gz 2>/dev/null | wc -l`
 Ngre=`ls $output_dir/sub-*/ses-*/anat/*GRE?.nii.gz 2>/dev/null | wc -l`
 Nbold=`ls $output_dir/sub-*/ses-*/func/*bold?.nii.gz 2>/dev/null | wc -l`
 Nmemp2rage=`ls $output_dir/sub-*/ses-*/anat/*MP2RAGE?.nii.gz 2>/dev/null | wc -l`
@@ -342,6 +343,7 @@ else
 #check if certain files exist that need further corrections: (the following simply suppresses stderr: 1>/dev/null 2>&1)
 Nfmaps=`ls $output_dir/sub-*/fmap/*phasediff.nii.gz 2>/dev/null | wc -l`
 NfmapsCase2=`ls $output_dir/sub-*/fmap/*twomagphase1.nii.gz 2>/dev/null | wc -l`
+NfmapsCase4=`ls $output_dir/sub-*/fmap/*epi.nii.gz 2>/dev/null | wc -l`
 Ngre=`ls $output_dir/sub-*/anat/*GRE?.nii.gz 2>/dev/null | wc -l`
 Nbold=`ls $output_dir/sub-*/func/*bold?.nii.gz 2>/dev/null | wc -l`
 Nmemp2rage=`ls $output_dir/sub-*/anat/*MP2RAGE?.nii.gz 2>/dev/null | wc -l`
@@ -382,6 +384,19 @@ fi
 fi
 
 
+if [ ! "$NfmapsCase4" = 0 ]
+then
+echo "  Running bids correction from phasediff fieldmap data..."
+
+if [ -n "$sessid" ]
+then
+parallel -a $heudiconv_subjlist -a $heudiconv_sesslist $popts "$execpath/etc/correctFieldMapCase4 $output_dir {1} {2} | tee -a $tuneup_log.{1}.{2} " 
+else
+parallel -a $heudiconv_subjlist  $popts "$execpath/etc/correctFieldMapCase4 $output_dir {1} | tee -a $tuneup_log.{1}" 
+fi
+
+fi
+
 
 if [ ! "$Ngre" = 0 -o ! "$Nmemp2rage" = 0 -o ! "$Nsa2rage_complex" = 0 -o ! "$Nmemprage" = 0 ]
 then
@@ -440,6 +455,9 @@ fi
 #merge any vNav files if they exist
 python3 $execpath/etc/merge_vNav.py $output_dir
 
+#average m3mprage images
+python3 $execpath/etc/memp2rage_bids_corrector.py $output_dir
+
 #remove scans.tsv files as they may be out of date after corrections
 rm -f $output_dir/*/*_scans.tsv $output_dir/*/*/*_scans.tsv