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example:bids [2018/10/21 14:57]
42.49.180.224 [Preparing a combined MEG/fMRI dataset for sharing]
example:bids [2018/09/19 14:54] (current)
robert [Step 6: create the sidecar files for each dataset]
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 The scripts are included on this page for completeness. You can also download them from our ftp server at ftp://​ftp.fieldtriptoolbox.org/​pub/​fieldtrip/​example/​bids The scripts are included on this page for completeness. You can also download them from our ftp server at ftp://​ftp.fieldtriptoolbox.org/​pub/​fieldtrip/​example/​bids
 </​note>​ </​note>​
-====== Preparing a combined MEG/fMRI dataset for sharing ======+==== Step 1: create empty directory structure ​====
  
-This example describes how to prepare a combined MEG/fMRI dataset for sharingThe study involved 204 subjects, which participated in either a auditory or a visual version of a language experiment. The data and the experiment are descriobed in more details in the references that you find at the end of this page+<​code>​ 
 +RAW=/project/​3011020.13/raw 
 +BIDS=/​project/​3011020.13/bids
  
-Although we acquired slightly more data, the part that we now want to share for these subjects consists of+for SUB in A2002 A2003 A2004 A2005 A2006 A2007 A2008 A2009 A2010 A2011 A2013 A2014 A2015 A2016 A2017 A2019 A2020 A2021 A2024 A2025 A2027 A2028 A2029 A2030 A2031 A2032 A2033 A2034 A2035 A2036 A2037 A2038 A2039 A2040 A2041 A2042 A2046 A2047 A2049 A2050 A2051 A2052 A2053 A2055 A2056 A2057 A2058 A2059 A2061 A2062 A2063 A2064 A2065 A2066 A2067 A2068 A2069 A2070 A2071 A2072 A2073 A2075 A2076 A2077 A2078 A2079 A2080 A2083 A2084 A2085 A2086 A2088 A2089 A2090 A2091 A2092 A2094 A2095 A2096 A2097 A2098 A2099 A2101 A2102 A2103 A2104 A2105 A2106 A2108 A2109 A2110 A2111 A2113 A2114 A2116 A2117 A2119 A2120 A2121 A2122 A2124 A2125 V1001 V1002 V1003 V1004 V1005 V1006 V1007 V1008 V1009 V1010 V1011 V1012 V1013 V1015 V1016 V1017 V1019 V1020 V1022 V1024 V1025 V1026 V1027 V1028 V1029 V1030 V1031 V1032 V1033 V1034 V1035 V1036 V1037 V1038 V1039 V1040 V1042 V1044 V1045 V1046 V1048 V1049 V1050 V1052 V1053 V1054 V1055 V1057 V1058 V1059 V1061 V1062 V1063 V1064 V1065 V1066 V1068 V1069 V1070 V1071 V1072 V1073 V1074 V1075 V1076 V1077 V1078 V1079 V1080 V1081 V1083 V1084 V1085 V1086 V1087 V1088 V1089 V1090 V1092 V1093 V1094 V1095 V1097 V1098 V1099 V1100 V1101 V1102 V1103 V1104 V1105 V1106 V1107 V1108 V1109 V1110 V1111 V1113 V1114 V1115 V1116 V1117 ; do 
 +mkdir -p $BIDS/​sub-$SUB/​meg 
 +mkdir -p $BIDS/​sub-$SUB/​func 
 +mkdir -p $BIDS/​sub-$SUB/​anat 
 +mkdir -p $BIDS/​sub-$SUB/​dwi 
 +done
  
-  * anatomical MRI +mkdir -p $BIDS/code 
-  * diffusion weighted MRI  +mkdir -p $BIDS/​stimuli 
-  * functional MRI +mkdir -p $BIDS/​source 
-    * resting state  +</​code>​
-    * functional task +
-  * MEG +
-    * resting state  +
-    * functional task+
  
-MEG was acquired with a 275 channel CTF system. MRI was acquired with a 3T Siemens scanner. For the coregistration of the MEG with the anatomical MRI, the headshape was recorded using a Polhemus electromagnetic tracker. Digital photo'​s of the anatomical landmark at both ears were taken. Furthermore,​ head localizer coils were used for MEG coregistration as usual. 
- 
-Simulus presentation was done using using [[https://​www.neurobs.com|NBS Presentation]]. For MEG the events are coded as triggers in the data set. Both for MEG and MRI the presentation log files are shared and used to create/​extend the //​events.tsv//​ sidecar files for the task data.  
- 
-The shared data is organized according to [[http://​bids.neuroimaging.io|BIDS]],​ the Brain Imaging Data Structure. This not only gives structure to the organization of the data files, but also helps to ensure that appropriate metadata and documentation are shared. We believe that this will facilitate reuse and increase the value of the shared data. 
- 
-&​lt;​note important&​gt;​ 
-At this moment the data sharing has not been totally completed. Right now we are working on a publication that describes the details of this dataset, and the data is currently under review. Once completed, the data will be published on the [[https://​www.ru.nl/​donders/​research/​data/​|Donders Repository]] with DOI http://​hdl.handle.net/​11633/​di.dccn.DSC_3011020.09_236. 
-&​lt;/​note&​gt;​ 
 ==== Step 2: collect and convert MRI data from DICOM to NIFTI ==== ==== Step 2: collect and convert MRI data from DICOM to NIFTI ====