MEG

Create a symbolic link to your raw data on the server

  • Create your own folder in neurospin/meg_tmp/ by typing
>> cd /neurospin/meg/meg_tmp/
>> mkdir your_folder
  • To avoid unnecessary occupation of disk space, DO NOT copy raw data files into your_folder. Create a symbolic link to it instead, by using the command "ln -s".
>>ln -s /neurospin/acquisition/neuromag/data/your_protocol_folder/your_subject_folder/date/raw_filename.fif
/neurospin/meg/meg_tmp/your_folder/new_raw_filename.fif
The symbolic link to your file will look like this:
>>new_raw_filename.fif@
  • NOTE: Choosing appropriate names for the symbolic links is IMPORTANT! You will use them throughout all the analysis processing steps. If you will use the fieldtrip-based pipeline of analysis, see here for organizing the file names and directories of your analysis. Choose simple and brief names, and replace the subject's id reference with a number: it will be easier to call them in the numerous steps of your analyses. Example: s02run3.fif may indicate the dataset from the 2nd subject, 3rd run.
  • Output files from your analyses should be saved in /neurospin/meg/meg_tmp/your_folder.

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TIP: to create a link to all .fif files in a directory at once:

1) either use the following bash script: Automatic scripts for symbolic links and maxfilter correction

2) or type the following code:

  1. Type csh to enter the C-shell
  2. then enter the following commands to create a simple loop (hit <return> after each line):

foreach i (/neurospin/acquisition/neuromag/data/[protocol]/[subject]/[date]/*.fif)
ln -s $i
end