Importing data from the Siemens Trio 3T

To import scans from the Trio3T (only works on the local network at Neurospin)

Create a text file list_subjects.txt following the instructions below
In a shell, run import_subjects_from_trio < list_subjects.txt

If the command "import_subjects_from_trio" is not available, install the scripts from Attach:import_exams_from_trio.tar.gz with the following commands:

mkdir -p $HOME/bin
tar -C $HOME/bin -xzf import_exams_from_trio.tar.gz

Structure of list_subjects.txt

Each line in the file list_subjects.txt indicates which imaging sessions to download for a given participant. The information is provided in columns as follow:

subject acq date nip anatsession funcsess1 namefuncsess1 funcsess2 namefuncsess2 ...

subject: name of the directory where to put this subject's data
acq: number of acquisition (one digit, usually '1')
date: date of exam in the format YYYYMMDD (e.g. 1 st April 2009 -> 20090401)
nip: "numero d'identification personnel" : subject identification number used on the imager
anatsession: number of the session containing the anatomical T1 scan (use two digits!!!, e.g. "02")
funcsess1: number of a session containing functional data (use two digits!!!, e.g. "02")
namefuncsess1: name of the directory that will contain the corresponding functional data (in fMRI/acquisition1)

It is possible to add as many (funcsess, namefuncsess) pairs to download more functional sessions (and different subjects can have different numbers of sessions)

# Example of list_subject.txt file:

suj01 1 20090303 jn070144 02 06 lang1 10 lang2 08 music1 12 music2 
suj03 1 20090303 jn070144 02 06 lang1 10 lang2 08 music1 12 music2 
suj04 1 20090503 mm234235 02 08 lang1 12 lang2 06 music1 10 music2
...

Notes:

- Selecting subjects

     1. Method 1: Lines starting with '#' are ignored, therefore add
     '#' in front of subjects you do not want to download

     2. Method 2: import_subjects_from_trio reads from the standard
     input; therefore use 'grep' to extracts relevant lines from
     list_subject_.txt.
     grep nip list_subjects.txt | import_subjects_from_trio

- File format:

  The imported image files are in the DICOM format,  you will probably
  need to convert them to analyze format. 
  1. Method 1: use the matlab/spm preprocessing script
  2. Method 2: use 'convert_mrdc_to_nifti'

Problems, questions -> christophe@pallier.org

Note: this page replaces the previous "Téléchargement des données et leur organisation"