How to make text data file for use in GingerALE

아래는 제가 현재 있는 UIC lab에서 다른 사람들에게 fMRI meta-analysis를 위하여 sleuth program에서 어떻게 text 파일을 만들어 내는 가에 대해서 설명한 글입니다.

영문으로 되어 있는 점 양해 바랍니다.

Steps for entering the data

Find the paper in the sleuth and use the sleuth if the paper is in the sleuth program.

If you find the wanted program from the sleuth, it will be displayed as follows:

Press the “Download checked” button. Look at the workspace.

Although there is just one paper, it is displayed in 4 rows (It has 4 experiments).

Here, click the export button.

We will use Talairach coordinate. If we use exploratory analysis and do not divide according to the types of experiments, we just divide all the results according to the subject groups. --> Select just like as mentioned above. By selecting the option – locations (GIngerALE Text), you can save the coordinate results as text file that can be used in the GingerALE.

(It is better to use the wordpad program to edit the txt files rather than word. In case of Microsoft word, there is a possibility to add unwanted format settings automatically into the txt file. This can be problematic in automated loading for gingerALE software.)

Manually input the data into the text file

You should identify following information – reference, type of experiments, subject groups, number of subjects and actual coordinates.

In this case, you need to use the format used in sleuth program gingerALE text.

For example,

// Reference=Talairach (If the reference coordinate is MNI, we need to convert it into Talairach in later step. If coordinates are written in MNI, you also need to specify where the coordinates came from - fsl or SPM.)

// Pavuluri, 2007: Angry Faces vs. Neutral Faces, Pediatric Bipolar Patients > Controls (This is important. By this information, we will decide into what text file we put this result.)

// Subjects=10 (This is important as the number of patients determines the statistical power of the meta-analysis.)

14        16        32 (Here place the coordinate written in the paper.) 13        -27       -13 33        -77       15 31        -73       11 -14       21        18 -15       -47       17 -35       -14       -26 -50       -46       -2

About reference, we can use MNI or Talairach coordinates. In many analysis program such as fsl (that I use) or SPM, MNI coordinate is commonly used. However, in GingerALE program, as the Talairach coordinates is well matched into Brodmann area, meta-analysis is commonly performed using Talairach space. For meta-analyses in Talairach space, we take MNI coordinates and convert them to Talairach space using the Lancaster (icbm2tal) transform. This conversion can be done using the ToolsàConvert foci option in GingerALE program.