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SearchAndView

Page history last edited by PBworks 13 years, 5 months ago

(1) Open up a BrainMap account at this website. You can find a copy of the Search&View manual here.

 

(2) Make a text file that has one row for each XYZ coordinate (input focus). Each row should have FOUR numbers: X-coordinate, Y-coordinate, Z-coordinate, and Study Code. XYZ coordinates should be in MNI space. The study codes should be positive consecutive integers, starting from 0 (not starting from 1!). Example . Let's assume for the sake of example that your text file is named Foci.txt.

 

(3) Run the command

 

wc Foci.txt

 

This should return three numbers. They are, in order: number of lines, number of words, and number of characters in the text file. The number of lines should equal the number of input foci. The number of words divided by the number of lines should be three, since there are three coordinates (XYZ) per line.

 

(4) Log onto one of the app servers (app1, app2, ..., app8).

 

(5) Bring up a shell (e.g., xterm or terminal), and at the prompt type

 

sav

 

to bring up Search&View. Two windows will pop up: the main Search&View window, and a login window.

 

(6) In the login window, log in using your BrainMap account and password.

 

(7) In the main Search&View window, click on the WorkSpace tab. Later on, you may want to re-load the workspace to go back to the analysis.

 

(8) Select File --> Open.... This will pop up a browser window. Browse to your XYZ input foci file, select it, then click on the Open button.

 

(9) Select File --> Save Workspace. This will pop up another browser window. Type in a desired filename (suggest with the file extension .wsp, for "workspace") to save this workspace.

 

(10) Click on the ALE tab.

 

(11) In top frame entitled ALE, enter an ALE Description and output file prefix ("ALE prefix"). Change the FWHM to whatever number you like. Click on the Apply papers from workspace button. Then click on the Compute button. Search&View will then create then ALE map, writing it out to disk in NIFTI format.

 

(12) In the frame entitled Permutation Testing, type in the number of Permutations you want (e.g., 10000), type in a desired output file prefix ("p-value prefix"), then click on the Compute button. This may take a long time to run; e.g., for 185 foci and 10000 simulations, it took about 6 hours and 40 minutes.

 

(13) In the frame entitled False Discovery Rate, type in the desired False Discovery Rate in the entry box entitled click q (FDR level). The default value of 0.05 is reasonable. Then, click on the Compute button. Two alternative p-value thresholds will be computed, pID (p-value threshold based on independence or positive dependence) and pN (nonparametric p-value threshold). You will need to choose one of these thresholds to use for the next step. The paper by Genovese et al. indicates that pID "is a reasonable assumption for many fMRI data sets." On the other hand, the BrainMap folks favor pN. The default method in SPM is pID. In the CSL in-house implementation of ALE, I have used SPM's code, so the CSL version of ALE is using pID.

 

(14) In the frame entitled Thresholding, type in your desired p-value in the entry box labeled Chosen p value. Enter a desired output file prefix in the entry box labeled Output prefix. Then click on the Compute button.

 

(15) In the frame entitled Clusters, type in the desired cluster size threshold in the entry box labeled Min. volume (mm^3). Enter a desired output file prefix in the entry box labeled Cluster prefix. Then click on the Compute button.

 

(16) Output images are in NIFTI format. Unfortunately, MEDx doesn't recognize this format. AFNI and later versions of SPM should be able to read in this format. Consider installing the free program MRIcron to use as a visualizer.

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