I am running a searchlight RSA analysis.

- I use 3dmaskdump to get the coordinates of every voxel in the brain mask. My understanding is that this outputs the coordinates in RAI orientation.

```
3dmaskdump -overwrite -mask /Users/lynna3/Documents/Projects/EF_Math/ref/mask/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD \
-noijk -xyz \
-o /Users/lynna3/Documents/Projects/EF_Math/Processed_Data/EF2001/Y1/proc/EF2001_NUM_Y1.results/RSA/tmp.n_voxel_coord_searchlight \
/Users/lynna3/Documents/Projects/EF_Math/ref/mask/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD
```

- I then loop through every voxel (e.g., -23.75 -2.5 -41) and use 3dmaskdump again to extract the data for the briks of interest in a 4mm sphere centered on the voxel of interest.

```
3dmaskdump -overwrite -quiet -nozero -noijk \
-mask /Users/lynna3/Documents/Projects/EF_Math/ref/mask/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD \
-xball -23.75 -2.5 -41 4 \
-o /Users/lynna3/Documents/Projects/EF_Math/Processed_Data/EF2001/Y1/proc/EF2001_NUM_Y1.results/RSA/tmp.roi_1 \
/Users/lynna3/Documents/Projects/EF_Math/Processed_Data/EF2001/Y1/proc/EF2001_NUM_Y1.results/stats.unsmoothed.trial.EF2001_REML_RAI+tlrc.BRIK"[2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75]"
```

- After fitting the model, I then use 3dUndump to write the model fit to the voxel of interest

```
3dUndump -overwrite -xyz -datum float \
-prefix /Users/lynna3/Documents/Projects/EF_Math/Processed_Data/EF2001/Y1/proc/EF2001_NUM_Y1.results/RSA/RSA_EF2001_Y1_Ratio_searchlight_4_tau_RAI \
-master /Users/lynna3/Documents/Projects/EF_Math/ref/mask/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD \
/Users/lynna3/Documents/Projects/EF_Math/Processed_Data/EF2001/Y1/proc/EF2001_NUM_Y1.results/RSA/RSA_EF2001_Y1_Ratio_searchlight_4_tau.txt
```

Here are a few questions I have to make sure I’m doing this correctly:

[ul]

[li] What is the unit of measure for the radius parameter? Is this in mm or voxels?

[/li][li] Which “-*ball” option should I use when feeding coordinates extracted in 3dmaskdump to 3dmaskdump? I’ve been using -xball because I passed the -xyz in the original 3dmaskdump, but I’m not sure if this is correct.

[/li][/ul]

Thanks in advance for your help,

Andrew