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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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aclynn11
May 04, 2023 01:02PM
I am running a searchlight RSA analysis.

1) 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

2) 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]"

3) 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:
  • What is the unit of measure for the radius parameter? Is this in mm or voxels?
  • 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.

Thanks in advance for your help,

Andrew
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Subject Author Posted

3dmaskdump to 3dmaskdump to 3dUndump

aclynn11 May 04, 2023 01:02PM

Re: 3dmaskdump to 3dmaskdump to 3dUndump

Daniel Glen May 04, 2023 10:07PM