Custom spherical ROI mask using centers from standard atlas

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1

Hi all,

I am using the 3dCM command to find the centers of left and right accumbens in the "FS.afni.MNI2009c_asym" atlas. I can see that these centers are getting correctly calculated and lie within the left and right accumbens in the aforementioned atlas.

3dCM -roi_vals 17 33 -Icent ~/abin/FS.afni.MNI2009c_asym.nii.gz > $fpath_roi_centers

I then use 3dUndump to create spherical ROIs of 5 mm diameter at these centers. The resulting spherical ROIs, however, lie a little far from the identified centers (there seems to be a translation error in position), which makes me think there was some problem with the axes used by 3dUndump to interpret the provided coordinates. The default orientation is "RAI" for 3dCM, and I can provide the same to 3dUndump, but the documentation says that the provided orientation will be overwritten by the orientation of the -master which is the "FS.afni.MNI2009c_asym" atlas.

3dUndump -prefix $basedir_dst/roi_mask_spherical_rewardnetw -master ~/abin/FS.afni.MNI2009c_asym.nii.gz -xyz -srad 5 $fpath_roi_centers

How can I fix this issue?

Thanks,
Robin

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2

Hi, Robin-

The output by 3dCM there is in RAI notation.

Therefore, add -orient RAI to your 3dUndump command. The output dataset grid will still match that of your -master .. dset. However, when reading in the xyz values, it will appropriately use RAI.

Thus, try:

3dUndump                                                               \
    -overwrite                                                         \
    -prefix    $basedir_dst/roi_mask_spherical_rewardnetw              \
    -master    ~/abin/FS.afni.MNI2009c_asym.nii.gz                     \
    -xyz                                                               \
    -orient    RAI                                                     \
    -srad      5                                                       \
    $fpath_roi_centers

--pt

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3

Thank you, Paul. That solved the issue!

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