afni.nimh.nih.gov

Adding on to Pete's numerous good suggestions...

For the regions you showed in the image, you can probably separate them with 3dmask_tool using erosion and dilation. That is one way to remove small necks of regions. So you might. try

3dmask_tool -dilate_inputs -3 3 -prefix MTlocal_nonecks.nii.gz -inputs MTclusts.nii.gz

Almost every atlas has some region related to MT/V5, and you can use these instead of the functional localizer or in combination if you want. You can peruse the list of atlas regions with whereami -show_atlas_code, or use whereami in the AFNI GUI to find the regions listed at the same coordinate (see example below). The Brainnetome and MNI_Glasser_HCP atlases have very different definitions for example. The HCP temporal regions are described here:

[www.ncbi.nlm.nih.gov]

whereami -space MNI -49 67 4
++ Input coordinates orientation set by default rules to RAI
+++++++ nearby Atlas structures +++++++

Original input data coordinates in MNI space

Focus point (LPI)=
    48.51 mm [R], -64.73 mm [P],   6.93 mm [S] {TLRC}
    49.00 mm [R], -67.00 mm [P],   4.00 mm [S] {MNI}
    49.00 mm [R], -71.00 mm [P],   9.00 mm [S] {MNI_ANAT}

Atlas MNI_Glasser_HCP_v1.0: Glasser HCP 2016 surface-based parcellation
   Focus point:  R_Medial_Superior_Temporal_Area
 * Within 1 mm: R_Area_FST
 * Within 2 mm: R_Area_V4t
 * Within 3 mm: R_Middle_Temporal_Area
 * Within 5 mm: R_Area_PH
 * Within 7 mm: R_Area_TemporoParietoOccipital_Junction_2

Atlas Brainnetome_1.0: Brainnetome MPM
   Focus point:  V5/MT+_right
 * Within 3 mm: A37dl_right
            -AND-  A39c_right
 * Within 5 mm: A37vl_right

Atlas CA_ML_18_MNI: Macro Labels (N27-MNI)
   Focus point:  Right Middle Temporal Gyrus
 * Within 5 mm: Right Middle Occipital Gyrus
 * Within 7 mm: Right Inferior Temporal Gyrus

Atlas CA_MPM_22_MNI: Eickhoff-Zilles MPM atlas
   Focus point:  Area_hOc5_(V5/MT)
 * Within 2 mm: Area_hOc4la

Atlas DD_Desai_MPM: Maximum probability maps of Desai DD and FS maps
   Focus point:  Right-Cerebral-White-Matter
 * Within 3 mm: ctx_rh_G_occipital_middle
 * Within 4 mm: ctx_rh_G_temporal_middle
 * Within 6 mm: ctx_rh_S_temporal_sup

Atlas DKD_Desai_MPM: Maximum probability maps of Desai DKD and FS maps
   Focus point:  Right-Cerebral-White-Matter
 * Within 2 mm: ctx-rh-lateraloccipital
 * Within 3 mm: ctx-rh-middletemporal
            -AND-  ctx-rh-inferiorparietal

Atlas CA_GW_18_MNIA: Cytoarch. Prob. Maps for gray/white matter
   Focus point:  grey   (p = 0.68)
            -AND-  white   (p = 0.31)

Atlas CA_N27_LR: Left/Right (N27) 1.8
   Focus point:  Right Brain

Atlas TT_Daemon: Talairach-Tournoux Atlas
   Focus point:  Right Middle Temporal Gyrus
            -AND-  Right Brodmann area 37
 * Within 3 mm: Right Middle Occipital Gyrus
            -AND-  Right Brodmann area 19
            -AND-  Right Brodmann area 39
 * Within 5 mm: Right Inferior Temporal Gyrus


******** Please use results with caution! ********
******** Brain anatomy is quite variable! ********
******** The database may contain errors! ********

---

As Pete said, to move these atlas regions to the native space of your subject, you would invert the transformations of the dataset computed by @SSwarper or auto_warp.py. An example script is shown here for @SSwarper:

[afni.nimh.nih.gov]

Also an example using auto_warp.py is shown here on one of the later slides:
[afni.nimh.nih.gov]

Note the atlas should be in the space of the template to which you have aligned. Also you should use a nearest neighbor interpolation with "3dNwarpApply -ainterp NN".



Edited 1 time(s). Last edit at 09/07/2021 11:05AM by Daniel Glen.