afni_proc.py example 11b with MNI space normalization

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1

Hi,

I have questions when I run afni_proc.py example 11b since I am trying to use MNI space instead of Talairach space

This is my afni_proc.py

afni_proc.py -subj_id FT.11b.rest
-blocks despike tshift align tlrc volreg blur mask regress
-copy_anat My_anat+orig
-dsets My_epi+orig.HEAD
-tcat_remove_first_trs 2
-align_opts_aea -cost lpc+ZZ
-tlrc_base MNI152_T1_2009c+tlrc
-tlrc_NL_warp
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-volreg_warp_dxyz 2.5
-mask_segment_anat yes
-mask_segment_erode yes
-mask_import Tvent template_ventricle_2.5mm+tlrc
-mask_intersect Svent CSFe Tvent
-regress_motion_per_run
-regress_ROI_PC Svent 3
-regress_ROI_PC_per_run Svent
-regress_make_corr_vols WMe Svent
-regress_anaticor_fast
-regress_censor_motion 0.2
-regress_censor_outliers 0.1
-regress_apply_mot_types demean deriv
-regress_est_blur_epits
-regress_est_blur_errts
-regress_run_clustsim yes

I just changed input datasets(epi and anat) and tlrc_base to MNI space.
For the Talairach space,
3dcalc -a ~/abin/TT_desai_dd_mpm+tlrc
-expr ‘amongst(a,152,170)’ -prefix template_ventricle
3dresample -dxyz 2.5 2.5 2.5 -inset template_ventricle+tlrc
-prefix template_ventricle_2.5mm

I need to use these command. But for MNI space, how can I modify these commands and afni_proc.py?
and why do we need to resample them in 2.5mm?

Thanks

2

Hello,

Sorry for being slow.

The goal here is to make a standard space ventricle mask, which you can intersect with the subjects CSF mask from 3dSeg, creating what should be a reasonable subject specific ventricle mask.

The one in standard space must of course be aligned with the chosen template, and it must also be on the same grid that your warped EPI data will be on, in order to apply it. To do this in MNI space, you must find a ventricle mask in MNI space (the TT_desai_dd_mpm dataset is not), and resample it to match the final grid of your analysis (in this case, 2.5 mm, though it is important to verify that the grid is an exact match).

In any case, start by finding a ventricle mask in MNI space. Do you have one?

  • rick