Hi all,

I'm now using AFNI to preprocess resting state fMRI data. As I cannot use FreeSurfer to segment tissues, I plan to use the example 11b to do preprocessing in afni_proc.py.

From the example, it tells us to import a ventricle mask from the template and then using TT space as illustration. And the template used is TT_desai_dd_mpm+tlrc. I'm wondering if there is any template in MNI space that I can use to extract the ventricle mask?

I have noticed that there are many templates including MNI and TT templates in abin folder. But don't know which one to use, since it seems that TT_desai_dd_mpm template is the probability map. And I also don't know the labels of ventricles in MNI space.

The afni_proc.py script I plan to use is as follows:

afni_proc.py -subj_id subj1 \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat subj1_anat.nii \
-dsets subj1_rest.nii \
-tcat_remove_first_trs 10 \
-align_opts_aea -cost lpc+ZZ \
-tlrc_base MNI_caez_N27+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

So use MNI space as the base space.

Do you have any idea about extracting ventricle from MNI template like the script as follows?
3dcalc -a ~/abin/TT_desai_dd_mpm+tlrc -expr 'amongst(a,152,170)' -prefix template_ventricle


Many thanks!


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