Hi, Osman-
I suggest you copy+paste the following text (which is your command, from above, just spaced out fairly uniformly) into a text file, say one called "do_ap.tcsh", so it is easier to fix and rerun, and generalize to process more subjects over time (the first line, which starts with odd characters, should be the very first thing in the new text file created):
#!/bin/tcsh
afni_proc.py \
-subj_id FT.11b.rest \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat anat+orig \
-dsets func+orig.HEAD \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ \
-tlrc_base TT_N27+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz 2.5 \
-blur_size 4 \
-mask_segment_anat yes \
-mask_segment_erode yes \
-mask_import Tvent template_ventricle_2.5mm+tlrc \
-mask_intersect Svent CSFe Tvent \
-mask_epi_anat yes \
-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 0.05 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim yes
Then, when you want to process this subject, you can type the following single line in the terminal:
tcsh do_ap.tcsh
Looking at your warnings and error messages, let's pick out a few to unpack:
+ This one with double asterisks can be fine---it is just reminding you to make sure that any associated stimulus timing files are also adjusted to match this removal of two initial time points (and since your run is like a resting state processing, with no stim files, then this should not be an issue to even need to verify):
** warning: removing first 2 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
+ this suggests that this file "template_ventricle_2.5mm+tlrc" does not exist on your system:
** cannot evaluate view of missing input: template_ventricle_2.5mm+tlrc
** in/out view change: NO-DSET -> +orig: mask_import_Tvent
This is not a file distributed with AFNI, so it would have to exist on your computer; how one could make this file is actually described at the top of this example 11b section here in the AP help:
[
afni.nimh.nih.gov]
+ these error message also relates to that same issue (a mask can't be made because the file doesn't exist):
** 3dinfo -d3: cannot get val list from NO-DSET NO-DSET NO-DSET, for dset template_ventricle_2.5mm+tlrc
** bad dims for -mask_import dataset:
template_ventricle_2.5mm+tlrc
import dims = None, analysis dims = [2.5, 2.5, 2.5]
** script creation failure for block 'mask'
To solve the above issue, you could follow the instructions at the top of the help section, which I noted above and copy+paste here:
AFNI currently does not have a good program to extract ventricles.
But it can make a CSF mask that includes them. So without FreeSurfer,
one could import a ventricle mask from the template (e.g. for TT space,
using TT_desai_dd_mpm+tlrc). For example, assuming Talairach space
(and a 2.5 mm^3 final voxel grid) for the analysis, one could create a
ventricle mask as follows:
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
Running that 3dcalc and 3dresample command should create template_ventricle_2.5mm, which you should then be able to use in your AP command.
--pt
