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April 20, 2022 07:25PM
Hi i try to do resting-state fmri analysis for a 25 subject. when i run the example of afni_proc.py 11b i get this output:

osman@osman-VirtualBox:~/sub08224$ 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
++ applying anaticor without label, using 3dSeg mask
** warning: removing first 2 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
-- will use min outlier volume as motion base
** cannot evaluate view of missing input: template_ventricle_2.5mm+tlrc
** in/out view change: NO-DSET -> +orig: mask_import_Tvent
-- tcat: reps is now 195
++ updating polort to 3, from run len 390.0 s
-- using non-linear template alignment
-- volreg: using base dset vr_base_min_outlier+orig
++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 2.5 mm tlrc voxels
-- applying anat warps to 1 dataset(s): anat
++ mask: using epi_anat mask in place of EPI one
-- masking: group anat = 'TT_N27+tlrc', exists = 1
** 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'
----------------------------------------------------------------------
** failed command (create_script):

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
----------------------------------------------------------------------
Subject Author Posted

afni_proc.py example 11b

osman April 20, 2022 07:25PM

Re: afni_proc.py example 11b

ptaylor April 21, 2022 09:55AM

Re: afni_proc.py example 11b Attachments

osman April 21, 2022 05:06PM

Re: afni_proc.py example 11b

ptaylor April 21, 2022 05:12PM

Re: afni_proc.py example 11b

osman April 21, 2022 05:48PM

Re: afni_proc.py example 11b Attachments

ptaylor April 21, 2022 09:28PM

Re: afni_proc.py example 11b Attachments

osman April 28, 2022 12:15PM

Re: afni_proc.py example 11b Attachments

ptaylor April 28, 2022 12:42PM

Re: afni_proc.py example 11b

rick reynolds April 28, 2022 01:06PM

Re: afni_proc.py example 11b Attachments

osman April 28, 2022 07:27PM

Re: afni_proc.py example 11b

osman April 28, 2022 07:30PM

Re: afni_proc.py example 11b

ptaylor April 29, 2022 08:49AM

Re: afni_proc.py example 11b

osman April 29, 2022 10:23AM

Re: afni_proc.py example 11b

ptaylor April 29, 2022 02:52PM



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