AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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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