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Dear AFNI users-

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Sincerely, AFNI HQ

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icupsy
October 01, 2019 05:02PM
Hi experts,
I try to run surface-based preprocessing on fMRI data. The script failed at reading input the surf.smooth.params.1D file and I check the file which turns out to be empty. I find a related topic on the board, it said that taking out some commands in SurfSmooth (-blurmaster and -detrend_master [afni.nimh.nih.gov]) but it did not work.
I tried to fix it but I can't find more related information. Could you please help me with it?

afni_proc.py

set subj = 18001
afni_proc.py -subj_id s0 -script proc.av -scr_overwrite \
-blocks tshift align tlrc volreg surf blur scale regress \
-copy_anat /Users/xc363/Desktop/ana/{$subj}/anat/{$subj}.anat.deob+orig \
-dsets \
/Users/xc363/Desktop/ana/{$subj}/func/{$subj}.run1+orig.HEAD \
/Users/xc363/Desktop/ana/{$subj}/func/{$subj}.run2+orig.HEAD \
/Users/xc363/Desktop/ana/{$subj}/func/{$subj}.run3+orig.HEAD \
/Users/xc363/Desktop/ana/{$subj}/func/{$subj}.run4+orig.HEAD \
-surf_anat /Users/xc363/Desktop/ana/{$subj}/freesurfer/SUMA/"$subj"_SurfVol.nii \
-surf_spec /Users/xc363/Desktop/ana/{$subj}/freesurfer/SUMA/"$subj"_?h.spec \
-tcat_remove_first_trs 0 \
-tlrc_base MNI152_T1_2009c+tlrc \
-align_opts_aea -cost lpc+ZZ \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 6.0 \
-regress_stim_times /Users/xc363/Desktop/ana/timeseries/ts_phon_A.1D \
/Users/xc363/Desktop/ana/timeseries/ts_phon_V.1D \
/Users/xc363/Desktop/ana/timeseries/ts_phon_AVC.1D \
/Users/xc363/Desktop/ana/timeseries/ts_phon_AVI.1D \
/Users/xc363/Desktop/ana/timeseries/ts_char_A.1D \
/Users/xc363/Desktop/ana/timeseries/ts_char_V.1D \
/Users/xc363/Desktop/ana/timeseries/ts_char_AVC.1D \
/Users/xc363/Desktop/ana/timeseries/ts_char_AVI.1D \
-regress_stim_labels phon_A phon_V phon_AVC phon_AVI char_A char_V \
char_AVC char_AVI \
-regress_basis 'BLOCK(20.8,1)' \
-regress_censor_motion 3.0 \
-regress_motion_per_run \
-regress_reml_exec \
-regress_make_ideal_sum sum_ideal.1D \
-regress_run_clustsim no \
-regress_opts_3dD \
-num_glt 2 \
-gltsysm 'SYM: phon_AVC -phon_AVI' -glt_label 1 'phon_con' \
-gltsysm 'SYM: char_AVC -char_AVI' -glt_label 2 'char_con'


This is the error message:
-- Error SurfSmooth (SUMA_SurfSmooth.c:1826):
Failed to read dset pb03.18001.lh.r01.surf.niml.dset
** ERROR: mri_read_ascii: can't read any valid data from file surf.smooth.params.1D
** FATAL ERROR: Can't read input file 'surf.smooth.params.1D'
Best,
Xin
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Subject Author Posted

Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

icupsy October 01, 2019 05:02PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

ptaylor October 02, 2019 10:59AM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

icupsy October 04, 2019 04:24PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

rick reynolds October 08, 2019 12:49PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

icupsy October 08, 2019 02:48PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

rick reynolds October 08, 2019 04:22PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

icupsy October 08, 2019 04:41PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

icupsy October 04, 2019 05:19PM

Re: Surface-based Preprocessing failed. surf.smooth.params.1D is empty and can't be read

rick reynolds October 02, 2019 11:30AM