Hi,
I'm trying to run a single subject surface analysis. I ran the script but it ended with this error message:
Done.
foreach hemi ( lh rh )
foreach run ( 01 )
3dVol2Surf -spec /usr/local/freesurfer/subjects/DM/SUMA/DM_lh.spec -sv DM_SurfVol_Alnd_Exp+orig -surf_A smoothwm -surf_B pial -f_index nodes -f_steps 10 -map_func ave -oob_value 0 -grid_parent pb02.DM.r01.volreg+tlrc -out_niml pb03.DM.lh.r01.surf.niml.dset
** ERROR: failed to open -sv dataset, DM_SurfVol_Alnd_Exp+orig
I suppose it's looking for the surface aligned with the experiment anatomy, is it right? Unfortunately I don't have any anatomical scan collected during the same session of my experiment... Is there a way in which I can run the analysis without using this anatomical scan?
Thanks
Francesca
#!/usr/bin/env tcsh
# created by uber_subject.py: version 0.36 (April 5, 2013)
# creation date: Thu Apr 16 15:13:01 2015
# set data directories
set top_dir = /usr/local
set anat_dir = $top_dir/freesurfer/subjects/DM/SUMA
set epi_dir = $top_dir/experiments/fcMovieCategory/localizer/DM
set stim_dir = $top_dir/experiments/fcMovieCategory/localizer/DM/event_files
# set subject and group identifiers
set subj = DM
set group_id = VisualLocalizer
# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg surf blur mask scale regress \
-copy_anat $anat_dir/DM_SurfVol+orig \
-tcat_remove_first_trs 2 \
-dsets $epi_dir/DM_localizer_siemens_run1_al+orig.HEAD \
-surf_anat $anat_dir/DM_SurfVol+orig \
-surf_spec $anat_dir/DM_?h.spec \
-align_opts_aea -giant_move \
-volreg_align_to third \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 3.0 \
-regress_stim_times \
$stim_dir/stim.01.fixation.1D \
$stim_dir/stim.02.face.1D \
$stim_dir/stim.03.house.1D \
$stim_dir/stim.04.body.1D \
$stim_dir/stim.05.tool.1D \
$stim_dir/stim.06.texture.1D \
-regress_stim_labels \
fixation face house body tool texture \
-regress_basis 'GAM' \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_opts_3dD \
-gltsym 'SYM: face-fixation' -glt_label 1 face-fixation \
-gltsym 'SYM: house-fixation' -glt_label 2 house-fixation \
-gltsym 'SYM: body-fixation' -glt_label 3 body-fixation \
-gltsym 'SYM: face-body' -glt_label 4 face-body \
-gltsym 'SYM: (0.2*face \
-0.2*house-0.2*body-0.2*tool-0.2*texture)-fixation' -glt_label 5 \
FHBTT-fixation \
-gltsym 'SYM: tool-fixation' -glt_label 6 tool-fixation \
-gltsym 'SYM: texture-fixation' -glt_label 7 texture-fixation \
-gltsym 'SYM: face-house' -glt_label 8 face-house \
-gltsym 'SYM: house-face' -glt_label 9 house-face \
-gltsym 'SYM: body-face' -glt_label 10 body-face \
-regress_reml_exec \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts
