Hi-
A couple comments, but these won't really be solutions, likely, just features:
1) You have two backslashes, separated by a space, in a row at the end of your first line: "\ \"
I just spaced the text out a bit here (without that double slash):
3dDeconvolve \
-input /mnt/analysis/sub-${subject}/func/sub-${subject}_scale.nii.gz \
-censor censor.1D \
-mask /mnt/analysis/sub-${subject}/func/sub-01_task-cyber_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz \
-polort 2 \
-num_stimts 2 \
-stim_times_AM1 1 /mnt/analysis/sub-${subject}/beh/test.1D 'dmBLOCK(1)' \
-stim_label 1 full \
-stim_times_AM1 2 \
/mnt/analysis/sub-${subject}/beh/tf_asd_${subject}_equal_play.txt \
'dmBLOCK(1)' \
-stim_label 2 equal \
-ortvec /mnt/analysis/sub-${subject}/func/confound_test.1D \
-gltsym 'SYM: +full -equal' \
-glt_label 1 full_exclude-equal_play \
-gltsym 'SYM: +equal -full' \
-glt_label 2 equal_play-full_exclude \
-fout \
-tout \
-x1D X.xmat.1D \
-xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subject \
-errts errts.${subject} \
-bucket stats.$subject
2) for choosing a duration modulation specification, these notes will likely be helpful:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/statistics/deconvolve_block.html
We generally recommend using dmUBLOCK() with a negative argument, whose magnitude is the mean stim duration.
3) You might want to specify the number of GLTs explicitly:
-num_glt 2
4) Your current GLTs are just sign-flips of each other. You shouldn't need to do that---we do 2sided testing by default, unlike in some other software. The importance and relevance of 2-sided testing in most MRI analyses is described here:
Chen G, Cox RW, Glen DR, Rajendra JK, Reynolds RC, Taylor PA (2019). A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests. Human Brain Mapping 40:1037-1043.
https://pubmed.ncbi.nlm.nih.gov/30265768/
5) I don't see any motion regressors there in the model?
--pt
Edited 1 time(s). Last edit at 01/04/2023 05:08PM by ptaylor.
