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

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evansorenson
August 23, 2021 01:43PM
Hello,

Did you ever figure this out? I have the same question. I have 8 different stimuli and 8 runs. Our input is a concatenation of the 8 runs using 3dTproject and we manually setup a -concat flag to tell 3dDeconvolve where the run breaks are for the 8 runs. I have 3dlss setup to loop through each stimulus and model only that specific condition with the stim_type_IM option. 

        3dTproject -input $(ls ${data}/sub-${subject}_task-ThalHi_run-*space-MNI152NLin2009cAsym_desc-preproc_bold*.nii.gz | sort -V) \
        -mask combined_mask+tlrc.BRIK \
        -polort 3 \
        -ort nuisance.1D \
        -prefix errts.nii.gz

        3dDeconvolve -input errts.nii.gz \
        -concat '1D: 0 216 432 648 864 1080 1296 1512' \
        -mask combined_mask+tlrc.BRIK \
        -censor censor.1D \
        -x1D dcb.xmat.1D \
        -local_times \
        -num_stimts 8 \
        -stim_times_IM  1 $stimuli[$i].1D.txt 'TENT(6, 20.4, 9)' -stim_label 1 $stimuli[$i] \
        -stim_times  2 $stimuli[get_stimuli_index($i, 1)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 2 $stimuli[get_stimuli_index($i, 1)] \
        -stim_times  3 $stimuli[get_stimuli_index($i, 2)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 3 $stimuli[get_stimuli_index($i, 2)] \
        -stim_times  4 $stimuli[get_stimuli_index($i, 3)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 4 $stimuli[get_stimuli_index($i, 3)] \
        -stim_times  5 $stimuli[get_stimuli_index($i, 4)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 5 $stimuli[get_stimuli_index($i, 4)] \
        -stim_times  6 $stimuli[get_stimuli_index($i, 5)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 6 $stimuli[get_stimuli_index($i, 5)] \
        -stim_times  7 $stimuli[get_stimuli_index($i, 6)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 7 $stimuli[get_stimuli_index($i, 6)] \
        -stim_times  8 $stimuli[get_stimuli_index($i, 7)].1D.txt 'TENT(6, 20.4, 9)' -stim_label 8 $stimuli[get_stimuli_index($i, 7)] \
        -x1D_stop \
        -allzero_OK \
        -jobs 4

        3dLSS -input errts.nii.gz \
        -matrix dcb.xmat.1D \
        -prefix dcb.LSS \
        -overwrite -verb
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Subject Author Posted

3dLSS design matrix input

jyaros September 05, 2020 01:29PM

Re: 3dLSS design matrix input

jyaros September 05, 2020 03:33PM

Re: 3dLSS design matrix input

jyaros September 11, 2020 02:52PM

Re: 3dLSS design matrix input

evansorenson August 23, 2021 01:43PM

Re: 3dLSS design matrix input

gang August 26, 2021 08:09AM