diff --git a/narps_open/pipelines/team_27SS.firstlevel b/narps_open/pipelines/team_27SS.firstlevel new file mode 100755 index 00000000..f536b331 --- /dev/null +++ b/narps_open/pipelines/team_27SS.firstlevel @@ -0,0 +1,66 @@ +#!/bin/tcsh + +# created by team 6VV2, reproduced by Narps reproducibility team +# creation date: 22 June 2023 +# read and ran by team_6VV2.py script +# version afni used by the team : AFNI Version 19.0.01 Tiberius +# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +# Last update: June 2023 + +# Store arguments (directory where to store results, subjects list, directory where data are stored) +set expdir="$1" +set subject="$2" +set datadir="$3" + + +afni_proc.py \ + -script ${expdir}/proc.${subject}.block \ + -scr_overwrite \ + -subj_id ${subject} \ + -out_dir ${expdir}/${subject}.results.block \ + -dsets ${datadir}/${subject}/func/${subject}_task-MGT_run-01_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-02_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-03_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-04_bold.nii.gz \ + -copy_anat ${datadir}/${subject}/anat/${subject}_T1w.nii.gz \ + -anat_has_skull yes \ + -blocks despike tshift align tlrc volreg blur mask scale regress \ + -despike_new yes \ + -tlrc_base MNI152_T1_2009c+tlrc \ + -tlrc_NL_warp \ + -align_opts_aea \ + -giant_move \ + -cost lpc+ZZ \ + -volreg_align_to MIN_OUTLIER \ + -volreg_tlrc_warp \ + -volreg_align_e2a \ + -blur_in_automask \ + -regress_stim_times \ + ${datadir}/${subject}/func/times+gain.1D \ + ${datadir}/${subject}/func/times+loss.1D \ + -regress_stim_types AM2 \ + -regress_stim_labels \ + GAIN \ + LOSS \ + -regress_basis \ + 'BLOCK(4,1)' \ + -mask_apply anat \ + -regress_motion_per_run \ + -test_stim_files no \ + -regress_opts_3dD \ + -GOFORIT 8 \ + -jobs 6 \ + -regress_censor_motion 0.2 \ + -regress_apply_mot_types demean deriv \ + -regress_censor_first_trs 3 \ + -regress_est_blur_errts \ + -execute + + +# extract beta values +3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] +3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] + +# convert BRIK to nii +3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index f536b331..41a56649 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -7,6 +7,16 @@ # version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus # Last update: June 2023 +""" +exemple run: +In a terminal, path /home/jlefortb/narps_open_pipelines, run: +/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/, sub-001, /home/jlefortb/narps_open_pipelines/data/original/ds001734/ + + +""" + + + # Store arguments (directory where to store results, subjects list, directory where data are stored) set expdir="$1" set subject="$2"