add stuff

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

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"