diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index 41a56649..435d6324 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -7,13 +7,11 @@ # 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/ +# exemple run: +# In a terminal, path /home/jlefortb/narps_open_pipelines, run: +# tcsh /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/ -""" @@ -67,10 +65,43 @@ afni_proc.py \ -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] +# # 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 +# # convert BRIK to nii +# 3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +# 3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc + + + +# run this file with "tcsh 6VV2_afni_proc.simple" + +# create 1D stimuli file : +# import pandas as pd + +# df_run1 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-01_events.tsv", sep="\t") +# df_run1 = df_run1[["onset", "gain", "loss"]].T +# df_run2 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-02_events.tsv", sep="\t") +# df_run2 = df_run2[["onset", "gain", "loss"]].T +# df_run3 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-03_events.tsv", sep="\t") +# df_run3 = df_run3[["onset", "gain", "loss"]].T +# df_run4 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-04_events.tsv", sep="\t") +# df_run4 = df_run4[["onset", "gain", "loss"]].T + +# df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) +# df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] +# df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) +# df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + +# df_gain.to_csv('/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/times+gain.1D', +# sep='\t', index=False, header=False) +# df_loss.to_csv('/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/times+loss.1D', +# sep='\t', index=False, header=False)