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adhdmedchal_makefsf_L2_GNGreg_mem11032019
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adhdmedchal_makefsf_L2_GNGreg_mem11032019
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#!/bin/sh
### FabScript runs FEAT for several runs and several subjects
### created by Adam, modified and commented by Fab
### v3 2004-10-07
### then by karin, 2-18-2005
### then by jess, 5-26-2006
### Again by Jess, 7-6-06 to include a junk variable in feat analysis
### again by jess 9-7-2006 to add a dated folder for FEATs
### again by jess 11-2-06 because need to redo using FLAME level 1 instead of fixed effects and only have one contrast (pos) because neg is done automatically
### now, by mackenzie 11-03-2019 to adapt to the ADHD Med Chal Study at UNC
###This version to run higher-level feat to average two runs of a task within each subject (LEVEL 2)
###F doanalysis command runs the other commands
doanalysis()
{
###F go in the directory subject/analysis
###F this saves the feat-reports in the analysis directory
###mkdir /space/raid4/data/poldrack/schizkids/$SUB/analysis/stop_signal/$FEAT_FOLDER/$RUN_NAME
#cd /space/raid4/data/poldrack/schizkids/$SUB/analysis/stop_signal/$FEAT_FOLDER/
cd /proj/cohenlab/projects/ADHDMedChal/ADHDMC_2019_Process/data_GLM/
###F the sed command replaces an old string in a text by a new string
###F read http://www.freeos.com/guides/lsst/ch07sec11.html for info
###F sed takes the FEAT text (yourdesign.fsf is a text) and changes the parameters
###F our model for MirrorReading experiment is Subject-11A/analysis/newrun1.fsf
###F the model for schizkids stop_signal is subject 30002_2/analysis/stop_signal/feats_11-2-06/ss_higher_level_feat.gfeat/design.fsf
###F NB: for shell, numbers starts from zero, not from 1
### [ADHD MED CHAL] the model for L2 is sub-1034_ses-01_gng_L2.fsf
### THIS USES RUN 01 and RUN 02 BY DEFAULT. WILL NEED TO MAKE THE OTHERS MANUALLY!!
############################## My Runs ##########################################
###F changes to be made for ss_higher_level_feat.gfeat (0)
#sed -e "s/30002_2/${SUB}/" -e "s/feats_11-2-06/${FEAT_FOLDER[0]}/" -e "s/ss_higher_level_feat/${RUN_NAME[0]}/" -e "s/30002_2/${SUB}/" -e "s/ss_run1.feat/${FIRST_INPUT_NAME[0]}/" -e "s/30002_2/${SUB}/" -e "s/ss_run2.feat/${SECOND_INPUT_NAME[0]}/" -e "s/30002_2/${EV_TITLE}/" -e "s/30002_2/${CONTRAST}/" /space/raid4/data/poldrack/schizkids/30002_2/analysis/stop_signal/feats_11-2-06/ss_higher_level_feat.gfeat/design.fsf > ${DESIGN_NAME[0]}.fsf
sed -e "s/sub-1034/${SUB}/g" -e "s/run-01/${FIRST_INPUT}/g" -e "s/run-02/${SECOND_INPUT}/g" -e "s/ses-01/${SESSMRI}/g" /proj/cohenlab/projects/ADHDMedChal/ADHDMC_2019_Process/data_GLM/sub-1034_ses-01_gng_L2.fsf > ${DESIGN_NAME}.fsf
### runs feat on each design matrix
#for j in 0; do feat ${DESIGN_NAME[j]}; done
}
############################## My Subjects ##########################################
########## [UCLA EXAMPLE SUBJECT] SUBJECT 30002_2 ##############
SUB="30002_2"
FEAT_FOLDER=(feats_11-2-06)
RUN_NAME=(ss_higher_level_feat)
FIRST_INPUT_NAME=(ss_run1.feat)
SECOND_INPUT_NAME=(ss_run2.feat)
EV_TITLE="30002_2"
CONTRAST="30002_2"
DESIGN_NAME=(design_higher_level_feat)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
#doanalysis
########## [ADHD MED CHAL] SUBJECT 1006 ##############
SUB="sub-1006"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1006_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
#doanalysis
########## [ADHD MED CHAL] SUBJECT 1005 SESSION 2 ##############
SUB="sub-1005"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1005_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1013 SESSION 2 ##############
SUB="sub-1013"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1013_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1016 SESSION 2 ##############
SUB="sub-1016"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1016_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1019 SESSION 2 ##############
SUB="sub-1019"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1019_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1020 SESSION 2 ##############
SUB="sub-1020"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1020_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1022 SESSION 2 ##############
SUB="sub-1022"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1022_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1023 SESSION 2 ##############
SUB="sub-1023"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1023_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1024 SESSION 2 ##############
SUB="sub-1024"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1024_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1025 SESSION 2 ##############
SUB="sub-1025"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1025_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1026 SESSION 2 ##############
SUB="sub-1026"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1026_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1027 SESSION 2 ##############
SUB="sub-1027"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1027_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1028 SESSION 2 ##############
SUB="sub-1028"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1028_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1029 SESSION 2 ##############
SUB="sub-1029"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1029_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1031 SESSION 2 ##############
SUB="sub-1031"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1031_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1034 SESSION 2 ##############
SUB="sub-1034"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1034_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1036 SESSION 2 ##############
SUB="sub-1036"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1036_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1038 SESSION 2 ##############
SUB="sub-1038"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1038_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1040 SESSION 2 ##############
SUB="sub-1040"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1040_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1042 SESSION 2 ##############
SUB="sub-1042"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1042_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1048 SESSION 2 ##############
SUB="sub-1048"
SESSMRI=(ses-02)
FIRST_INPUT=(run-02)
SECOND_INPUT=(run-03)
DESIGN_NAME=(sub-1048_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1049 SESSION 2 ##############
SUB="sub-1049"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1049_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1050 SESSION 2 ##############
SUB="sub-1050"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1050_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1064 SESSION 2 ##############
SUB="sub-1064"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1064_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1065 SESSION 2 ##############
SUB="sub-1065"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1065_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1067 SESSION 2 ##############
SUB="sub-1067"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1067_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1068 SESSION 2 ##############
SUB="sub-1068"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1068_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1070 SESSION 2 ##############
SUB="sub-1070"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1070_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1071 SESSION 2 ##############
SUB="sub-1071"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1071_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1077 SESSION 2 ##############
SUB="sub-1077"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1077_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1081 SESSION 2 ##############
SUB="sub-1081"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1081_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1083 SESSION 2 ##############
SUB="sub-1083"
SESSMRI=(ses-02)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1083_ses-02_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1010 SESSION 1 ##############
SUB="sub-1010"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1010_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1026 SESSION 1 ##############
SUB="sub-1026"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1026_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1031 SESSION 1 ##############
SUB="sub-1031"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1031_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1038 SESSION 1 ##############
SUB="sub-1038"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1038_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1042 SESSION 1 ##############
SUB="sub-1042"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1042_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis
########## [ADHD MED CHAL] SUBJECT 1048 SESSION 1 ##############
SUB="sub-1048"
SESSMRI=(ses-01)
FIRST_INPUT=(run-01)
SECOND_INPUT=(run-02)
DESIGN_NAME=(sub-1048_ses-01_gng_L2)
###F if you don't want to process a sub, deactivate "doanalysis" using "#"
doanalysis