Update generate_initial_data/README formating

Presently the crucial commands at the end of the https://git.fmrib.ox.ac.uk/falmagro/ukb_unconfound_v2/-/raw/master/generate_initial_data/README.md aren't treated as preformatted, and so all the commands are combined in a jumble. This PR makes these commands preformatted. (Also, one redirect is missing from the first line; that's fixed in the PR (but not in the example below).

E.g. compare

cat $subjDir/subj.txt | grep "^2" $CONFDATA/subj.txt cat $CONFDATA/subj.txt | awk -F "" '{print $2$3$4$5$6$7$8}' > $CONFDATA/subj_2.txt bool_files.sh $CONFDATA/subj.txt $SUBJECTS_DIR/subj.txt cp A_and_B.txt $CONFDATA/FS_subj.txt rm A_*txt B_not_A.txt

to

cat $subjDir/subj.txt | grep "^2" $CONFDATA/subj.txt
cat $CONFDATA/subj.txt | awk -F "" '{print $2$3$4$5$6$7$8}' > $CONFDATA/subj_2.txt
bool_files.sh $CONFDATA/subj.txt $SUBJECTS_DIR/subj.txt
cp A_and_B.txt $CONFDATA/FS_subj.txt
rm A_*txt B_not_A.txt

generate_initial_data/README.md

@@ -33,7 +33,8 @@ To run these scripts, you would need:
 
 - Run in this order:
 
-cat $subjDir/subj.txt | grep "^2" $CONFDATA/subj.txt
+```
+cat $subjDir/subj.txt | grep "^2" > $CONFDATA/subj.txt
 cat $CONFDATA/subj.txt | awk -F "" '{print $2$3$4$5$6$7$8}' > $CONFDATA/subj_2.txt
 bool_files.sh $CONFDATA/subj.txt $SUBJECTS_DIR/subj.txt
 cp A_and_B.txt $CONFDATA/FS_subj.txt
@@ -56,5 +57,6 @@ cd gen_STRUCTMOTION;      ./script_STRUCTMOTION.sh ;      cd ..
 cd gen_TE_fMRI;           ./script_TE_fMRI.sh ;           cd ..
 cd cd gen_SCALING;        ./script_SCALING.sh ;           cd ..
 cd gen_NEWEDDY;           ./script_NEWEDDY.sh ;           cd ..
+```
 
 - Change the permissions of the files in $CONFDATA