forked from tommysprague/preproc_shFiles
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsurf_to_vol_SEalign.sh
185 lines (130 loc) · 6.49 KB
/
surf_to_vol_SEalign.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
#!/bin/bash
# run like
# surf_to_vol_SEalign.sh vRF_tcs CC RF1 blur 5
# -OR
# surf_to_vol_SEalign.sh vRF_tcs CC RF1 surf
# smooth on the SUMA surface
#
# adapted from surfsmooth.sh, from KD
# adapted from surfsmooth_tcs.sh, from TCS
# TCS, 4/10/2017
# UDPATED TCS 7/21/2017 for PRISMA Multiband data (processed w/ afni_proc.py)
# UPDATED TCS 9/11/2017 for sub-session spin-echo alignment
#
# attempts to do parallel processing (this step is *very* slow)
#
# assumes you have a subj directory like:
# SUBJ
# - ANATSUBJ [symlink to shared SUBJECTS_DIR]
# --- SUMA
# ------ ANATSUBJ_lh/rh.spec
# ------ ANATSUBJ_SurfVol+orig.
# - FUNCsess
# --- SUBJ_FUNCsess.results/pb0X.SUBJ_FUNCsess.?h.r0?.[surf/blur].niml.dset
#
# data have already been smoothed in the surface from afni_proc.py, so here we're just projecting back into volume
#
# Proceeds by doing this for LH, RH independently (due to how SUMA handles things),
# then combining these images and saving as a new _ss.nii.gz dataset
#
#
# meant to be run from subj ROOT directory
#
# At conclusion of vol --> surf --> vol transforms, resulting nii.gz's are poorly built - they're
# missing info about # TRs and they're written to 5D
# - loops through runs within session and 'squeezes' the nifti using preproc_mFiles toolbox niftiSqueeze
# - looks up TR from the $FUNCSESS and uses that to reset TR value in nifti
# - transforms data to RAI, which is the final space we want *all* data in
#
# TODO: make a version of this that projects into a different gridparent
# DATAROOT is global variable set before running scripts
#DATAROOT=/deathstar/data
#ROOT=/deathstar/data/vRF_tcs
EXPTDIR=$1
ROOT=$DATAROOT/$EXPTDIR
SUBJ=$2
FUNCSESS=$3
ANATSUBJ=${SUBJ}anat
#TR=$4 # TODO: figure out how to get this dynamically per run (hard w/ parallel command...)
SOURCESTR=$4
FWHM=$5
#CORES=8
ALL_PREPROC_DIR=$(ls -d $ROOT/$SUBJ/$FUNCSESS/${SUBJ}_${FUNCSESS}*.results)
# OR ss5
if [[ $SOURCESTR = blur ]]; then
#statements
PBNUM=pb04
FUNCSUFFIX=ss$FWHM
elif [[ $SOURCESTR = surf ]]; then
#statements
PBNUM=pb03
FUNCSUFFIX=surf
fi
#FUNCSUFFIX=ss5 # when saving (bar_widht_1_XXX), what to use? usually surf or ss$FWHM
#SOURCESTR=blur # pb0X.$SOURCESTR.niml.dset (typically blur or surf)
#PBNUM=pb04 # pb03, surf OR pb04, blur
FUNCPREFIX_lh=$ROOT/$SUBJ/$FUNCSESS/${SUBJ}_${FUNCSESS}*.results/$PBNUM.${SUBJ}_${FUNCSESS}*.lh.r*.$SOURCESTR.niml.dset
FUNCPREFIX_rh=$ROOT/$SUBJ/$FUNCSESS/${SUBJ}_${FUNCSESS}*.results/$PBNUM.${SUBJ}_${FUNCSESS}*.rh.r*.$SOURCESTR.niml.dset
FUNCPREFIX=${SUBJ}_${FUNCSESS} #"pb04.CCpp2_CMRR4_unwarp_ss.lh.r03.blur.niml.dset"
cd $ROOT/$SUBJ/$FUNCSESS
# need this to have all the runs (within their individual .results directories)
# should include: pb03.CC_MGSMap1.lh.r01
rm $ROOT/$SUBJ/$FUNCSESS/func_list_lh.txt; for FUNC in $FUNCPREFIX_lh; do printf "%s\n" $FUNC | cut -f -5 -d . >> $ROOT/$SUBJ/$FUNCSESS/func_list_lh.txt; done
rm $ROOT/$SUBJ/$FUNCSESS/func_list_rh.txt; for FUNC in $FUNCPREFIX_rh; do printf "%s\n" $FUNC | cut -f -5 -d . >> $ROOT/$SUBJ/$FUNCSESS/func_list_rh.txt; done
# list of runs
rm $ROOT/$SUBJ/$FUNCSESS/run_list.txt; for FUNC in $FUNCPREFIX_lh; do printf "%s.%s\n" $FUNC | cut -f 5 -d . >> $ROOT/$SUBJ/$FUNCSESS/run_list.txt; done
# list of output filenames
# want it to look like : CC_MGSMap1.r01 ($SUBJ_$FUNCSESS.$RUN)
# just make it, don't try to chop up (too tricky w/ SE)
#rm $ROOT/$SUBJ/$FUNCSESS/func_list.txt; for FUNC in $FUNCPREFIX_lh; do printf "%s.%s\n" $FUNC | cut -f 3,5 -d . >> $ROOT/$SUBJ/$FUNCSESS/func_list.txt; done
rm $ROOT/$SUBJ/$FUNCSESS/func_list.txt; for FUNC in $(cat run_list.txt); do printf "${SUBJ}_$FUNCSESS.$FUNC\n" $FUNC >> $ROOT/$SUBJ/$FUNCSESS/func_list.txt; done
# move a volreg run (pb02) to FUNCSESS, rename appropriately`
#3dcopy $PREPROC_DIR/pb02.${SUBJ}_${FUNCSESS}.r01.volreg+orig $ROOT/$SUBJ/$FUNCSESS/${FUNCPREFIX}_r01.nii.gz
3dcopy $(ls $ROOT/$SUBJ/$FUNCSESS/${SUBJ}_${FUNCSESS}*.results/pb02.${SUBJ}_${FUNCSESS}*.r01.volreg+orig* | head -1) $ROOT/$SUBJ/$FUNCSESS/${FUNCPREFIX}_r01.nii.gz
TR=$(3dinfo -tr $ROOT/$SUBJ/$FUNCSESS/${FUNCPREFIX}_r01.nii.gz)
# how many runs? that's how many cores we want
CORES=$(cat $ROOT/$SUBJ/$FUNCSESS/func_list.txt | wc -l)
cd $ROOT/$SUBJ
# something like this works: cat ./func_list_lh.txt | parallel -C / echo printf "%s" {-1} | cut -f 3- -d .
# convert this back into vol (unsmoothed)
cat ./$FUNCSESS/func_list_lh.txt | parallel -P $CORES -C / \
3dSurf2Vol \
-spec ./${ANATSUBJ}/SUMA/${ANATSUBJ}_lh.spec \
-surf_A smoothwm \
-surf_B pial \
-sv ./${ANATSUBJ}/SUMA/${ANATSUBJ}_SurfVol+orig. \
-grid_parent ./${FUNCSESS}/${FUNCPREFIX}_r01.nii.gz \
-map_func ave \
-f_steps 10 \
-prefix ./${FUNCSESS}/{-1}_$FUNCSUFFIX.nii.gz \
-sdata ./${FUNCSESS}/{-2}/{-1}.$SOURCESTR.niml.dset
# convert this back into vol (unsmoothed)
cat ./$FUNCSESS/func_list_rh.txt | parallel -P $CORES -C / \
3dSurf2Vol \
-spec ./${ANATSUBJ}/SUMA/${ANATSUBJ}_rh.spec \
-surf_A smoothwm \
-surf_B pial \
-sv ./${ANATSUBJ}/SUMA/${ANATSUBJ}_SurfVol+orig. \
-grid_parent ./${FUNCSESS}/${FUNCPREFIX}_r01.nii.gz \
-map_func ave \
-f_steps 10 \
-prefix ./${FUNCSESS}/{-1}_$FUNCSUFFIX.nii.gz \
-sdata ./${FUNCSESS}/{-2}/{-1}.$SOURCESTR.niml.dset
# RENAME THEM TO SOMETHING SENSICAL
# TODO: figure out how to dynamically change pb03/pb04?
cat ./$FUNCSESS/run_list.txt | parallel -P $CORES \
mv ./$FUNCSESS/$PBNUM.$FUNCPREFIX*.rh.{}_$FUNCSUFFIX.nii.gz ./$FUNCSESS/rh_${FUNCPREFIX}.{}_$FUNCSUFFIX.nii.gz
#mv $(ls ./$FUNCSESS/$PBNUM.$FUNCPREFIX*.rh.{}_$FUNCSUFFIX.nii.gz | head 1) ./$FUNCSESS/rh_${FUNCPREFIX}.{}_$FUNCSUFFIX.nii.gz
cat ./$FUNCSESS/run_list.txt | parallel -P $CORES \
mv ./$FUNCSESS/$PBNUM.$FUNCPREFIX*.lh.{}_$FUNCSUFFIX.nii.gz ./$FUNCSESS/lh_${FUNCPREFIX}.{}_$FUNCSUFFIX.nii.gz
cat ./$FUNCSESS/func_list.txt | parallel -P $CORES \
3dcalc -prefix ./${FUNCSESS}/{}_$FUNCSUFFIX.nii.gz -a ./${FUNCSESS}/lh_{}_$FUNCSUFFIX.nii.gz -b ./${FUNCSESS}/rh_{}_$FUNCSUFFIX.nii.gz -expr "'(a+b)/(notzero(a)+notzero(b))'"
# NOTE: very hard to get this to work w/ parallel, so dropping it for now
#squeeze & reset TR [[_surf]]
for FUNC in $(cat ./$FUNCSESS/func_list.txt);
do
matlab -nosplash -nodesktop -r "setup_paths_RFs; nii=niftiRead('./${FUNCSESS}/${FUNC}_$FUNCSUFFIX.nii.gz'); nii=niftiSqueeze(nii,${TR}); niftiWrite(nii,'./${FUNCSESS}/${FUNC}_$FUNCSUFFIX.nii.gz'); exit;";
done
# finally, put them in RAI (preferred by vista; all ROIs in this orientation)
cat ./$FUNCSESS/func_list.txt | parallel -P $CORES \
3dresample -overwrite -prefix ./${FUNCSESS}/{}_$FUNCSUFFIX.nii.gz -orient rai -inset ./${FUNCSESS}/{}_$FUNCSUFFIX.nii.gz