forked from jrasero/Predicting-icns
-
Notifications
You must be signed in to change notification settings - Fork 0
/
shen_time_series_native_task_icafix.sh
113 lines (84 loc) · 4.28 KB
/
shen_time_series_native_task_icafix.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
#!/bin/bash
subjectlist=s1200_unrelated_r227.txt
DBHOST=https://db.humanconnectome.org
PROJECT=HCP_1200
REST_URL_PREFIX=$DBHOST/data/archive/projects/$PROJECT/subjects
hcp_fix_dir=~/fix1.065
while read -r subject;
do
echo "starting with subject $subject..."
mkdir -p data/data_task_icafix/sub-$subject
mkdir -p data/data_task_icafix/sub-$subject/temp
temp_path=data/data_task_icafix/sub-$subject/temp
subject_url_prefix=$REST_URL_PREFIX/$subject/experiments/${subject}_CREST/resources/${subject}_CREST/files
file_relative_path=MNINonLinear/Results/tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz
output_file=data/data_task_icafix/sub-$subject/temp/tfMRI_MOTOR_LR.nii.gz
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data_task_icafix/temp.log
rm -r data/data_task_icafix/sub-$subject
continue
fi
file_relative_path=MNINonLinear/xfms/standard2acpc_dc.nii.gz
output_file=data/data_task_icafix/sub-$subject/temp/standard2acpc_dc.nii.gz
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data_task_icafix/temp.log
rm -r data/data_task_icafix/sub-$subject
continue
fi
file_relative_path=T1w/T1w_acpc_dc.nii.gz
output_file=data/data_task_icafix/sub-$subject/temp/T1w_acpc_dc.nii.gz
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data_task_icafix/temp.log
rm -r data/data_task_icafix/sub-$subject
continue
fi
file_relative_path=MNINonLinear/Results/tfMRI_MOTOR_LR/Movement_Regressors.txt
output_file=data/data_task_icafix/sub-$subject/temp/Movement_Regressors.txt
#curl -u jrasero:hcp667333202 -o $output_file $subject_url_prefix/$file_relative_path
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data/data_task_icafix/temp.log
rm -r data/data_task_icafix/sub-$subject
continue
fi
file_relative_path=MNINonLinear/T1w_restore_brain.nii.gz
output_file=data/data_task_icafix/sub-$subject/temp/T1w_restore_brain.nii.gz
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data/data_task_icafix/temp.log
rm -r data_task_icafix/sub-$subject
continue
fi
file_relative_path=MNINonLinear/wmparc.nii.gz
output_file=data/data_task_icafix/sub-$subject/temp/wmparc.nii.gz
if curl -u jrasero:hcp667333202 -o $output_file --fail $subject_url_prefix/$file_relative_path; then
echo "URL for file exist"
else
echo "$subject does not have file $file_relative_path" >> data/data_task_icafix/temp.log
rm -r data/data_task_icafix/sub-$subject
continue
fi
echo "applying FIX-ICA..."
. $hcp_fix_dir/hcp_fix $temp_path/tfMRI_MOTOR_LR.nii.gz 2000
echo "resampling T1 to 2mm resolution..."
fsl5.0-flirt -in $temp_path/T1w_acpc_dc.nii.gz -ref $temp_path/T1w_acpc_dc.nii.gz -interp spline -applyisoxfm 2.0 -out $temp_path/T1w_acpc_dc_2mm.nii.gz
echo "changing fMRI to this T1 volume space..."
fsl5.0-applywarp -i $temp_path/tfMRI_MOTOR_LR_hp2000_clean.nii.gz -o $temp_path/tfMRI_MOTOR_LR_native.nii.gz -r $temp_path/T1w_acpc_dc_2mm.nii.gz \
-w $temp_path/standard2acpc_dc.nii.gz --interp=spline
echo "trasforming shen partellation to native space..."
fsl5.0-applywarp -i data/atlas/shen_2mm_268_parcellation.nii.gz -o $temp_path/shen_2mm_268_parcellation_native.nii.gz -r \
$temp_path/T1w_acpc_dc_2mm.nii.gz -w $temp_path/standard2acpc_dc.nii.gz --interp=nn
echo "extracting roi time series..."
fsl5.0-fslmeants -i $temp_path/tfMRI_MOTOR_LR_native.nii.gz -o data/data_task_icafix/sub-$subject/func_mean.txt \
--label=$temp_path/shen_2mm_268_parcellation_native.nii.gz --transpose
echo "subject $subject finished. Deleting temporary files..."
rm -r $temp_path
done < $subjectlist