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neuroimagen:bioface_tbss

TBSS (proyecto BIOFACE)

tbss_1_preproc

[osotolongo@detritus bioface]$ mkdir bftbss
[osotolongo@detritus bioface]$ cd bftbss/
[osotolongo@detritus bftbss]$ cp ../working/*FA* ./
[osotolongo@detritus bftbss]$ tbss_1_preproc *.nii.gz
processing 0002_dti_FA
processing 0003_dti_FA
processing 0004_dti_FA
processing 0005_dti_FA
processing 0006_dti_FA
...
...
...

tbss_2_reg

[osotolongo@detritus bftbss]$ tbss_2_reg -T
0002_dti_FA_FA_to_target
0003_dti_FA_FA_to_target
0004_dti_FA_FA_to_target
0005_dti_FA_FA_to_target
0006_dti_FA_FA_to_target
...
...
...

tbss_3_postreg

[osotolongo@detritus bftbss]$ tbss_3_postreg -T
using pre-chosen target for registration
transforming all FA images into MNI152 space
0002_dti_FA_FA
0003_dti_FA_FA
0004_dti_FA_FA
0005_dti_FA_FA
...
....
...

tbss_4_prestats

[osotolongo@detritus bftbss]$ tbss_4_prestats 0.2
creating skeleton mask using threshold 0.2
creating skeleton distancemap (for use in projection search)
projecting all FA data onto skeleton
 
now run stats - for example:  
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V
(after generating design.mat and design.con)

Test con lenguaje

[osotolongo@detritus bftbss]$ head bioface_data.csv 
PSubject,Subject,Edad,Sexo,Estudios,FACEmem
B001,0001,64,1,11,13
B002,0002,53,2,9,48
B003,0003,60,2,8,10
B004,0004,64,2,7,21
B005,0005,62,2,16,30
B006,0006,64,2,5,25
B007,0007,62,2,11,39
B008,0008,58,2,11,45
B009,0009,51,2,11,28
[osotolongo@detritus bftbss]$ grep -f subjects.list bioface_data.csv > sub_bioface_data.csv
[osotolongo@detritus bftbss]$ head sub_bioface_data.csv
B002,0002,53,2,9,48
B003,0003,60,2,8,10
B004,0004,64,2,7,21
B005,0005,62,2,16,30
B006,0006,64,2,5,25
B007,0007,62,2,11,39
B008,0008,58,2,11,45
B009,0009,51,2,11,28
B010,0010,62,2,6,17
B011,0011,54,2,16,67

Redo

[osotolongo@detritus bftbss]$ grep -v "`awk -F',' '{print $2}' sub_bioface_data.csv`" subjects.list 
0032

Borro el 0032 de subjects.list, y

[osotolongo@detritus bftbss]$ for x in `cat subjects.list`; do cp ../working/${x}_dti_FA.nii.gz ./; done
[osotolongo@detritus bftbss]$ awk -F"," '{print $3,$4,$5,$6}' sub_bioface_data.csv > comp_data.dat
[osotolongo@detritus bftbss]$ head comp_data.dat
53 2 9 48
60 2 8 10
64 2 7 21
62 2 16 30
64 2 5 25
62 2 11 39
58 2 11 45
51 2 11 28
62 2 6 17
54 2 16 67
[osotolongo@detritus bftbss]$ Text2Vest comp_data.dat design.mat
[osotolongo@detritus bftbss]$ head design.mat
/NumWaves 4
/NumPoints 83
/Matrix
53 2 9 48
60 2 8 10
64 2 7 21
62 2 16 30
64 2 5 25
62 2 11 39
58 2 11 45
[osotolongo@detritus bftbss]$ cat model.con
0 0 0 1
0 0 0 -1
[osotolongo@detritus bftbss]$ Text2Vest model.con design.con
[osotolongo@detritus bftbss]$ cat design.con
/NumWaves 4
/NumPoints 2
/Matrix
0 0 0 1
0 0 0 -1

y repito todos los pasos.

[osotolongo@detritus bftbss]$ tbss_1_preproc *.nii.gz
...
[osotolongo@detritus bftbss]$ tbss_2_reg -T
...
[osotolongo@detritus bftbss]$ tbss_3_postreg -T
...
[osotolongo@detritus bftbss]$ tbss_4_prestats 0.2
...

Statistics

ahora ejecuto el randomise,

[osotolongo@detritus bftbss]$ randomise -i stats/all_FA_skeletonised.nii.gz -o bftbss -m stats/mean_FA_skeleton_mask -d design.mat -t design.con -n 1000 --T2 -V
randomise options: -i stats/all_FA_skeletonised.nii.gz -o bftbss -m stats/mean_FA_skeleton_mask -d design.mat -t design.con -n 1000 --T2 -V 
Loading Data: 
Data loaded
4.97831e+111 permutations required for exhaustive test of t-test 1
Doing 1000 random permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
Starting permutation 4
Starting permutation 5
...
...
...

Vamos a mirarlo,

[fsluser@FSLVm7_64 bftbss]$ fslview_deprecated /usr/local/fsl/data/standard/MNI152_T1_1mm stats/mean_FA_skeleton -l Green -b 0.2,0.7 bftbss_tfce_corrp_tstat1 -l Red-Yellow -b 0.95,1

y hacemos un tbss_fill,

[osotolongo@detritus bftbss]$ tbss_fill bftbss_tfce_corrp_tstat1 0.95 stats/mean_FA tbss_fill

para verlo mejor,

[fsluser@FSLVm7_64 bftbss]$ fslview_deprecated stats/mean_FA stats/mean_FA_skeleton -l Green -b 0.2,0.8 tbss_fill -l Red-Yellow -b 0.05,0.2

neuroimagen/bioface_tbss.txt · Last modified: 2020/09/02 10:22 by osotolongo