neuroimagen:bioface_vbm
Table of Contents
VBM para BIOFACE y FACEMemory
El procedimiento general para VBM puede verse aqui y aqui. Esta pagina solo recoge las particularidades para BIOFACE.
Limpiando, cortando, pegando y haciendo la tabla
[osotolongo@detritus vbmmem]$ awk -F"," '{print $3","$5","$6","$7","$24}' ../bioface_np.csv > bioface_mem.csv [osotolongo@detritus vbmmem]$ head bioface_mem.csv Subjecte,Edad,Sexo,Años_Estudios,Resultado B001,64,1,11,13 B002,53,2,9,48 B003,60,2,8,10 B004,64,2,7,21 B005,62,2,16,30 B006,64,2,5,25 B007,62,2,11,39 B008,58,2,11,45 B009,51,2,11,28
que guay, mezcla de catalan,castellano, una Ñ! en los headers, pa volverse loco. Esto lo edito a mano.
[osotolongo@detritus vbmmem]$ head bioface_mem.csv PSubject,Edad,Sexo,Estudios,FACEmem B001,64,1,11,13 B002,53,2,9,48 B003,60,2,8,10 B004,64,2,7,21 B005,62,2,16,30 B006,64,2,5,25 B007,62,2,11,39 B008,58,2,11,45 B009,51,2,11,28
Los codigos estan aqui:
[osotolongo@detritus vbmmem]$ head ../bioface_mri.csv 0001;B001 0002;B002 0003;B003 0004;B004 0005;B005 0006;B006 0007;B007 0008;B008 0009;B009 0010;B010
Damos formato y unimos,
[osotolongo@detritus vbmmem]$ sed 's/;/,/g' ../bioface_mri.csv > bioface_join.csv [osotolongo@detritus vbmmem]$ sed -i '1iSubject,PSubject' bioface_join.csv [osotolongo@detritus vbmmem]$ head -n 5 bioface_join.csv Subject,PSubject 0001,B001 0002,B002 0003,B003 0004,B004 [osotolongo@detritus vbmmem]$ join -t"," -1 2 -2 1 bioface_join.csv bioface_mem.csv > bioface_data.csv [osotolongo@detritus vbmmem]$ head -n 5 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
Data Matrix
Aqui construimos la matriz de design.mat,
[osotolongo@detritus vbmmem]$ awk -F"," '{print $3,$4,$5,$6}' bioface_data.csv | tail -n+2 > vbm_data.dat [osotolongo@detritus vbmmem]$ head vbm_data.dat 64 1 11 13 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 [osotolongo@detritus vbmmem]$ Text2Vest vbm_data.dat design.mat [osotolongo@detritus vbmmem]$ head design.mat /NumWaves 4 /NumPoints 94 /Matrix 64 1 11 13 53 2 9 48 60 2 8 10 64 2 7 21 62 2 16 30 64 2 5 25 62 2 11 39
y el design.con,
[osotolongo@detritus vbmmem]$ cat contrast_model.txt 0 0 0 1 0 0 0 -1 [osotolongo@detritus vbmmem]$ Text2Vest contrast_model.txt design.con [osotolongo@detritus vbmmem]$ cat design.con /NumWaves 4 /NumPoints 2 /Matrix 0 0 0 1 0 0 0 -1
BET
Trae las imagenes de FS,
[osotolongo@detritus vbmmem]$ for x in `awk -F"," {'print $2'} bioface_data.csv | tail -n +2`; do get_fsbrain.sh bioface ${x} /nas/data/bioface/vbmmem/struc; done [osotolongo@detritus vbmmem]$ cd struc/ [osotolongo@detritus struc]$ for x in `awk -F"," {'print $2'} ../bioface_data.csv | tail -n +2`; do a="$a ${x}_struc ${x}_struc_brain"; done [osotolongo@detritus struc]$ slicesdir -o -e 0.1 $a
parece OK, asi que seguimos,
Template
[osotolongo@brick01 vbmmem]$ fslvbm_2_template -n 0001_struc 0002_struc 0003_struc ... ... ... 0093_struc 0094_struc 0095_struc Running segmentation: ID=10918 Running initial registration: ID=14147 Creating first-pass template: ID=21513 Running registration to first-pass template: ID=23634 Creating second-pass template: ID=44624 Study-specific template will be created, when complete, check results with: fslview struc/template_4D_GM and turn on the movie loop to check all subjects, then run: fslview /usr/local/fsl/data/standard/tissuepriors/avg152T1_gray struc/template_GM to check general alignment of mean GM template vs. original standard space template.
Esto no funciona.Hay problemas con FAST y estas imagenes. Workaround: Hacking FSLVBM
Traigo la GM de FS,
[osotolongo@detritus vbmmem]$ for x in `awk -F"," {'print $2'} bioface_data.csv | tail -n +2`; do get_gm.sh bioface ${x} /nas/data/bioface/vbmmem/struc; done
y hago el procedimiento alternativo
[osotolongo@detritus vbmmem]$ fslvbm_2_template_alt -n
PreProc
esta parte es igual,
$ fslvbm_3_proc
no tiene problemas porque lo que se hace es registrar al template comun que ya hemos creado.
randomise
Aqui es donde esta el meollo de los modelos. Podemos cambiar la variable de estudio, los contrastes, etc, siempre y cuando los sujetos a estudiar no cambien.
osotolongo@detritus:vbmmem$ head design_rlpp.mat /NumWaves 4 /NumPoints 94 /Matrix 64 1 11 13 53 2 9 48 60 2 8 10 64 2 7 21 62 2 16 30 64 2 5 25 62 2 11 39 osotolongo@detritus:vbmmem$ randomise -i stats/GM_mod_merg_s2.nii.gz -o stats/fslvbm_rlpp_s2 -m stats/GM_mask -d design_rlpp.mat -t design.con -n 5000 -T -V osotolongo@detritus:vbmmem$ autoaq -i stats/fslvbm_rlpp_s2_tfce_corrp_tstat1.nii.gz -t 0.95 -o reports/hoca_rlpp_s2_report.txt -a "Harvard-Oxford Cortical Structural Atlas" 2>/dev/null osotolongo@detritus:vbmmem$ autoaq -i stats/fslvbm_rlpp_s2_tfce_corrp_tstat1.nii.gz -t 0.95 -o reports/hosa_rlpp_s2_report.txt -a "Harvard-Oxford Subcortical Structural Atlas" 2>/dev/null
 |  |  |
||
=====[ stats/fslvbm_rlpp_s2_tfce_corrp_tstat1.nii.gz | Harvard-Oxford Cortical Structural Atlas ]===== ClusterIndex Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm) 16 14080 0.996 56 6 -16 -0.145 -26.3 -7.85 15 1133 0.984 12 -30 48 -1.25 -42.3 38.7 14 449 0.984 48 -56 32 52.2 -58.3 28.6 .... Structures to which each center of mass belongs to: 16,-0.145,-26.3,-7.85,Harvard-Oxford Cortical Structural Atlas,No label found! 15,-1.25,-42.3,38.7,Harvard-Oxford Cortical Structural Atlas,69% Cingulate Gyrus, posterior division, 23% Precuneous Cortex 14,52.2,-58.3,28.6,Harvard-Oxford Cortical Structural Atlas,41% Angular Gyrus, 30% Lateral Occipital Cortex, superior division .....
O cambiamos a otra variable,
osotolongo@detritus:vbmmem$ head design_rlpn.mat /NumWaves 4 /NumPoints 94 /Matrix 64 1 11 0 53 2 9 2 60 2 8 0 64 2 7 0 62 2 16 0 64 2 5 0 62 2 11 5 osotolongo@detritus:vbmmem$ randomise -i stats/GM_mod_merg_s2.nii.gz -o stats/fslvbm_rlpn_s2 -m stats/GM_mask -d design_rlpn.mat -t design.con -n 5000 -T -V
Amnesico y no amnesico
Amnesico,
[osotolongo@brick03 grupos]$ awk -F"," '{if ($2=="1") print $1}' amnesia.csv > amnesico.list [osotolongo@brick03 grupos]$ grep -f amnesico.list bioface_data.csv > amnesico_bioface_data.csv [osotolongo@brick03 grupos]$ header=`head -n 1 bioface_data.csv` [osotolongo@brick03 grupos]$ sed -i "1i$header" amnesico_bioface_data.csv [osotolongo@brick03 grupos]$ head amnesico_bioface_data.csv PSubject,Subject,Edad,Sexo,Estudios,FACEmem B002,0002,53,2,9,48 B004,0004,64,2,7,21 B005,0005,62,2,16,30 B010,0010,62,2,6,17 B012,0012,61,1,12,16 B013,0013,58,2,10,51 B014,0014,62,1,8,22 B017,0016,64,2,20,4 B018,0017,62,2,8,15
No amnesico,
[osotolongo@brick03 grupos]$ awk -F"," '{if ($2=="2") print $1}' amnesia.csv > noamnesico.list [osotolongo@brick03 grupos]$ grep -f noamnesico.list bioface_data.csv > noamnesico_bioface_data.csv [osotolongo@brick03 grupos]$ sed -i "1i$header" noamnesico_bioface_data.csv [osotolongo@brick03 grupos]$ head noamnesico_bioface_data.csv PSubject,Subject,Edad,Sexo,Estudios,FACEmem B001,0001,64,1,11,13 B003,0003,60,2,8,10 B006,0006,64,2,5,25 B007,0007,62,2,11,39 B008,0008,58,2,11,45 B009,0009,51,2,11,28 B011,0011,54,2,16,67 B015,0015,59,2,14,57 B020,0019,64,2,8,13
neuroimagen/bioface_vbm.txt · Last modified: 2021/03/22 15:23 by osotolongo