neuroimagen:fs_group_analysis
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Table of Contents
FreeSurfer Group Analysis
FSDG
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat
Primero hay que construir el archivo de diseño del experimento,
[osotolongo@detritus fsdg]$ head codes.csv Subject,PSubject 0001,F001 0002,F002 0003,F003 0004,F004 0005,F005 0006,F006 0007,F007 0008,F008 0009,F009 [osotolongo@detritus fsdg]$ head demographics.csv PSubject,edat_v0,Anyos_Escolaridad_FAC_v0,Sex_1H_0M_v0 F001,71,8,0 F002,70,12,1 F003,70,8,0 F004,76,16,0 F005,68,20,1 F006,64,14,0 F007,59,19,1 F008,55,16,0 F009,67,16,0 [osotolongo@detritus fsdg]$ join -t"," -1 2 -2 1 codes.csv demographics.csv | awk -F"," '{print "facehbi_"$2","$3","$4","$5}' | sed 's/facehbi_Subject/Variables/;s/edat_v0/Age/;s/Anyos_Escolaridad_FAC_v0/Education/;s/Sex_1H_0M_v0/Gender/' | sed 's/facehbi_\([^,]*\),/Input facehbi_\1 Main /; s/,/ /g' > body.csv [osotolongo@detritus fsdg]$ head body.csv Variables Age Education Gender Input facehbi_0001 Main 71 8 0 Input facehbi_0002 Main 70 12 1 Input facehbi_0003 Main 70 8 0 Input facehbi_0004 Main 76 16 0 Input facehbi_0005 Main 68 20 1 Input facehbi_0006 Main 64 14 0 Input facehbi_0007 Main 59 19 1 Input facehbi_0008 Main 55 16 0 Input facehbi_0009 Main 67 16 0 [osotolongo@detritus fsdg]$ cat headers.txt GroupDescriptorFile 1 Title FACEHBI_all Class Main [osotolongo@detritus fsdg]$ cat headers.txt body.csv > facehbi.fsdg [osotolongo@detritus fsdg]$ head facehbi.fsdg GroupDescriptorFile 1 Title FACEHBI_all Class Main Variables Age Education Gender Input facehbi_0001 Main 71 8 0 Input facehbi_0002 Main 70 12 1 Input facehbi_0003 Main 70 8 0 Input facehbi_0004 Main 76 16 0 Input facehbi_0005 Main 68 20 1 Input facehbi_0006 Main 64 14 0
GLM Analysis (mri_glmfit)
Primero construimos los contrastes, diciendole a FS cual es la variable que nos interesa, en este caso la edad,
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
[osotolongo@detritus fsdg]$ cat facehbi.mtx 0 1 0 0
Ahora vamos a correr el modelo con este contraste,
[osotolongo@detritus fsdg]$ mris_preproc --fsgd facehbi.fsdg --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.facehbi.age.thickness.10.mgh [osotolongo@detritus fsdg]$ mri_glmfit --y lh.facehbi.age.thickness.10.mgh --fsgd facehbi.fsdg --C facehbi.mtx --surf fsaverage lh --cortex --glmdir lh.facehbi.age.glmdir
Para usar freeview me he tenido que ir a la FSL VM
[fsluser@FSLVm7_64 fsdg]$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.facehbi.age.glmdir/facehbi/sig.mgh:overlay_threshold=4,5 -viewport 3d
Cambiando el overlay threshold para que muestre toda la significancia,
Ejemplo, fijando uncorrected p<0.001,
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Clusterwise Correction for Multiple Comparisons
Ahora voy a buscar los clusters con una p>0.05
[osotolongo@detritus fsdg]$ mri_glmfit-sim --glmdir lh.facehbi.age.glmdir --cache 4 neg --cwp 0.05 --2spaces
A ver,
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.ocn.annot -viewport 3d
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También hay un resumen de los clusters que se han encontrado a esta significancia,
[osotolongo@detritus fsdg]$ cat lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.cluster.summary # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ # $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ # CreationTime 2020/06/11-08:12:12-GMT # cmdline mri_surfcluster.bin --in lh.facehbi.age.glmdir/facehbi/sig.mgh --mask lh.facehbi.age.glmdir/mask.mgh --cwsig lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.cluster.mgh --sum lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.cluster.summary --ocn lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.masked.mgh --no-fixmni --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --csdpdf lh.facehbi.age.glmdir/facehbi/cache.th40.neg.pdf.dat --vwsig lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.voxel.mgh --vwsigmax lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.voxel.max.dat --oannot lh.facehbi.age.glmdir/facehbi/cache.th40.neg.sig.ocn.annot --bonferroni 2 --surf white # cwd /nas/data/facehbi/fsdg # sysname Linux # hostname detritus.fundacioace.com # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.facehbi.age.glmdir/facehbi/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /nas/data/subjects # SearchSpace_mm2 75610.7 # SearchSpace_vtx 147840 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign neg # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 2.34317 at vertex 124430 # Overall min -11.9208 at vertex 75951 # NClusters 27 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -6.017 60982 491.13 -47.9 -18.5 -2.1 0.00020 0.00000 0.00040 1098 -5034.35 superiortemporal 2 -11.921 75951 428.53 -31.7 -41.3 -9.1 0.00020 0.00000 0.00040 941 -6762.90 parahippocampal 3 -7.640 112606 361.05 -20.6 -99.6 -2.3 0.00020 0.00000 0.00040 432 -2179.37 lateraloccipital 4 -5.486 105941 331.99 -17.1 -32.3 56.5 0.00020 0.00000 0.00040 865 -3748.97 precentral 5 -5.449 35788 316.75 -44.9 6.5 -23.4 0.00020 0.00000 0.00040 611 -2771.80 superiortemporal 6 -7.472 67375 290.75 -20.6 30.7 50.4 0.00020 0.00000 0.00040 424 -2270.56 superiorfrontal 7 -4.824 159440 286.63 -8.8 -58.3 11.9 0.00020 0.00000 0.00040 622 -2552.03 precuneus 8 -6.970 138044 273.27 -30.3 -20.0 68.2 0.00020 0.00000 0.00040 626 -3090.95 precentral 9 -6.527 35125 264.21 -35.4 -12.7 18.8 0.00020 0.00000 0.00040 820 -4057.14 insula 10 -5.259 113827 256.47 -58.3 -17.5 -17.2 0.00020 0.00000 0.00040 522 -2207.87 middletemporal 11 -6.063 142574 227.96 -18.1 -91.7 16.1 0.00020 0.00000 0.00040 329 -1494.23 lateraloccipital 12 -4.901 142130 215.89 -61.7 -35.5 5.4 0.00020 0.00000 0.00040 478 -2005.09 bankssts 13 -7.124 88387 197.22 -10.7 -56.5 26.6 0.00020 0.00000 0.00040 436 -2167.82 precuneus 14 -5.977 112248 187.37 -31.2 -83.9 6.5 0.00040 0.00000 0.00080 312 -1449.31 lateraloccipital 15 -5.741 127670 174.29 -54.6 -0.9 -30.3 0.00080 0.00040 0.00140 210 -946.11 middletemporal 16 -5.957 110612 155.97 -44.6 23.1 18.8 0.00180 0.00100 0.00260 258 -1195.22 parsopercularis 17 -5.156 102514 136.16 -22.9 56.1 15.5 0.00459 0.00340 0.00579 163 -710.54 rostralmiddlefrontal 18 -5.618 43104 128.92 -24.3 6.2 48.4 0.00619 0.00479 0.00759 289 -1317.77 caudalmiddlefrontal 19 -5.445 91005 128.90 -21.8 -66.5 0.5 0.00619 0.00479 0.00759 285 -1241.01 lingual 20 -4.760 47386 121.71 -8.2 33.1 33.9 0.00759 0.00599 0.00918 190 -780.64 superiorfrontal 21 -4.778 107013 120.23 -19.8 -83.3 38.4 0.00798 0.00639 0.00958 223 -941.62 superiorparietal 22 -4.954 58975 118.93 -10.8 25.6 -17.8 0.00818 0.00659 0.00978 269 -1155.28 medialorbitofrontal 23 -4.799 38711 117.04 -60.9 -46.0 -1.9 0.00898 0.00739 0.01077 232 -956.50 bankssts 24 -6.095 1815 116.62 -47.1 -19.1 56.1 0.00918 0.00739 0.01097 319 -1485.15 postcentral 25 -4.976 77509 113.61 -35.6 37.8 13.2 0.01057 0.00878 0.01236 190 -814.05 rostralmiddlefrontal 26 -4.228 51760 87.69 -45.5 -72.1 10.1 0.02524 0.02247 0.02800 140 -552.81 inferiorparietal 27 -6.056 126177 68.80 -27.1 -68.1 22.7 0.04898 0.04508 0.05288 181 -854.08 superiorparietal
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