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--- neuroimagen:pgs [2022/01/29 09:50]
osotolongo [comparando]
+++ neuroimagen:pgs [2022/05/10 09:20]
osotolongo [comparando]
@@ Line 151: / Line 151: @@
 plot(w$WM.hypointensities, w$WMH, main="WMH comparison pgs VS FS", xlab="Freesurfer WMH", ylab="pgs WMH", pch=15, col="blue")
 abline(wl$coefficients[1],wl$coefficients[2],col="red",lwd=3)
-text(2500,25000, bquote(R^2 == .(round(pwl$adj.r.squared, digits=3))))
+text(2500,25000, bquote(R^2 == .(round(pwl$adj.r.squared, digits=3))), cex=2)
 dev.off()
@@ Line 159: / Line 159: @@
 {{:neuroimagen:wmh_comparing.png?600|}}
+===== WMH on tracts =====
+**Nota:** El T1 original no se registra bien a espacio MNI (o viceversa). Hay que usar el T1 preprocesado de FS.
+<code bash>
+[osotolongo@brick03 output]$ mri_convert --in_type mgz --out_type nii --conform /old_nas/subjects/bioface_0020/mri/T1.mgz 0020_tmp.nii.gz
+[osotolongo@brick03 output]$ fslreorient2std 0020_tmp 0020_struct
+[osotolongo@brick03 output]$ antsRegistrationSyNQuick.sh -d 3 -t s -f 0020_struct.nii.gz -m /old_nas/bioface/bids/sub-0020/anat/sub-0020_T1w.nii.gz -o 00020_T12struct_warp_
+[osotolongo@brick03 output]$ antsRegistrationSyNQuick.sh -d 3 -t s -f 0020_struct.nii.gz -m /usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz -o 00020_MNI2struct_warp_
+[osotolongo@brick03 output]$ antsApplyTransforms -d 3 -i 0020_WMH.nii.gz -r 0020_struct.nii.gz -t 00020_T12struct_warp_1Warp.nii.gz -t 00020_T12struct_warp_0GenericAffine.mat -n GenericLabel -o 0020_WMH_in_struct.nii.gz
+[osotolongo@brick03 output]$ antsApplyTransforms -d 3 -i /usr/local/fsl/data/atlases/JHU/JHU-ICBM-labels-1mm.nii.gz -r 0020_struct.nii.gz -t 00020_MNI2struct_warp_1Warp.nii.gz -t 00020_MNI2struct_warp_0GenericAffine.mat -n GenericLabel -o 0020_labels_in_struct.nii.gz
+</code>
+{{:neuroimagen:testing_wmh_on_icbm.png?800|}}

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