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neuroimagen:pgs [2022/01/29 17:20]
osotolongo [comparando]
neuroimagen:pgs [2022/05/10 09:20] (current)
osotolongo [comparando]
Line 159: Line 159:
  
 {{:neuroimagen:wmh_comparing.png?600|}} {{: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|}}
neuroimagen/pgs.txt ยท Last modified: 2022/05/10 09:20 by osotolongo