Practicum Neuro-Imaging MRI
Master Klinische Neuropsychologie 2020/2021 – Vrije Universiteit Amsterdam
Samenvatting Stansterk
Blauwe markering = handeling in FSL
Practicum 5: Understand the structure of a 3D MRI scan, learn to navigate in a standard brain, work
with brain atlases
FSL openen via terminal XQuartz, FSLeyes openen via ‘fsleyes’ intypen in terminal.
“nii” = Nifti format; standaard voor MRI data.
“gz” = file is compressed
Nu kijken naar bestand “MNI152_T1_1mm.nii.gz” à Gemiddelde van 152 hersenen.
Do you expect more alignment (= less blurring) between different brains at central or at peripheral regions of
the brain? à Centrale regios zullen meer alignt zijn.
The 152 different brains have all been transformed into the same space. There is less variation near the
center of these brains than in the individual gyri and sulci. Therefore, there is more overlap (and less
blurring) between brains at central compared to peripheral regions.
Klik op (i) = algemene info, info over voxels, oriëntatie.
X-as = dim1
Y-as = dim2
Z-as = dim3
1 voxel = 1 mm x 1 mm x 1 mm = kubieke millimeter = 1 mm3
Een brein image is ongeveer 7 liter.
,“Storage order = Radiological” = rechter kant van het brein is aan de linker kant van het plaatje.
X = rechts
Y = front
Z = top
Coördinaten (0,0,0) = Centrum van afbeelding. Dichtbij de Anterior Commissure (AC).
Coördinaten (0,2,-4) = AC.
Due to the "nodding" of the head (i.e., chin on chest), the cerebellum is slightly more superior in this image.
Due to the "nodding" of the head (i.e., chin on chest), the posterior end of the corpus callosum is slightly
more superior in this image.
The anterior end of the corpus callosum is at about y = +32 mm, the posterior end is at about y = -43 mm.
We have to add the 1 mm slice right in the middle at y = 0, which leads to a length of 32+43+1 = 76 mm.
“Ga naar coördinaat (…) Welke structuur is dit?” à Benoem Rechts of Links!
, Atlas informatie: Settings à OrthoView1 à Atlas panel
Note that this is a probabilistic atlas: the further removed from the center of a region, the smaller the
probability that a voxel is part of this region, and the darker the color. The white colors in the center have a
very high probability of belonging to this structure.
As the names imply, the Harvard-Oxford Cortical Atlas contains cortical grey matter structures, and the
Harvard-Oxford Subcortical atlas contains subcortical grey matter structures.
Master Klinische Neuropsychologie 2020/2021 – Vrije Universiteit Amsterdam
Samenvatting Stansterk
Blauwe markering = handeling in FSL
Practicum 5: Understand the structure of a 3D MRI scan, learn to navigate in a standard brain, work
with brain atlases
FSL openen via terminal XQuartz, FSLeyes openen via ‘fsleyes’ intypen in terminal.
“nii” = Nifti format; standaard voor MRI data.
“gz” = file is compressed
Nu kijken naar bestand “MNI152_T1_1mm.nii.gz” à Gemiddelde van 152 hersenen.
Do you expect more alignment (= less blurring) between different brains at central or at peripheral regions of
the brain? à Centrale regios zullen meer alignt zijn.
The 152 different brains have all been transformed into the same space. There is less variation near the
center of these brains than in the individual gyri and sulci. Therefore, there is more overlap (and less
blurring) between brains at central compared to peripheral regions.
Klik op (i) = algemene info, info over voxels, oriëntatie.
X-as = dim1
Y-as = dim2
Z-as = dim3
1 voxel = 1 mm x 1 mm x 1 mm = kubieke millimeter = 1 mm3
Een brein image is ongeveer 7 liter.
,“Storage order = Radiological” = rechter kant van het brein is aan de linker kant van het plaatje.
X = rechts
Y = front
Z = top
Coördinaten (0,0,0) = Centrum van afbeelding. Dichtbij de Anterior Commissure (AC).
Coördinaten (0,2,-4) = AC.
Due to the "nodding" of the head (i.e., chin on chest), the cerebellum is slightly more superior in this image.
Due to the "nodding" of the head (i.e., chin on chest), the posterior end of the corpus callosum is slightly
more superior in this image.
The anterior end of the corpus callosum is at about y = +32 mm, the posterior end is at about y = -43 mm.
We have to add the 1 mm slice right in the middle at y = 0, which leads to a length of 32+43+1 = 76 mm.
“Ga naar coördinaat (…) Welke structuur is dit?” à Benoem Rechts of Links!
, Atlas informatie: Settings à OrthoView1 à Atlas panel
Note that this is a probabilistic atlas: the further removed from the center of a region, the smaller the
probability that a voxel is part of this region, and the darker the color. The white colors in the center have a
very high probability of belonging to this structure.
As the names imply, the Harvard-Oxford Cortical Atlas contains cortical grey matter structures, and the
Harvard-Oxford Subcortical atlas contains subcortical grey matter structures.
