External Email - Use Caution
Dear FreeSurfer Experts,
I have a question regarding how the hypothalamus volumes are calculated
using the hypothalamic subunits function, as opposed to the ScLimbic deep
learning tool which is only currently available in the dev version of
Freesurfer.
My project consists of measuring the volume of the hypothalamus, so I
thought of running both algorithms and comparing results to ensure they
were consistent. However, they are quite different and I was wondering if
there are certain flags/options I should be adding to ensure that the
results will relate to each other and why that is the case. What is the key
difference in how the hypothalamus is calculated by both these methods? How
do I ensure my results are robust/trustworthy? What does noMB mean in the
ScLimbic results?
I have tried running the ScLimbic function using the original T1 and the
--conform flag to make sure that the voxels were isotropic, and then
retried by using the nu.mgz as input (as that's what the hypothalamus
subunits function uses).
Here are the results (also attached):
HYPOTHALAMIC SUBUNITS
subject left anterior-inferior left anterior-superior left posterior left
tubular inferior left tubular superior right anterior-inferior right
anterior-superior right posterior right tubular inferior right tubular
superior whole left whole right
test 19.88 25.155 136.715 145.785 131.879 20.078 29.209 134.882 161.009
133.293 459.414 478.471
SC LIMBIC (T1-W and --conform)
# Subcortical Limbic Volumetric Stats
# Created by mri_sclimbic_seg
# NRows 12
# NTableCols 5
# ColHeaders Index SegId NVoxels Volume_mm3 StructName
1 26 469 471.6122 Left-Nucleus-Accumbens
2 58 460 459.8144 Right-Nucleus-Accumbens
3 819 588 571.3680 Left-HypoThal-noMB
4 820 631 586.4990 Right-HypoThal-noMB
5 821 667 707.3562 Left-Fornix
6 822 631 700.7991 Right-Fornix
7 843 58 60.5358 Left-MammillaryBody
8 844 57 64.1979 Right-MammillaryBody
9 865 414 396.2163 Left-Basal-Forebrain
10 866 448 450.1535 Right-Basal-Forebrain
11 869 165 170.6947 Left-SeptalNuc
12 870 151 157.4303 Right-SeptalNuc
SC LIMBIC (nu.mgz input)
# Subcortical Limbic Volumetric Stats
# Created by mri_sclimbic_seg
# NRows 12
# NTableCols 5
# ColHeaders Index SegId NVoxels Volume_mm3 StructName
1 26 513 519.7247 Left-Nucleus-Accumbens
2 58 526 537.3985 Right-Nucleus-Accumbens
3 819 575 570.7261 Left-HypoThal-noMB
4 820 613 604.3893 Right-HypoThal-noMB
5 821 657 675.3337 Left-Fornix
6 822 663 691.8721 Right-Fornix
7 843 51 53.4853 Left-MammillaryBody
8 844 58 61.4891 Right-MammillaryBody
9 865 473 483.7591 Left-Basal-Forebrain
10 866 487 496.4204 Right-Basal-Forebrain
11 869 145 153.3073 Left-SeptalNuc
12 870 138 142.8245 Right-SeptalNuc
I'm also not sure exactly what the flag "--crop" means for the hypothalamic
subunits function. I left it to the default value of 184 but how will
changing this affect my final result?
Below are also my codes for all three functions:
mri_segment_hypothalamic_subunits --s ${subjid} --sd ${sd} --crop 184
mri_sclimbic_seg --i ${sd}/${subjid}/mri//T1.mgz --o
${sd}/${subjid}/mri/sclimbic.mgz --write_volumes --conform
mri_sclimbic_seg --i ${sd}/${subjid}/mri//nu.mgz --o
${sd}/${subjid}/mri/sclimbic.mgz --write_volumes
Any help is appreciated.
Thank you,
Asmin
UCL Queen Square Institute of Neurology