Hey everyone, I am a newbie to FreeSurfer.
I have 3D T1 brain MRI scans and I am trying to find out whether it is possible:
- to compute the volume of White Matter in each lobe in the brain
- to compute the total volume of each brain lobes (frontal, temporal, parietal, occipital)
I have played around with FastSurfer and I could only retrieve volume measurements for grey matter in each structure as in below:
# TableCol 1 ColHeader Index
# TableCol 1 FieldName Index
# TableCol 1 Units NA
# TableCol 2 ColHeader SegId
# TableCol 2 FieldName Segmentation Id
# TableCol 2 Units NA
# TableCol 3 ColHeader NVoxels
# TableCol 3 FieldName Number of Voxels
# TableCol 3 Units unitless
# TableCol 4 ColHeader Volume_mm3
# TableCol 4 FieldName Volume
# TableCol 4 Units mm^3
# TableCol 5 ColHeader StructName
# TableCol 5 FieldName Structure Name
# TableCol 5 Units NA
# NRows 95
# NTableCols 5
# ColHeaders Index SegId NVoxels Volume_mm3 StructName
1 2 3807115 140581.7 Left-Cerebral-White-Matter
2 4 498466 18406.4 Left-Lateral-Ventricle
3 5 33594 1240.5 Left-Inf-Lat-Vent
4 7 255397 9430.8 Left-Cerebellum-White-Matter
5 8 1155735 42676.7 Left-Cerebellum-Cortex
6 10 152104 5616.6 Left-Thalamus
7 11 70545 2604.9 Left-Caudate
8 12 103646 3827.2 Left-Putamen
9 13 43968 1623.6 Left-Pallidum
10 14 53316 1968.7 3rd-Ventricle
11 15 58740 2169.0 4th-Ventricle
12 16 445190 16439.1 Brain-Stem
13 17 57581 2126.2 Left-Hippocampus
14 18 24383 900.4 Left-Amygdala
15 24 38501 1421.7 CSF
16 26 6575 242.8 Left-Accumbens-area
17 28 80921 2988.1 Left-VentralDC
18 31 18823 695.1 Left-choroid-plexus
19 41 3889755 143633.2 Right-Cerebral-White-Matter
20 43 410483 15157.5 Right-Lateral-Ventricle
21 44 31962 1180.2 Right-Inf-Lat-Vent
22 46 251077 9271.3 Right-Cerebellum-White-Matter
23 47 1177394 43476.5 Right-Cerebellum-Cortex
24 49 153444 5666.1 Right-Thalamus
25 50 77346 2856.1 Right-Caudate
26 51 105713 3903.6 Right-Putamen
27 52 46690 1724.1 Right-Pallidum
28 53 75332 2781.7 Right-Hippocampus
29 54 33662 1243.0 Right-Amygdala
30 58 7971 294.3 Right-Accumbens-area
31 60 80156 2959.8 Right-VentralDC
32 63 19054 703.6 Right-choroid-plexus
33 77 49491 1827.5 WM-hypointensities
34 1002 67264 2483.8 ctx-lh-caudalanteriorcingulate
35 1003 141168 5212.8 ctx-lh-caudalmiddlefrontal
36 1005 96267 3554.8 ctx-lh-cuneus
37 1006 47102 1739.3 ctx-lh-entorhinal
38 1007 157488 5815.4 ctx-lh-fusiform
39 1008 230355 8506.1 ctx-lh-inferiorparietal
40 1009 257262 9499.7 ctx-lh-inferiortemporal
41 1010 52854 1951.7 ctx-lh-isthmuscingulate
42 1011 249137 9199.6 ctx-lh-lateraloccipital
43 1012 181901 6716.9 ctx-lh-lateralorbitofrontal
44 1013 120600 4453.3 ctx-lh-lingual
45 1014 93576 3455.4 ctx-lh-medialorbitofrontal
46 1015 265404 9800.3 ctx-lh-middletemporal
47 1016 37252 1375.6 ctx-lh-parahippocampal
48 1017 101207 3737.2 ctx-lh-paracentral
49 1018 86829 3206.3 ctx-lh-parsopercularis
50 1019 39598 1462.2 ctx-lh-parsorbitalis
51 1020 77496 2861.6 ctx-lh-parstriangularis
52 1021 44040 1626.2 ctx-lh-pericalcarine
53 1022 248824 9188.1 ctx-lh-postcentral
54 1023 77850 2874.7 ctx-lh-posteriorcingulate
55 1024 296595 10952.1 ctx-lh-precentral
56 1025 198120 7315.8 ctx-lh-precuneus
57 1026 73995 2732.3 ctx-lh-rostralanteriorcingulate
58 1027 226243 8354.3 ctx-lh-rostralmiddlefrontal
59 1028 523951 19347.4 ctx-lh-superiorfrontal
60 1029 225321 8320.2 ctx-lh-superiorparietal
61 1030 394746 14576.4 ctx-lh-superiortemporal
62 1031 253965 9377.9 ctx-lh-supramarginal
63 1034 29789 1100.0 ctx-lh-transversetemporal
64 1035 129757 4791.4 ctx-lh-insula
65 2002 45353 1674.7 ctx-rh-caudalanteriorcingulate
66 2003 147259 5437.7 ctx-rh-caudalmiddlefrontal
67 2005 97577 3603.1 ctx-rh-cuneus
68 2006 33476 1236.1 ctx-rh-entorhinal
69 2007 173818 6418.4 ctx-rh-fusiform
70 2008 299415 11056.2 ctx-rh-inferiorparietal
71 2009 282156 10418.9 ctx-rh-inferiortemporal
72 2010 53373 1970.9 ctx-rh-isthmuscingulate
73 2011 246604 9106.1 ctx-rh-lateraloccipital
74 2012 165797 6122.2 ctx-rh-lateralorbitofrontal
75 2013 127622 4712.6 ctx-rh-lingual
76 2014 93788 3463.2 ctx-rh-medialorbitofrontal
77 2015 282547 10433.3 ctx-rh-middletemporal
78 2016 32751 1209.4 ctx-rh-parahippocampal
79 2017 92852 3428.7 ctx-rh-paracentral
80 2018 93695 3459.8 ctx-rh-parsopercularis
81 2019 42767 1579.2 ctx-rh-parsorbitalis
82 2020 77958 2878.7 ctx-rh-parstriangularis
83 2021 47708 1761.7 ctx-rh-pericalcarine
84 2022 228996 8455.9 ctx-rh-postcentral
85 2023 72251 2667.9 ctx-rh-posteriorcingulate
86 2024 293416 10834.7 ctx-rh-precentral
87 2025 251924 9302.6 ctx-rh-precuneus
88 2026 44554 1645.2 ctx-rh-rostralanteriorcingulate
89 2027 209536 7737.3 ctx-rh-rostralmiddlefrontal
90 2028 540823 19970.5 ctx-rh-superiorfrontal
91 2029 247506 9139.4 ctx-rh-superiorparietal
92 2030 390136 14406.2 ctx-rh-superiortemporal
93 2031 215034 7940.4 ctx-rh-supramarginal
94 2034 26958 995.5 ctx-rh-transversetemporal
95 2035 139923 5166.8 ctx-rh-insula
And here are the commands I used:
#1
bash run_fastsurfer.sh --t1 '8_sag_mprage.nii.gz' --sd fastsurfer/output --sid 1 --vox_size 0.333 --seg_only --no_cereb --no_biasfield --py /debug-LbfMcKxW-py3.10/bin/python --viewagg_device cpu
#2
mri_segstats --seg aparc.DKTatlas+aseg.deep.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum cortical_stats.txt
Is there a way to get the same kind of data but for white matter? And is it possible to get the volume of each brain lobes?
Also, if no, is there any software that would allow me to do that?
Please let me know if you need further clarifications
Kind Regards