looks like it is only different in the first or second decimal place, is that right? If so, then it is acceptable.
On 8/22/2024 4:11 PM, Sneha Pandya wrote:
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Dear team,
A] I am running mri_gtmpvc on our data and need to extract stats data that is in the similar format as gtm.stats.dat file from non-pvc corrected PET data, in the sense getting mean regional uptake from non-pvc PET data alongside region names, volumes, var, etc information using ROIs from gtmseg.
mri_gtmpvc command (turned off PVC):
mri_gtmpvc --i PET.nii.gz --reg PET_to_nu.reg.lta --seg ${ FreeSurferDir }/mri/gtmseg.mgz --default-seg-merge --auto-mask ${FWHM} .01 --psf 0 --no-tfe --no-rescale --save-input --o nopvcoutput
I tried this with following approaches as suggested in the forum:
1] mri_convert nopvc.nii.gz --ascii nopvc_1.stats.dat
2] mri_segstats --i input.nii.gz --seg aux/seg.nii.gz --ctab aux/seg.ctab --excludeid 0 --sum nopvc_2.stats.dat
On comparing mean uptake between nopvc_1.stats.dat and nopvc_2.stats.dat, I see that values are similar but not same. Is this expected?
Head of nopvc_1.stats.dat:
54832.960938
65543.554688
59080.023438
75662.140625
47840.519531
61120.222656
66590.773438
69356.742188
58847.007812
65715.578125
Head of nopvc_2.stats.dat:
Index
SegId
NVoxels
Volume_mm3
StructName
Mean
StdDev
Min
Max
Range
1
2
106905
223886.7
Left-Cerebral-White-Matter
54832.95
8839.049
15160.92
96317.77
81156.85
2
7
7723
16174
Left-Cerebellum-White-Matter
65543.57
10289.78
26951.39
90987.36
64035.97
3
8
24806
51950.2
Left-Cerebellum-Cortex
59079.91
14349.17
13388.75
107889.7
94500.95
4
10
3427
7177
Left-Thalamus
75662.06
13054.39
33599.36
105854.3
72254.89
5
11
1813
3796.9
Left-Caudate
47840.52
10624.56
19515.38
88224.69
68709.31
6
12
2280
4774.9
Left-Putamen
61120.21
8453.317
43591.13
83701.97
40110.84
7
13
976
2044
Left-Pallidum
66590.77
5816.431
50056.58
83431.62
33375.04
8
16
6686
14002.2
Brain-Stem
69356.77
16951.96
20199.62
115301.7
95102.11
B] Also, when we turn off PVC with “--psf 0 --no-tfe” flags, SGTM is still performed right whose regional data is saved in gtm.stats.dat file? If we perform RBV PVC does it in addition affect in anyway SGTM outputs (i.e gtm.stats.dat)?
C] Is there a way to erode only reference region in the mri_gtmpvc command both when PVC is performed (SGTM or RBV) and with no PVC? If not, is there a way to do so after running mri_gtmpvc to rescale PVC’ed and non-PVC’ed uptake with eroded cerebellum derived from gtmseg? I have extracted eroded GM cerebellum from gtmseg using mri_binarize and then planning to use that eroded GM cerebellum mask to rescale PVC’ed/non-PVC’ed regional uptake, not sure if it is the right approach.
mri_binarize command:
mri_binarize --i ${FreeSurferDir}/mri/gtmseg.mgz --o CerebellumGrayMatterMaskEroded_gtmseg.mgz --match 8 47 --erode 2
Thank you,
Sneha
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