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