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