External Email - Use Caution
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