External Email - Use Caution

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. - > looks like it is only different in the first or second decimal place, is that right? If so, then it is acceptable. Yes, that’s correct its different in the first/second place. Just for understanding, why would we expect these differences?

Not, sure if other previous questions were received so reposting them: 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

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, August 23, 2024 6:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] petsurfer questions - No PVC stats file in the similar format as gtm.stats.dat

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: External Email - Use Caution Dear team, A] I am running mri_gtmpvc on our data and need

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:

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

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