External Email - Use Caution Hi Freesurfer team,
Just wanted to bump this to see if anyone had any thoughts. Thanks, Adam On Tue, Jan 29, 2019 at 10:21 AM Adam Martersteck <[email protected]> wrote: > Hi FreeSurfer team, > I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage paper: > > 1) It looks like the 2 rigid transforms created during mri_gtmpvc found at > [$pvc_directory/aux/anat2bbpet.lta] and [$pvc_directory/aux/bbpet2anat.lta] > are misnamed and the file names should be swapped. I noticed this isn’t a > problem during mri_vol2surf (e.g. the PetSurfer wiki) because mri_vol2surf > is “smart” and will automatically detect and invert the transform -- but it > was causing problems for me when I used them during mri_vol2vol thinking > the bbpet2anat.lta was from pet space to anat space. I apologize if you > already knew about this – I couldn’t find anything in the FSv6 “Known > Issues” or on the PetSurfer page. > > 2) I am using the MG PVC stream and a fairly conservative GM PVF threshold > of 30% (similar to Doug’s paper). I noticed when the PVF is < 0.3 it sets > the corrected [mg.nii.gz] image to zero in those voxels. Intuitively, I > would have thought this would just “cap” all values < 0.3 to 0.3 and divide > voxels by 0.3 to get a MG corrected voxel. I went back to Doug’s paper and > found, indeed, the paper says, *“In this study, we varied the threshold > from 1% to 50%. The TACs in voxels that did not meet this criterion were > set to zero.”* > > So when I take the mg.nii.gz and use vol2surf as Doug did, I get a > significant number of “patches” of zero values across the cortex (see > attached image; every voxel along the normal is zero). I would then have > smoothed this surface -- artificially lowering the entire neighborhood of > vertices. Did you guys do something else for the Neuroimage paper when you > were going from vol2surf? Or did you smooth the zeroes into the surrounding > vertices? Maybe this isn't a problem in healthy brains and the projfrac 0.5 > voxel is always a non-zero? > > Since I am working with significantly atrophied Alzheimer brains -- would > “capping” the PVF make sense here to balance over correcting noise while > avoiding non-zero vertices? Is there a command in fscalc to set all values > between 0.0001 and 0.3 to 0.3 so I could do this? > > Thanks! > Adam >
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