help > MCALT in AFNI
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Apr 10, 2019 03:04 PM | Kamil Grajski - NuroSci, LLC
MCALT in AFNI
Thank you for this important contribution to neuroimaging tools for
analysis of older populations. Am looking to confirm rsfMRI
results previously obtained on an ADNI dataset with AFNI using
MNI152 atlas. Does anyone have experience applying MCALT in
AFNI? I may need just a bit of hand-holding here, but is it
correct that in order to use ./MCALT_T1.nii it needs to be
skullstripped first? - KAG
Apr 10, 2019 04:04 PM | Kamil Grajski - NuroSci, LLC
RE: MCALT in AFNI
Or...to answer my own question, is the template obtained by
applying the brain mask (./MCALT_brainmask.nii) to ./MCALT_T1.nii?
Apr 10, 2019 04:04 PM | Christopher Schwarz - Mayo Clinic
RE: MCALT in AFNI
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Originally posted by Kamil Grajski:
I don't have a lot of experience with AFNI, but for the direct question of how to get a skull-stripped version, then I agree with your suggestion. You can either use MCALT_brainmask to to exclude voxels that are mostly CSF, or MCALT_TIV to include the original signal for voxels that are mostly CSF and within the TIV.
Best,
Chris
Originally posted by Kamil Grajski:
Or...to answer my own question, is the template
obtained by applying the brain mask (./MCALT_brainmask.nii) to
./MCALT_T1.nii?
I don't have a lot of experience with AFNI, but for the direct question of how to get a skull-stripped version, then I agree with your suggestion. You can either use MCALT_brainmask to to exclude voxels that are mostly CSF, or MCALT_TIV to include the original signal for voxels that are mostly CSF and within the TIV.
Best,
Chris
Apr 10, 2019 05:04 PM | Kamil Grajski - NuroSci, LLC
RE: MCALT in AFNI
Got it! Many thanks for speedy reply.