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Dear Dr. Douglas N Greve,
Thank you for your attention and reply and it is really helpful.
Best,
Yu-Wei
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: 27 June 2021 16:42:45
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question about partial volume corrections with
PETSurfer
On 6/21/2021 12:13 PM, Yu-Wei Chang wrote:
External Email - Use Caution
External Email - Use Caution
Dear PetSurfer and Freesurfer Developers,
I would like to run partial volume corrections on amyloid PET images (from
ADNI) with PetSurfer.
I have downloaded the amyloid PET images that were intensity normalized to the
cerebellar GM.
However, I noticed that the PVC analysis in PetSurfer uses the Pons as a
reference region.
I don't have much experience with PET analyses but I was wondering
1.1 If I should use the same reference region for the PVC?
This is a biological question, not a technical one. If they used cerebellum,
probably good to stick with that
1.2 If so, how can I change the Pons for the Cerebellar GM in the commands on
the website?
I found a similar question raised in the forum (MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1u8lWqzGoNh6_E_LJdUs5VjA67_kFxQRh5wLYmksWJr86Abo_BWzbY5JSC880m45K5E79RaLMA-2d6YB5YpmGJGlBOQ2deoNxLuqSxMH775HioLZSkdcLG4A0Hu9cS5k0eR9kV5YVGzPSL1tLEwB-Q_o-AQSyntUS-CT519v_XPWmt4YJC2ajejIo4xPS-XiSC3j0HNlx31zpOMyVQ0eoCzCNh64wRMeDJOoPWGAbxcZtvv_6mz8syGcBKju4tEm2TAih5Ao26GAbi05RO27GIA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52918.html<https://secure-web.cisco.com/1ZlB3PzPmZnYFpKkL_LMunStJKeDgVzSjzFa3rVWrk5e5OXDg8sn2fECIW_80d1NtvqZ-MkovTawCi5Ch6uXXNSPFsodmBDCzlqAXmixjSWeeB8j5mJwcowB1fFCZ-hNp30G4ggxBUyy-t-bRYq6qZjhVq-Pp68NdB5rW_rqHpJVd-teN4JhrfBtauoGOq1hYOmEuSd5EpeiCbmMMjmIxC1cn-IOZXDrmaTa9EP5q5w9i_r8GjaJ9Psv3EX4a6G-JxFjhLA5wbt78-mptx9YvVA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52918.html>)
and the provided solution is to add ‘--rescale 7 8 46 47’ for left and right
cblum wm and gm.
2.1 Does ‘--rescale 7 8 46 47’ suit my question 1?
Yes
2.2 If so, where can I find the whole list of ids that specify every brain
region in the left and right hemispheres?
Look in gtmseg.ctab in $SUBJECTS_DIR/subject/mri
Thank you.
Best,
Yu-Wei
****************************
Yu-Wei Chang 張育瑋
Doctoral student
UNIVERSITY OF GOTHENBURG
Department of Physics
Gothenburg, Sweden
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