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?
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 (https://secure-web.cisco.com/1ZlB3PzPmZnYFpKkL_LMunStJKeDgVzSjzFa3rVWrk5e5OX...) 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?
2.2 If so, where can I find the whole list of ids that specify every brain region in the left and right hemispheres?
Thank you.
Best,
Yu-Wei
**************************** Yu-Wei Chang 張育瑋 Doctoral student
UNIVERSITY OF GOTHENBURG Department of Physics Gothenburg, Sweden
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://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52918.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wjK_yk2HoCgSqX04o05x5Sc-YFFlqAWFLLeX1Xw-8VWtRl...
External Email - Use Caution
Dear Dr. Douglas N Greve,
Thank you for your attention and reply and it is really helpful.
Best,
Yu-Wei
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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_kFxQRh5wLYmksWJr86Ab...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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wjK_yk2HoCgSqX04o05x5Sc-YFFlqAWFLLeX1Xw-8VWtRl...
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Yu-Wei Chang