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Thank you very much for your response Doug.
What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)? And what value of PSF should we specify to calculate this ratio? To my knowledge, this is an acquisition related parameter and if I set it to 0 I will turn off PVC.
Best wishes, Marina.
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Douglas N. Greve https://secure-web.cisco.com/1y-OD2P8BWHc0h287Xl8Diwwr6Ds9fMYa9s6RyGJbPbpYxPx3JIc0yXalZqJbTpbdASEaa25SaBP6BZrHh-ckK9p4KmnrShTPTQiliqNt53IQS-Nt9lXFyYjh1H-dvtew0E4TqUxoTOVFhv7rJ-6DRtsxXI2z7M7kmh0G-0fbXwUCvMVpzejl0P1NsyVLpV9ursv_ygJ4U3V8PPFuwvpjgnggz4XzNrQVMrPi_bwVsq_SYagZvcsSCa9LQjJZuuQlU73tJUifxBLb186MvX9zSw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522 Mon, 31 May 2021 17:39:23 -0700 https://secure-web.cisco.com/1cF0PzjgERhEsaW2ZJdBauXH4XR9YM93MndhHQk1vpHHyUUh9bnoJo1CrDyz0L9jR435cYmwLHKL1Z8ixRosfFwRa2NeA6nyAGSrA4aRke_mbKOGQmyHedBGFwRHNPrRV406w6eF0h5KCyNHpEajspNVvXE-3tAtnO87o54yNOHGv77Cv41TBCisFGTpIttO8yQHYH98UwscMRW5WzKsD425FeG8aoL0xD4o_zi2edkEoIY2y1H6L1aggLPectASboZKHVwgZYfe_8dGfBTUAuA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210531
Yes, you can use PETsurfer. I would apply it to the ratio
On 5/28/2021 10:25 AM, Marina Fernández wrote:
External Email - Use Caution
Dear experts,
I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*.
Can I use the PVC functions of PetSurfer for this purpose? And in case I can:
Should I apply PVC only on T1? Or also in T2?
Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)?
Any other advice for calculating myelin maps would be welcome.
Thank you in advance,
Marina
*Link:
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On 6/1/2021 10:19 AM, Marina Fernández wrote:
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Thank you very much for your response Doug.
What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)?
I've never done it before. I usually use MG (this will only work for gray matter). If you need white matter, then RBV I guess.
And what value of PSF should we specify to calculate this ratio? To my knowledge, this is an acquisition related parameter and if I set it to 0 I will turn off PVC.
Yes, set psf to 0. It will still correct for the tissue fraction effect (unless you also add --no-tfe).
Best wishes, Marina.
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Douglas N. Greve https://secure-web.cisco.com/1y-OD2P8BWHc0h287Xl8Diwwr6Ds9fMYa9s6RyGJbPbpYxPx3JIc0yXalZqJbTpbdASEaa25SaBP6BZrHh-ckK9p4KmnrShTPTQiliqNt53IQS-Nt9lXFyYjh1H-dvtew0E4TqUxoTOVFhv7rJ-6DRtsxXI2z7M7kmh0G-0fbXwUCvMVpzejl0P1NsyVLpV9ursv_ygJ4U3V8PPFuwvpjgnggz4XzNrQVMrPi_bwVsq_SYagZvcsSCa9LQjJZuuQlU73tJUifxBLb186MvX9zSw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522 Mon, 31 May 2021 17:39:23 -0700 https://secure-web.cisco.com/1cF0PzjgERhEsaW2ZJdBauXH4XR9YM93MndhHQk1vpHHyUUh9bnoJo1CrDyz0L9jR435cYmwLHKL1Z8ixRosfFwRa2NeA6nyAGSrA4aRke_mbKOGQmyHedBGFwRHNPrRV406w6eF0h5KCyNHpEajspNVvXE-3tAtnO87o54yNOHGv77Cv41TBCisFGTpIttO8yQHYH98UwscMRW5WzKsD425FeG8aoL0xD4o_zi2edkEoIY2y1H6L1aggLPectASboZKHVwgZYfe_8dGfBTUAuA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210531
Yes, you can use PETsurfer. I would apply it to the ratio On 5/28/2021 10:25 AM, Marina Fernández wrote:
External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*.Can I use the PVC functions of PetSurfer for this purpose? And in case I can: Should I apply PVC only on T1? Or also in T2? Which T1 should I use? The original T1 or the T1 with corrections (for example, the nu.mgz file that is corrected for variations in intensity)? Any other advice for calculating myelin maps would be welcome. Thank you in advance, Marina *Link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com <http://secure-web.cisco.com>" claiming to be* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262571/#R48 <https://secure-web.cisco.com/1QZOfvqmKfuLQOn-6qhxRHDDmKDXv8lZm-TGv73nobyUAH1I0oIKrmMHLBbHemda3zQlTVUP27c-_ekOM7GMkDS3_FSSl-zdKBGWuydiuynTR5i6c5iRPQBGY8-Ik3sdoQWdcb9MQ0-rKS0nRtBBtlZHi4FwU1YrjGqd9HjzDIBiNvvz0lSr47uLM9P-9B573D_4JfmbQT9SyEBo6SRUgMj6asmEOSQoRzk_Bu9ZbNkTuboF_mufZy0ggT5jhqptutYORJtSkIP3S4h5Z8fVGNQ/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48> <https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48 <https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48>>
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Marina Fernández