External Email - Use Caution
Dear FS experts,
I hope this email finds you all doing well. I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me.
1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)? * I read through https://secure-web.cisco.com/1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5yx... but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google. 2. How do you tell if it worked? I saw https://secure-web.cisco.com/1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmns... this previous post but it does not seem to have been answered.
Any assistance would be greatly appreciated.
Thank you so much!
All the best, Emily Harriott PhD student, Vanderbilt University
Hello Emily,
To clone voxels from your T1.mgz -> brainmask.mgz:
1. select brainmask.mgz as your active volume 2. click on 'Voxel Edit' -> 'Clone Voxel' 3. set T1.mgz as the reference volume 4. shade desired voxels to clone
I would recommend having your brainmask on top of the T1, as well as changing the opacity (and possibly the colormap) of the brainmask. Place the cursor in the voxels you have cloned to check the value is the same in both the target and reference volumes.
Best, Jackson ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harriott, Emily M emily.m.harriott@vanderbilt.edu Sent: Tuesday, February 28, 2023 5:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] more detailed instructions for cloning voxels & confirmation that the cloning worked
External Email - Use Caution
Dear FS experts,
I hope this email finds you all doing well.
I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me.
1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)? * I read through MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/VoxelE...https://secure-web.cisco.com/1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5yxKkzbcbGLX9un1PEHP6pGkr4BnnRfhRLb9ALVzgvYGJNRIxXJ-E2ozgNJcylTntvEp2Ycpy_Bx-zvs2agCjmG40KAePC5w_5Kgr-V07QnDQvMdGuukkxDYmI6yds4pmvU2Zgl0jrnFZcBLCJgBbAq3CrSKKWaGeqj1_4OMWhb9bH8dEnbwRpNAq7n1QredI3ey-drRTa6x9edLY2mgv5D0UjAXZ7bs-b90qAKENlV1E8SFAAs9E1Np0Bx0p0xL0zsEhAxcQn3m8RTnEU6FANXTunqPUgDDq68EEpwUbXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FVoxelEdit but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google. 2. How do you tell if it worked? I saw 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/msg56601.htmlhttps://secure-web.cisco.com/1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmnsRoBR_KsILBOCNRp19OF-B5qG89-_q3lidCoftze1HYTV7vL0Z7z7B5fiWe-DLNyg8r8SehP1Gs8sU6ViExQXhpZ--t1_N-_Qz8ShETFAL69my5mzpCPm6VT5HK7xfRf1jFNoIqZmPGHZMaoSRPsFSYO9Fal3dOxgJIIkSQca_XKOZz-d-8HTa5GpbmHTf-8gE8Z7A5_4xFERTyJ5fmf1fqPh3Iv_8ukxTtuIdOgLfXdSNGp3eTnVFSgbFnKeWh36yTx9haqNynDo9AJAJhaDc3qIVz9fueCzuWESlXMg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56601.html this previous post but it does not seem to have been answered.
Any assistance would be greatly appreciated.
Thank you so much!
All the best,
Emily Harriott
PhD student, Vanderbilt University
External Email - Use Caution
Dear Dr. Nolan,
Thank you so much for your help; I really appreciate it.
I’m currently using a heat color map for brainmask.mgz and the grayscale color map for T1.mgz.
After shading (step 4), should I expect to see the newly cloned voxels (perhaps as red voxels added to brainmask.mgz) immediately? Or, nothing actually appears after shading and the cloned voxels added to brainmask.mgz only appear in brainmask.mgz after another run of recon-all?
Also, what do you mean by “Place the cursor in the voxels you have cloned to check the value is the same in both the target and reference volumes.”? What value?
Thank you so much! Emily Harriott
From: Nolan, Jacksonmailto:JNOLAN5@mgh.harvard.edu Sent: Thursday, March 2, 2023 5:16 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Cc: Harriott, Emily Mmailto:emily.m.harriott@vanderbilt.edu Subject: Re: [Freesurfer] more detailed instructions for cloning voxels & confirmation that the cloning worked
Hello Emily,
To clone voxels from your T1.mgz -> brainmask.mgz:
1. select brainmask.mgz as your active volume 2. click on 'Voxel Edit' -> 'Clone Voxel' 3. set T1.mgz as the reference volume 4. shade desired voxels to clone I would recommend having your brainmask on top of the T1, as well as changing the opacity (and possibly the colormap) of the brainmask. Place the cursor in the voxels you have cloned to check the value is the same in both the target and reference volumes.
Best, Jackson
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harriott, Emily M emily.m.harriott@vanderbilt.edu Sent: Tuesday, February 28, 2023 5:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] more detailed instructions for cloning voxels & confirmation that the cloning worked
External Email - Use Caution
Dear FS experts,
I hope this email finds you all doing well.
I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me.
1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)?
* I read through MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1zMq8YO0tpEGlKk0HoaYICoJ2GBTe2Zfcjw1BniPnodvXjD...https://secure-web.cisco.com/1g6hYvQ5fFFjoFxT-ueIUccJ3eOoleNow9uGEHMOkAzsei5Z5hAiciSjOF81FK5pg46CTnY9_IC1dQdgndFIdjGsXIN4chxOVbJ2xOsCElYr-kruqmy8Z7Hm47LAIy4W_WSrNUPf3AIOSQyK4FDvlvbJSbs32O2tSsdrAchhx-ylinl7_eMZlw3o6XfiN7Vf-odkXN5hZvwXzZWlwKqWwhmKTlNHRrGbprhrBEmqXxxfukvvIxcyINmofGYxqst1KVdCGdKQwIl4totSxeRdrzSMdBQTG0yEgsVOpkBsLg9Yfwa2jL3vrfEaNjSZctC3ZF00JujexyL3Bsl7aAB7VNQ/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1edlOGwMXoyYaTFLL7CtR8DWHAzxHsiS014OXifU0XBn5yxKkzbcbGLX9un1PEHP6pGkr4BnnRfhRLb9ALVzgvYGJNRIxXJ-E2ozgNJcylTntvEp2Ycpy_Bx-zvs2agCjmG40KAePC5w_5Kgr-V07QnDQvMdGuukkxDYmI6yds4pmvU2Zgl0jrnFZcBLCJgBbAq3CrSKKWaGeqj1_4OMWhb9bH8dEnbwRpNAq7n1QredI3ey-drRTa6x9edLY2mgv5D0UjAXZ7bs-b90qAKENlV1E8SFAAs9E1Np0Bx0p0xL0zsEhAxcQn3m8RTnEU6FANXTunqPUgDDq68EEpwUbXg%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FFreeviewGuide%25252FFreeviewTools%25252FVoxelEdit%26data%3D05%257C01%257Cemily.m.harriott%2540vanderbilt.edu%257C62b46cef4c134723ac2808db1b742a31%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C638133957959807287%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252FGs4w8Mw%252BDtVggVNKAgfS7dVVEwWCUFBJgcKUfquVhU%253D%26reserved%3D0 but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google.
1. How do you tell if it worked? I saw MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1q5o33LsadH2Co-Hw9bw99Kfr83o0aV-0UjyphQyjgF09qp...https://secure-web.cisco.com/1EoKcIUpGiuX6kUS4_MLZdDB8cr2dwglmM_p6uEUHoW2T9dh9bekjwPit3hRuMMTi7lwlWnECN0umzaFDzaKxmPS68fBU4F9on26oI7tOx8DIUohj3T3OE-WQoHOzZKXeMg-MpRJ6aLMMoCyAEtlwQ2tsBB7PFvkwJwpCfv9ngq9OJ6p0z5rFzq1PkXEtqpH0vsUbEOUf6HFMBdhcRVDw95zYLeHnLqoQ7-4W-nZ7rnZ3XZwPI-qXmySOGD1cjDY1o_43ri96JixSB9M8Gwn8MwJME5UxcbZ_KK55M5FA7sKynxwGi5SjehSCoHpNXA5Lv8aq7WwxnjQs5OSrZcDATw/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1FkHM4e40vXk3f7s77S0LuFO0Duz3wB6sJb6MPMmOOUvmnsRoBR_KsILBOCNRp19OF-B5qG89-_q3lidCoftze1HYTV7vL0Z7z7B5fiWe-DLNyg8r8SehP1Gs8sU6ViExQXhpZ--t1_N-_Qz8ShETFAL69my5mzpCPm6VT5HK7xfRf1jFNoIqZmPGHZMaoSRPsFSYO9Fal3dOxgJIIkSQca_XKOZz-d-8HTa5GpbmHTf-8gE8Z7A5_4xFERTyJ5fmf1fqPh3Iv_8ukxTtuIdOgLfXdSNGp3eTnVFSgbFnKeWh36yTx9haqNynDo9AJAJhaDc3qIVz9fueCzuWESlXMg%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Ffreesurfer%252540nmr.mgh.harvard.edu%25252Fmsg56601.html%26data%3D05%257C01%257Cemily.m.harriott%2540vanderbilt.edu%257C62b46cef4c134723ac2808db1b742a31%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C638133957959807287%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D6zXGtarBF%252B3admEdpemM1tSwX9nRH0r3cSub%252B%252FIpitg%253D%26reserved%3D0 this previous post but it does not seem to have been answered.
Any assistance would be greatly appreciated.
Thank you so much!
All the best,
Emily Harriott
PhD student, Vanderbilt University The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1j7wCeBkJRbzraBDPf9nSiil5xg8-th4dADxdIE25ZB4iuN...https://secure-web.cisco.com/1xWdFO2fA0P3TT5NXrFVOag-2pPLfRiDHn6A5Rewl7ToYon9rtj-H0vDCg44jUjWb5MDg5yPBKbBSMEDKD5W8YLIvQSrQqHiksobijOsV5v7lkN-eDSHKAtWmae6xREhXkT2u-fVy4UupG9IqTZNGiDrkPjwoZQlm4_4I1UgYLWeYLoH044sdKUx8BZOChToyD7pjOCPXxX74B4Mf73L1rRiMeB0xMLppFdhJC4by-E2Qvk1B5WNbNsVAadY7-NBSyLlDTWpqn4dlk2m32-wIsLuNjBtm4iSzqWgL5vEM1T3x1ilpexocZAcffSpT3OgWif0JzUF5bKaEtbiw8dSlDw/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C01%257Cemily.m.harriott%2540vanderbilt.edu%257C62b46cef4c134723ac2808db1b742a31%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C638133957959807287%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DXHvdvlLzssdhxOsl8Nz4W4t8tAB%252FZiThjF9MkpD%252B6nE%253D%26reserved%3D0 .
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freesurfer@nmr.mgh.harvard.edu
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Harriott, Emily M -
Nolan, Jackson