External Email - Use Caution Hi Lilla,
Thanks a lot for your help! isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label Do I put the labels 7,8,46,47 where it says labels in the code above? Can I use the ROI files for co-registration into the diffusion space and then tractography? Get Outlook for iOS<https://secure-web.cisco.com/1gqN3EUycQThQVGuEVVLF26HprGoX4yNvtzkB7mw66mArVWqe1ua47g4eK6B2ZnKZ78e3qDdGU2KBt2rnm5gXHyuA7KwCMae-5WV4Dll9B8G1aMcJceC1Bwtd6_JsxXHKf1x2rHHgx04v5i02K7SZ3weUKjlhLLnKj6LTiz91ZRV0e6ii4Cz8Ns9Ht61DrxIi55Rto1bA6VBLaeMT8WN1cd5Pylob6TDmz5o79f3Ln2M7U2HHiY_UjrRlO_nO0sL26L_-mEtR_7gjouG9l8_Ihg/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> Sent: Sunday, May 16, 2021 10:49:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation Yes, you can use that one as well. Lilla ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ar...@cam.ac.uk> Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Sorry for another message, I have the aparc + aseg file, is that the file I should use? Get Outlook for iOS<https://secure-web.cisco.com/147PXKkFY6kebtynYSivzZJLuEDgG0lD53ixLapqXi0ddfjq_-5ccN6Kg5Wwbh15wUijedAouXUMgGYryi4GHuciIvz68lHI1JoaAryp25P5kc0NwjRirPjUBwXey23W6cB3O3nUbpamWt3Y6DtncsUND9EObf74KTxYhBSOafqKtk8eu4pugY6OP0PlcFad1dZ-raNEpBJXFiFy2B1pAqqZ2_ctY8SO8pNA4cnh38yGH7-J_z-1QoQ9NNgFUWqI7p4HVyTHhyEJ3Na_bEv3TDw/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ar...@cam.ac.uk> Sent: Sunday, May 16, 2021 10:37:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution Hi Lilla, Thanks a lot for your help! isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label Do I put the labels 7,8,46,47 where it says labels in the code above? Can I use the ROI files for co-registration into the diffusion space and then tractography? Thanks! Regards, Akila From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> Date: Sunday, 16 May 2021 at 22:25 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation The labels that you are looking for are: 7,8, 46, 47 You can use the below command isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label in order to get these from the aseg volume. That will result in 4 ROI files that you can use in your further analysis. Lilla ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ar...@cam.ac.uk> Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Hi Lilla, That would be ideal! Thanks Akila Get Outlook for iOS<https://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> Sent: Sunday, May 16, 2021 5:22:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation Is your question then how to isolate the cerebellar WM/GM labels from aseg? Lila ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ar...@cam.ac.uk> Sent: Friday, May 14, 2021 12:13 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Hey, Thanks for your message. Yes I have! Akila From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> Date: Friday, 14 May 2021 at 16:44 To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation Hi Akila, Have you run recon_all on your structural data? Lilla ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ar...@cam.ac.uk> Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. It would be great if you could give me advice and any feedback about the pipeline. Thanks for your help! Regards, Akila
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