Hi Donovan - That's interesting, is there a way you can share the cross and long dirs of this subject with me? The data look good based on the cross tracts, so I suspect there might be an issue with a registration or other step that comes before the tract reconstruction, and that affects only the long stream.
Thanks! Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Donovan Roediger roedi004@umn.edu Sent: Wednesday, March 16, 2022 2:03 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA longitudinal - weird tracts
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Hello Anastasia,
I ran TRACULA (7.2.0) twice on the same dataset, once as cross-sectional and once as longitudinal. The cross sectional tracts look OK, but the longitudinal output looks very bad for every subject. Below are summaries of my workflows along with links to screenshots of the resulting tracts. Can you tell what I'm doing to mess up the longitudinal stream?
Cross sectional TRACULA: 1) Structural and diffusion data preprocessed using HCP 4.0.1 (which includes cross-sectional recon-all with FS 6.0) 2) Thalamic segmentation was run using FreeSurfer 7.2.0. 3) Cross sectional TRACULA (7.2.0) was run using the HCP-cleaned diffusion data. Default settings used except doeddy=0 because eddy was run as part of HCP preprocessing. IMAGE: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/12fAumCxWwdNzVSMZP9mKcmaTqsxP01oD/viewhttps://secure-web.cisco.com/13BZ6YlVnYcAOxNoC1FBf0K8tfLvVUgG_XzJ51MPZJ5fE68WILWzsybN0GpSP1erIUeKk7-HtFX3hAI4vzcWOaT7uC09PukR4GdFt-EoQCtqsBTO3qI5LEvkL9t3LWmh9wkM-m5t3_jfd0lPPbZIOJTCsDgKOQ8qdAvKNkZ4aTYjrDOZkoM17qc_cLSNdSilfB_uQnQYMllmqiMx21EaTr2JPlMBcLgUqvnydp-OfKi4WkJsGwjkSC3pqF_gjS3jHKPRMLQRxLIEdtIl-Eja3RvrnSI3QR16SAfsprLOsuz8sbcsOx5AiZr1cWDZnXRAf8UeNrNCW95r83yE7AmljVuL-aDNEyxDZ0OlF-d3NAwE/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F12fAumCxWwdNzVSMZP9mKcmaTqsxP01oD%2Fview
Longitudinal TRACULA: 1) Structural and diffusion data preprocessed using HCP 4.0.1 (which included cross-sectional recon-all with FS 6.0). 2) Longitudinal recon-all was run under FreeSurfer 6.0 starting with the HCP FreeSurfer cross-sectional outputs. 3) Thalamic segmentation was run on the ".long" subjects using FreeSurfer 7.2.0. 4) Longitudinal TRACULA (7.2.0) was run using the HCP-cleaned diffusion data. Default settings used except doeddy=0 because eddy was run as part of HCP preprocessing. IMAGE: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/14OjjOqWAAywNCAquA7BRe1Nnsy7JPRJk/viewhttps://secure-web.cisco.com/1us4Dr6uNFzuOYt72IbrjF1_SvArR22k16JUpH4ZBPgF2WV62r1N3XmMQq1t57Y7iTEU_sO0k6HmrH46cVdhN9Vovzvut9nHlVUsMhpHsU5FtcrXEUmS2JtWnEs2MMSbNAbFHoJW_W51THBa9gjUh64WGpvFrAIyGkki3Qt2eDl9LHUp7OYchU9k_5okkt9XRi_-dwVf2fG1yCBiuwE8_7m8Pd4R9T_oo9CT0I9kXsi8ClDjSM3Z8mDaCpelqrd-urcgoOwq8dn6osbRKwKfDr6rSdNjUi7OIvcFoRtWUhuykU8uezQ_5jzCk1x3WmbcOSaSv6i7IHMJQAvGqs6Z-xzKKo1La7oW8CM_uUXVpFzQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F14OjjOqWAAywNCAquA7BRe1Nnsy7JPRJk%2Fview
Thanks so much! Donovan
-- Donovan Roediger Neuroimaging Analyst | Psychiatry | psychiatry.umn.eduhttp://secure-web.cisco.com/1XUdWsTie5QlwBj9f61BHiVYk8RaruC4rpqsiO8n9f-UyLCYcrkzK2jw0zSbvsx5XYr5Z4qCZNs4798yL6cnocCQaX6sXfatp6ZNdPzosLCRSVWHYt1MDEogbn63TyBJ5cC8JSYOXxIFMuNgdpkmX0XVM_Z93WFbQQzsQL5zifUT_eAewpiwo8UPYMFsxoPHU6fa9Zgmjkm_FBx-2M7lvc8XnO4kNxWToOe3sGxVgUWUieq82fNbt3xOCtfHqBbM9IVEgKCIc2GsWvwWHO0rH0MVvGlMamXDWWyuOZGe8GHMAqlZQuReuCeAyc1uKlZWho1k7_ocknrN-ZsL7nbRv7ncjUAsCXu61uuMt4u4WAbY/http%3A%2F%2Fpsychiatry.umn.edu University of Minnesota Medical School | med.umn.eduhttp://secure-web.cisco.com/1S_BJlSQ2NSw1kMVllZXzgNqCqDU_5lhSQ24tpZ0hy94dFVD0Tqke-h7u_9ebCIUHdbBJwoIwbxZ4q6ggUnoIyKSh0IPwT4vV9ZBFofgNTD97ZSut14ia1uXM_3NDQqLHvuHtWe9f_CsRvqJjVrpzi0wBksyp7sUXFVa3C_CmLIuFSwHP5nMoD-GvlQc8dWtSiUpmtHPbeeesyQzg05PziQd2Q8_7dbmwLvvC0mHiM6BhepifW5QIDK_p_qwQMqoypKTftduhuebfv_kVz__yDD8NkQiQ-Y5DY4-lUQeuFhSamjd3c_-KmpIaowM_Ddt8PLOlv-g9RMqP5L1cq1AR8JhCHW_k0eN27EXPmpxe9E4/http%3A%2F%2Fmed.umn.edu | 612-626-5064 staff biohttps://secure-web.cisco.com/1IdZ5gFMBKeiXOXZZl8u_Lmu2Itqgjp8vqJbAswnHrkh98m9ZXoILXUpGo8TM5CTJHBTv65PVhNU_2BMmJZlVpF1u_d0kJqjK5gUM4RlTTTB7tdxgO2IVpql1FuC0JGX88jmG5TXt5yQtEbBI1wEe0DwDe8mc0bIzRMTVgf8GHASacA3LY3TcJ34jCu3btGjURHEfawRu-Tr_HaMV8xP6Htc39HH9zslKTSpPhQdEtoFglQB9fxIoZpz8CqMR1matQenqgNv4EZ9UfH-RXVNWcaBNpg83jM6Ofi5IAMjTiaiUZfQkXjndhPTC6WikK21sdL8sRntkZo1ivBjAXWNaMuBHg-Bftb8JHWjPcCcjumY/https%3A%2F%2Fmed.umn.edu%2Fbio%2Fpsychiatry-staff%2Fdonovan-roediger | he, him, his