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Thank you, Anastasia. I emailed you off-list with a link to our data.
djr
On Wed, Mar 16, 2022 at 1:03 PM Donovan Roediger roedi004@umn.edu wrote:
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:
- 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: https://secure-web.cisco.com/1-sjZQvXljDNiCmjPmky_iAlXAQNXAv3ozZOl8D_fAugyKZ...
Longitudinal TRACULA:
- 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: https://secure-web.cisco.com/1XErg-f5naJbI7U1JRSOIq_9GJ7HzxrxGsDNY6uFnbwSs4G...
Thanks so much! Donovan
-- Donovan Roediger Neuroimaging Analyst | Psychiatry | psychiatry.umn.edu University of Minnesota Medical School | med.umn.edu | 612-626-5064 staff bio https://secure-web.cisco.com/13sNXjL0Aq1YWYB4xrD1Pkv-2AchfervPP5zunnx_4FfQFQLhxyEwrQXHQ7HfZSEI3fb60mWM68A911LV7tmZmFtyOsm3FSgUfuyGDqioApcTbBBATMR9nd-LW9JKUlIAxo2ol4ZEipx7iwQxNGoL7EMBcAcIZcnX2q0h4p_0OSsZh30NpaJdLZ9gmRbv1g9REV6XDUZmwpBVQJbynmsdEolbx64FE0LqdZObJJNQKtm_M9jmTRplXO5SSMeeKMePwuJsWkyMZUitcEWfkVk4_4mtTNKsfkifAJV22gQKyyQoZ6oi9dzDzWJokt8qIEguh4iHuSZ9bLCDYPb_fgObS7zGbjpl49RFty9hu6e1QWY/https%3A%2F%2Fmed.umn.edu%2Fbio%2Fpsychiatry-staff%2Fdonovan-roediger | he, him, his