Re: [Freesurfer] Coordinates in TRACULA group analysis

Thanks, Anastasia I know that TRACULA use probabilistic tractography but if ROIs are not set how determine the origin and the end of a certain tract? I think that the first we have to determine the origin and the end of the tract, the second it constructs possible pathway not with the

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic model of how likely each tract is to go through or next to each of the labels of the freesurfer subcortical segmentation and cortical parcellation, as a function of position along the trajectory of the tract. Best,

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anastasia, Thank you! It seems work well!! I have another question. Are ROIs for automatic tractography in TRACULA the same ROIs presented in Wakana et al. 2007? Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里

[Freesurfer] Siemens SPECTRA 3T - Help with sequences

Dear colleagues, I’m a researcher psychiatrist who is currently testing image acquisitions with different sequences on a Siemens 3T SPECTRA scanner. I would like to learn from you if any of you had experience with this scanner in the collection of high-resolution structural images (MPRAGE), DTI,

[Freesurfer] group analysis/ region of interest (ROI) approach

Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Longitudinal single time point cross sectional comparison

Dear Freesurfer users, I have longitudinal data with three time points but want to run a cross sectional comparison on the first instance between group on just one time point (using QDEC). Any Idea on how I could do that on longitudinal data. Thanks for your help. Emmanuel Nwosu

Re: [Freesurfer] error during longitudinal -long stream

Hi Martin， I tried 2 times again (run 4 analysis at the same time). This time, it works well, The link to fsaverage is automatically created. I did not replicate the error message. Thank you so much! Best, Jinsong On Fri, Jul 29, 2016 at 11:44 AM, Martin Reuter

[Freesurfer] Running recon-all with T1 and FLAIR

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when

Re: [Freesurfer] significance overlay in freeview

Dear Ruopeng, Yes, I'm running FS 5.3. :) But then how can I see the correct significance overlay? Cause even when leaving out some commands (which may or may not work in 5.3), freeview does load, but seems to only display the DK-atlas on fs average (... and gets stuck sometimes too), as I

[Freesurfer] Where are time series from adjusted (post selxavg3) ROIs

Dear Freesurfer experts I have been going through the documentation trying to figure out how to extract the time series for an ROI (Posteriorcingulate) after removing the regressors that I put in my mkanalysis-sess. I have run the selxavg3. 1. Is this time course what is in the