[Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Anastasia! I will go backwards with increasing difficulty for me to understand everything: 4. I see, yes this would not make sense. Thank you for the explanation! 3. With fslview I will have to run through 393,120 slices, then. (72 slices in z-direction for our 70 DWI scans for tp1 and tp2 fo

[Freesurfer] tracall longitudinal default options

Hi all! I am almost ready to do my first longitudinal run with Tracula. I guess that for the remaining insecurities it is probably best to stick with the default options but I'd like to be more confident with it and just wanted to ask which option to choose and why or why not: My config file conta

Re: [Freesurfer] tracall longitudinal default options

Thank you so much for your help! :) - Field inhomogeneity: great, I'll stick with the default option then - Number of sticks: thank you..I had a look at Figures 8 and 9 in the mentioned paper..and this does not look good: we have 60 non b0 images with a b-value of 700 and the dwi_snr text file in

[Freesurfer] Tracula longitudinal "nan" values for highest probability path

Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them "nan"-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the c

Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path

Hi Anastasia, the files are here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr The base is here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB Freesurfer outputs: /autofs/cluster/lazar/proj

[Freesurfer] long_mris_slopes sign of do-rate

Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experiment