Dear FreeSurfer TRACULA experts,
I am new to FreeSurfer and using TRACULA to process DTI data. From the mail-archive, I understand TRACULA mainly needs the aparc+aseg output from recon_all in order to run. Using the recon_all output information, I was able to complete the 3 steps in TRACULA, but only after switching from the 7.1.1 version to the 6.0.5.1 version of FreeSurfer. I have the following questions about TRACULA:
1. Some of the tutorial files that are needed to run the TRACULA tutorial are not there upon downloading or do not match the tutorial instructions. Is there an updated version of the tutorial instructions that match the current files? 2. Do you have insight as to why TRACULA -prep exits with ERRORS when it's run with version 7.1.1 of FreeSurfer, but exits without errors when it's run with version 6.0.5.1? Reviewing the scripts, it seems the most notable difference are the values for i_ras, j_ras, and k_ras. Version 6.0.5.1 gives varying numbers, while version 7.1.1 gives values of -1, 0, or 1. 3. I came across the webpage introducing version 7.2 with substantial updates for TRACULA after having run my dataset with version 6.0 (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes). It states, "Unless the new features are employed, recon-all will give the same exact result as 7.1.1 and 7.1.0." Is this also true for TRACULA? Would you advise rerunning my dataset with version 7.2 of TRACULA (or even 7.3, but the recent release notes for this version didn't mention TRACULA changes)? 4. Is there another location to find the dwi_motion_byvol.txt output file? Currently the instructions say it should be located in the /subject#/dmri folder but only the dwi_motion.txt can be found there (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs). 5. For some subjects with visible motion distortions in manual quality check, I ran TRACULA as a second QC measure. However, they are still given a score of 0 and 1 for percent bad slices and average dropout score, respectively, according to the dwi_motion.txt. In fact, for all the subjects I ran, they all received those scores with the exception of one subject, who actually had minimal motion artifacts in manual QC. I'm not sure how to interpret this and was wondering if you could please advise. 6. While combing through the mail-archive to better understand how to use TRACULA, I noticed dt_recon being mentioned with TRACULA processing. Is this a step that needs to be completed before running TRACULA? Or is it part of an older version of processing that is already built into the updated versions 6.0+ of TRACULA?
Thank you in advance for your time!
Warm regards, Diana