Hi Tamara,
1. brainmask.mgz
2. yes, as you will get your final measures from the long output stats. Take a look at how aseg edits are done in the regular cross stream. In long it would work the same (just with passing -long and then instead of -all you just do the last steps to recompute the stats). If you cannot find this on the wiki. Ask again here without longitudinal (just how to do aseg edits and what steps to run after that).
3. see earlier mail. If the long look OK, the rest should have worked basically.
Best Martin
On Oct 19, 2016, at 7:06 PM, Tamara Tavares ttavare@uwo.ca wrote:
Hello,
I am interested in looking at ventricular changes over time and thus, have ran the longitudinal stream on my participants scans. As suggested online, I am checking the ventricular segmentation in the longitudinal outputs and am planning on making any edits to the longitudinal stream if the segmentation of the ventricles are incorrect. I have a few questions related to this:
To check the segmentations, should I overlay the aseg.mgz with the brainmask.mgz or the brainmask_SubjID-Temp.mgz?
If I find that the segmentation of the ventricle is incorrect, should I make edits to the aseg output in the longitudinal outputs? What command line would I use to re-do the longitudinal stream with the corrected segmentation?
After looking to see whether there are errors in the longitudinal recon-all script output, are there any other things I should check to ensure that the base and longitudinal stream ran correctly?
Thank you in advance for your help! Tamara
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