I want to preprocess and analyze group differences in cortical surface area and so far, I used freesurfer's recon-all and -qcache for preprocessing. As far as I understodd, it basically does a lot of different steps for you, from motion correction to skull stripping to smoothing.
Are there any other / up-to-date tutorials or other ways of doing structural preprocessing?
Hi,
You can try FSL pre-processing for artefact corrections and start with the FS processing stage 2 directly.
Cheers
Would you recommend FSL rather than FS for motion correction? I am asking because all the data is already preprocessed fully with FS, but we wanted to make sure we didn't miss THE better software/function to do the preprocessing before continuing.
I would also recommend checking out CAT12:
http://www.neuro.uni-jena.de/cat/index.html#SBM
i've been using CIVET and SurfStat for cortical thickness, but it also does surface analysis http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET it's an online pipeline which does the preprocessing automatically, you upload the images and it returns all sorts of data
I specifically use SPM12 for preprocessing VBM analysis of structural MRI data or T1 images. Is there any other way we can do that more manageable?
I used freesurfer now, but it is probably a little less user-friendly than an SPM12 toolbox as there is no GUI...
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