-cubic only affects the very first part of the stream, so it should not affect processing when you re-run after edits

-custom-tal-atlas also only affect the first part of the stream

-qcache should only be run after you have done all of your processing. If you do not re-run it, then qdec will use the data from the initial execution (ie, it will not have your edits)

-pctsurfcon and -cortparc3 may be redundant depending upon how your run recon-all after edits

-mprage is more complicated because it is used at several places in the stream. In general, you should use it every time you run recon-all

On 5/14/19 3:04 PM, Aaron Tanenbaum wrote:

External Email - Use Caution

Hello freesurfers, Our lab has been using freesurfer 5.3 for a while. We use the following flag when we run the initial recon-all

-mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon -custom-tal-atlas TRIO_PIB_NDC_as_mni_average_305

However i have found out that we do not use any of these flags when we have we rerun recon-all after making standard edits. So my question is do any of these flags need to be used when rerun recon-all?

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