External Email - Use Caution

Dear Freesurfer experts,

I am attempting to run an old-fashioned polar angle retinotopy analysis through FsFast.

Unsurprisingly, the tutorials I've found on the topic are somewhat outdated (>10 years ago) and seem to suggest employing flags that are no longer valid in mkanalysis-sess.

For instance, it seems that -ncycles is no longer a valid flag, instead giving -retinotopy with the period of a cycle seems to be sufficient. Yet, from my understanding, this implies giving a -tpef flag pointing to a file that has the timepoints to exclude (i.e. before and and after the wedge stimulus has been displayed, in my case both 'off' periods last 12 seconds).

My functional images have gone through fmriprep, so are already preprocessed and have the motion parameters estimated. Accordingly, I have put these in a file to give through the flag -extreg to mkanalysis-sess. However, I get the "flag unrecognized" error if I attempt to include it in my call. Is there some other way to do this?

Moreover, the wiki page on mkanalysis-sess mentions that retinotopy runs must be analyzed through sfa-sess command, yet a tutorial I've found employs selxavg3-sess, I assume this is wrong? Telling the difference between the two based on their pages in the wiki is challenging.

Many thanks in advance for any help you may provide.

Best,

Stefano Ioannucci