I am attempting to pre-process my data using the TORTOISE documentation. The recommendation is to “axialize” the data using the AFNI script fat_pre_axialize_anat.tcsh, however I am unable to locate this script even examining the latest version. For that matter, I can’t find any of the scripts recommended here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Prepreprocessing.html#. Do I need to download something in addition to the precompiled AFNI binaries?
Thanks in advance!
Righty-o. So, that documentation was a first draft at making wrapper scripts for going from DICOMs up to TORTOISE and FreeSurfer usage for combining structural + DWI processing and analyses. On the “Overview” page before that, there actually is a script tarball of several tcsh-scripts that are referred to there. They were not put into the main distribution because they were still in flux, basically.
Since that time, those scripts have been greatly expanded (both in number and in functioning), and TORTOISE itself has been released in version 3.0 for which DIFF_PREP and DR_BUDDI are command line processable: hooooorrraaaaayy! I am waiting for a couple small updates to TORTOISE to allow for easier scripting, and then there will be a new set of documentation+examples for processing, including scripts for basic running of TORTOISE3.0.
Therefore, I wouldn’t recommend using the older scripts at this point, but instead to use the updated versions, which are pretty much stabilized in development for being releasable in the main source. If you like, this can be discussed more offline.
Hi Paul, do you have an update on this? I’m going round in circles trying to find fat_pre_axialize_anat.tcsh, fat_pre_t2w_from_t1w.tcsh etc? Thanks! L
Thanks! I was using fat_pre_* rather than fat_proc_*