Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz,
included the same labels and followed the same lookup table as the OG
aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we
recommend also running the thalamic nuclei segmentation, as it helps with the
accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios
<dimitriosalexopou...@wustl.edu>
Sent: Wednesday, October 20, 2021 2:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
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Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from
the standard structural output from FS 7.1.1., and specifically for the
relative positions (left, right, anterior, etc.) of each tract with respect to
the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline
that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
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