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Hi Freesurfer Developers,
I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat, and I was wondering how to best visualize and interpret the results of the cluster-wise correction in freeview.
I referenced this page ( https://secure-web.cisco.com/1rtane6ARuP3X8AuU2py8u1aHHy9K5qYs7DI1jVqCAg3GHW...), which describes how to do this for uncorrected statistics, and used dmri_trk2trk to try to embed the *perm.th13.abs.sig.cluster.mgh files produced by mri_glmfit-sim into the template .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".display.trk). I also embedded the *perm.th13.abs.sig.cluster.mgh files into the mean path .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".mean.trk).
However, I'm noticing inconsistencies in the location along the tract of significant clusters between the projection of the uncorrected statistics in freeview, projection of the corrected statistics in freeview, and the cluster location as indicated by the cluster summary file (*perm.th13.abs.sig.cluster.summary.txt).
I've attached the cluster summary file for FA in the rh.cst tract as an example. My understanding is that for pathways with superior-inferior orientation, points along the tract are ordered from superior to inferior. Given that this significant cluster is at a VoxX of 68 (of 80 total points along the tract), I would have thought that this cluster would be located at a more inferior position along the right cst -- instead, the cluster appears to be located superiorly (trk files for uncorrected and corrected statistics for this pathway are attached). Similar to this FS user ( https://secure-web.cisco.com/1MD72Ga_1F-Q0FFmEMhYJe7s5dOdRHRhGL2ZDfR5AWgoROs...), I'm wondering: (1) Am I missing something regarding this embedding process? (2) Is it appropriate to embed the *perm.th13.abs.sig.cluster.mgh file to visualize the results of the cluster-wise correction?
Please let me know if there is any other information or attachments you'd like me to provide. Any thoughts on where I might be going wrong would be greatly appreciated. Thank you!
Best, Makenna
*Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin