External Email - Use Caution
Hello Bruce,
Thank you very much for your quick response.
I do have another point of confusion regarding the BA.thresh.annot file. When visualised in Freeview (using Bert as the example), the BA.thresh annotation file labelled the medially located structure as the perirhinal cortex and the laterally located structure as the entorhinal cortex.
I find that quite puzzling as I understand their relative anatomical location to be the reverse; I would really appreciate it if you could clarify why it is labelled as such in the annot file?
Again, thank you for your time in helping me understand this.
Cheers, Yi-Leng
On Tue, Feb 5, 2019, 04:26 Bruce Fischl <fischl@nmr.mgh.harvard.edu wrote:
Hi Yi-Leng
the annot file contains the label with the max p-value at each location. The thresholded .label files are computed to have the surface area that matches the average of the training labels, so they will not be the same.
cheers Bruce
On Tue, 5 Feb 2019, Yi Leng Fung wrote:
External Email - Use CautionDear FreeSurfer Developers,
Prior to extracting the gray volume numbers of the entorhinal and
perirhinal cortex from
?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and
perirhinal cortex on the
?h.BA.thresh.annot on Freeview. However, I noted that their locations on
the annot file did not
correspond to the (non-overlapping) locations indicated
by ?h.entorhinal.thresh.label and
?h.perirhinal.thresh.label.
I have also loaded the annot files and label files from the fully
recon-ed subject named "bert" on
Freeview and observed the same mismatch in the labeling. I am curious
why this might be the case.
I have searched the archive and have not been able to find any similar
queries on this, hence it would be
of tremendous help if someone could clarify this observation. If it is
of interest, I am running
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04.
Thank you for your assistance and I look forward to hearing from you.
Best regards, Yi-Leng
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