4 Feb
2019
4 Feb
'19
9:03 p.m.
thanks. It is almost certainly a bug in recon-all. I'm testing a fix tomorrow and hopefully we can have one out to you (and the rest of the list) by tomorrow.
Sorry! Bruce On Tue, 5 Feb 2019, Yi Leng Fung wrote:
External Email - Use Caution
[3a1715320c6fbab489126e656ad6e765d6e0a6ee.png?u=328927] Hello Bruce,
Yep, the exvivo entorhinal thresh label overlay on the perirhinal annotation. I have attached a screenshot of it for your reference.
Cheers, Yi-Leng
On Tue, Feb 5, 2019 at 12:31 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yi-Leng
eek! Can you verify that the lh.entorhinal_exvivo.thresh.label is correct? Does it overlay on the perirhinal annotation? thanks Bruce On Tue, 5 Feb 2019, Yi Leng Fung wrote: > > External Email - Use Caution > > [3f1a37b0d4514e4a90a5d3340afcefe6c789830e.png?u=328927] > Hello All, > > Here it is, both are from bert. > > Thank you for looking into this. > > Cheers, > Yi-Leng > > On Tue, Feb 5, 2019 at 7:47 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Yi-Leng > > can you send us an image of the parcellaton on an inflated surface so we > can see? > > thanks > Bruce > > > On Tue, 5 Feb 2019, Yi Leng Fung wrote: > > > > > 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 Caution > > > > > > Dear 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 > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer