External Email - Use Caution Hello Bruce,
I am just checking in as I am curious if there has been any update available regarding the entorhinal and perirhinal annot/labelling? I hope I haven't missed anything. Thank you! Yi Leng On Sun, Feb 10, 2019, 16:32 Yi Leng Fung <yf...@student.unimelb.edu.au> wrote: > > Hello Bruce, > > I have uploaded a tarred and gzipped subject onto the ftp site. Do let me > know if there is anything else I could help with. > > Cheers, > Yi Leng > > > On Sat, Feb 9, 2019 at 2:25 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Yi-Leng >> >> can you upload the worst subject to our ftp site (the entire gzipped and >> tarred subject dir please). >> >> cheers >> Bruce >> On Fri, 8 Feb 2019, Yi Leng Fung wrote: >> >> > >> > External Email - Use Caution >> > >> > [64b4f0f085b91c1f8130601d2cf65e8861fc5b7f.png?u=328927] >> > Hello Bruce, >> > >> > On all four of our studies, the labels and the annot look similar in >> the sense that almost the entire >> > rh.perirhinal_exvivo.thresh.label was contained within the >> rh.entorhinal_exvivo.thresh.label (screenshot of the >> > right hemisphere with labels and annot attached for your reference). >> The resulting annot label shows an extremely >> > under-represented perirhinal on the right hemispheres. The left >> hemispheres did not show such a dramatic overlap. >> > >> > Cheers, >> > Yi-Leng >> > >> > >> > On Fri, Feb 8, 2019 at 3:44 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> > Do the labels look better than the annot? >> > >> > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung <yf...@student.unimelb.edu.au> >> wrote: >> > >> > External Email - Use Caution >> > >> > Hello FreeSurfer team, >> > >> > Thank you for providing the recon-all patch. We have applied this to >> four studies and have seen a >> > notable difference between in the representation of entorhinal over >> perirhinal on the right hemisphere >> > labelling on each analysis ran. The left hemisphere appears to have >> less overlap. >> > >> > I have attached a screenshot of both hemispheres to demonstrate. Would >> really appreciate any feedback. >> > Thanks! >> > >> > Cheers, >> > Yi-Leng >> > >> > >> > On Wed, Feb 6, 2019 at 3:11 AM Hoopes, Andrew <ahoo...@mgh.harvard.edu> >> wrote: >> > >> > Hi Yi Leng, there’s a recon-all patch for 6.0 at >> > >> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all. >> You can >> > update it with: >> > >> > >> > >> > cd ${FREESURFER_HOME}/bin >> > >> > mv recon-all recon-all.backup >> > >> > curl >> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all >> -o >> > recon-all >> > >> > chmod +x recon-all >> > >> > >> > >> > Let us know if that works! >> > >> > >> > >> > thanks >> > >> > Andrew >> > >> > >> > >> > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yi >> Leng Fung >> > <yf...@student.unimelb.edu.au> >> > Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> >> > Date: Monday, February 4, 2019 at 9:17 PM >> > To: FS Help <freesurfer@nmr.mgh.harvard.edu> >> > Cc: Jean Augustinack <j...@nmr.mgh.harvard.edu> >> > Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and >> > ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label >> > >> > >> > >> > External Email - Use Caution >> > >> > Image removed by sender. >> > >> > Thank you! >> > >> > >> > >> > Cheers, >> > >> > Yi Leng >> > >> > >> > >> > >> > >> > On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> > >> > 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 < >> fis...@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 < >> fis...@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 < >> fis...@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 >> > > >> > > >> > >_______________________________________________ >> > 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 >> > >> > <screenshot_20190207_rh_perirhinal_obscured_recon-all_patch.png> >> > >> > _______________________________________________ >> > 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 > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
