22 Feb
2019
22 Feb
'19
10:38 a.m.
Hi Yi Leng
no, I guess the thing to do for now is use the labels, which appear reasonable, and not the .annot
cheers Bruce On Fri, 22 Feb 2019, Yi Leng Fung wrote:
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 yfung@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 fischl@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 <fischl@nmr.mgh.harvard.edu> wrote: > Do the labels look better than the annot? > > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung <yfung@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 <AHOOPES@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-bounces@nmr.mgh.harvard.edu> on behalf of Yi Leng Fung > <yfung@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 <jean@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 <fischl@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 <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 > > > > > >_______________________________________________ > 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