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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
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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 inflatedsurface 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 theBA.thresh.annot file. When visualised in
Freeview > (using Bert as > > the example), the BA.thresh annotation file labelled themedially located structure as the
perirhinal > cortex and > > the laterally located structure as the entorhinalcortex.
> > > > I find that quite puzzling as I understand theirrelative anatomical location to be the
reverse; I > would really > > appreciate it if you could clarify why it is labelled assuch in the annot file?
> > > > Again, thank you for your time in helping me understandthis.
> > > > 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 maxp-value at each location.
> > The thresholded .label files are computed to havethe surface area that
> > matches the average of the training labels, sothey 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 ofthe entorhinal and perirhinal cortex
from > > > ?h.BA_exvivo.thresh.stats file, I was examiningthe entorhinal and perirhinal cortex
on the > > > ?h.BA.thresh.annot on Freeview. However, I notedthat their locations on the annot
file did > not > > > correspond to the (non-overlapping) locationsindicated by ?h.entorhinal.thresh.label
and > > > ?h.perirhinal.thresh.label. > > > > > > I have also loaded the annot files and labelfiles from the fully recon-ed subject
named > "bert" on > > > Freeview and observed the same mismatch inthe labeling. I am curious why this might
be the > case. > > > > > > I have searched the archive and have not beenable to find any similar queries on
this, hence > it > > would be > > > of tremendous help if someone could clarify thisobservation. 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 forwardto 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
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