External Email - Use Caution
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 athttps://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 curlhttps://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 YiLeng 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 CautionImage 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 afix
tomorrow and hopefully we can have one out to you (and the rest ofthe
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 theperirhinal 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 thelh.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 aninflated 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 regardingthe BA.thresh.annot
file. When visualised in > Freeview > > (using Bert as > > > the example), the BA.thresh annotation filelabelled the medially
located structure as the > perirhinal > > cortex and > > > the laterally located structure as theentorhinal cortex.
> > > > > > 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 islabelled as such in
the annot file? > > > > > > Again, thank you for your time in helping meunderstand 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 themax p-value at
each location. > > > The thresholded .label files are computedto have the surface
area that > > > matches the average of the traininglabels, so they will not
be the same. > > > > > > cheers > > > Bruce > > > > > > > > > On > > > Tue, 5 Feb 2019, Yi Leng Fung wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > Dear FreeSurfer Developers, > > > > > > > > Prior to extracting the gray volumenumbers of the
entorhinal and perirhinal cortex > from > > > > ?h.BA_exvivo.thresh.stats file, I wasexamining 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 andlabel files from the
fully recon-ed subject > named > > "bert" on > > > > Freeview and observed the same mismatchin the labeling. I
am curious why this might > be the > > case. > > > > > > > > I have searched the archive and have notbeen able to find
any similar queries on > this, hence > > it > > > would be > > > > of tremendous help if someone couldclarify 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 lookforward 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
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