Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 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 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
wrote:
> Do the labels look better than the annot?
>
> On Feb 6, 2019, at 10:15 PM, Yi Leng Fung
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
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: on behalf of Yi
Leng Fung
>
> Reply-To: FS Help
> Date: Monday, February 4, 2019 at 9:17 PM
> To: FS Help
> Cc: Jean Augustinack
> 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
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.
> >
>
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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
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
> 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
>> wrote:
>> > Do the labels look better than the annot?
>> >
>> > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung
>> 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
>> 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: on behalf of Yi
>> Leng Fung
>> >
>> > Reply-To: FS Help
>> > Date: Monday, February 4, 2019 at 9:17 PM
>> > To: FS Help
>> > Cc: Jean Augustinack
>> > 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
>> 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
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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
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
> wrote:
> > Do the labels look better than the annot?
> >
> > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung
> 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
> 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: on behalf of Yi
> Leng Fung
> >
> > Reply-To: FS Help
> > Date: Monday, February 4, 2019 at 9:17 PM
> > To: FS Help
> > Cc: Jean Augustinack
> > 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
> 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
> > >
> > >
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 wrote:
Do the labels look better than the annot?
On Feb 6, 2019, at 10:15 PM, Yi Leng Fung 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 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: on behalf of Yi Leng Fung
Reply-To: FS Help
Date: Monday, February 4, 2019 at 9:17 PM
To: FS Help
Cc: Jean Augustinack
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 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
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
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
> >
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
Do the labels look better than the annot?
> On Feb 6, 2019, at 10:15 PM, Yi Leng Fung
> 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
>> 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: on behalf of Yi Leng Fung
>>
>> Reply-To: FS Help
>> Date: Monday, February 4, 2019 at 9:17 PM
>> To: FS Help
>> Cc: Jean Augustinack
>> Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and
>> ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
>>
>>
>>
>> External Email - Use Caution
>>
>>
>>
>> Thank you!
>>
>>
>>
>> Cheers,
>>
>> Yi Leng
>>
>>
>>
>>
>>
>> On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl
>> 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
>> > 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
>> > 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.thres
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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: on behalf of Yi Leng Fung
Reply-To: FS Help
Date: Monday, February 4, 2019 at 9:17 PM
To: FS Help
Cc: Jean Augustinack
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
mailto: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
> mailto: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
> mailto: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
> mailto: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,
> > > >
> >
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
External Email - Use Caution Thank you! Cheers, Yi Leng On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl 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 > 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
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 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 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 > 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 > >
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 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 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
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 > 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
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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 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
Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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
