Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
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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
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
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 CautionDear 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
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
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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 CautionHello 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 eachlocation.
The thresholded .label files are computed to have the surface areathat
matches the average of the training labels, so they will not bethe 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 entorhinaland perirhinal cortex from
> ?h.BA_exvivo.thresh.stats file, I was examining the entorhinaland perirhinal cortex on the
> ?h.BA.thresh.annot on Freeview. However, I noted that theirlocations on the annot file did not
> correspond to the (non-overlapping) locations indicatedby ?h.entorhinal.thresh.label and
> ?h.perirhinal.thresh.label. > > I have also loaded the annot files and label files from thefully recon-ed subject named "bert" on
> Freeview and observed the same mismatch in the labeling. I amcurious why this might be the case.
> > I have searched the archive and have not been able to find anysimilar queries on this, hence it
would be > of tremendous help if someone could clarify this observation. Ifit is of interest, I am running
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu16.04.
> > Thank you for your assistance and I look forward to hearing fromyou.
> > 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
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
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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 surfaceso 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 entorhinal cortex. > > I find that quite puzzling as I understand their relativeanatomical location to be the reverse; I
would really > appreciate it if you could clarify why it is labelled as such inthe 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 ateach location.
> The thresholded .label files are computed to have thesurface area that
> matches the average of the training labels, so they willnot 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 theentorhinal and perirhinal cortex from
> > ?h.BA_exvivo.thresh.stats file, I was examining theentorhinal and perirhinal cortex on the
> > ?h.BA.thresh.annot on Freeview. However, I noted thattheir locations on the annot file did
not > > correspond to the (non-overlapping) locations indicatedby ?h.entorhinal.thresh.label and
> > ?h.perirhinal.thresh.label. > > > > I have also loaded the annot files and label files fromthe 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 tofind 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 onUbuntu 16.04.
> > > > Thank you for your assistance and I look forward tohearing 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
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
External Email - Use Caution
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
> > >_______________________________________________ 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
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.edumailto: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.edumailto: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<mailto: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<mailto: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<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: 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 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
> > >_______________________________________________ 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
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 CautionHello 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 CautionThank 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
External Email - Use Caution
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 CautionHello 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: 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 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 regarding theBA.thresh.annot file. When visualised in
Freeview > (using Bert as > > the example), the BA.thresh annotation file labelledthe medially 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 labelledas such 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, Inoted that 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 clarifythis 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
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
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.labelExternal 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
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
> > >_______________________________________________ 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
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 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 restof 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 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 understandtheir relative
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 withthe max 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 onFreeview. 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 havenot been 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 Ilook 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
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Hoopes, Andrew -
Yi Leng Fung