subject:"Re\: \[Freesurfer\] Hippocampal Subfields Segmentation"

Re: [Freesurfer] hippocampal subfields segmentation

2012-01-26 Thread Koen Van Leemput

Hi Joana,

The smallness of our CA1 compared to other protocols seems to be
caused by disagreements in the fields of where the subfield boundaries
should be located. I've talked to several experts on this and they all
are confident that their own definition is the only "right" one. :-)

As for the atlas our manual segmentations are based on, I believe it's
Duvernoy but I'm cc-ing Jean Augustinack and Brad Dickerson who know
more about this.

Hope this helps,

Koen


On Thu, Jan 26, 2012 at 9:54 AM, JOANA BRAGA PEREIRA
 wrote:
> Dear Koen & Freesurfers,
>
> I've been working with the GEMS tool for hippocampal subfields
> segmentation and have a question I would like to ask you all.
>
> I've noticed that the CA1 sector appears to be quite small compared to
> other subfields (CA2-3 seems to be the largest), while previous
> studies suggest that it should be the largest subfield of the
> hippocampus. Why?
>
> On the other hand, I have read the paper by Van Leemput et al. [2009]
> and how the subfields were initially delineated and was wondering what
> atlas was the manual tracing based on?
>
> Many thanks!
>
> joana
>
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] hippocampal subfields segmentation

2012-01-26 Thread Joana Braga Pereira

Dear Koen,

Thanks! I will wait for Dr. Augustinack and Dr. Dickerson's answers.

joana

2012/1/26 Koen Van Leemput 

> Hi Joana,
>
> The smallness of our CA1 compared to other protocols seems to be
> caused by disagreements in the fields of where the subfield boundaries
> should be located. I've talked to several experts on this and they all
> are confident that their own definition is the only "right" one. :-)
>
> As for the atlas our manual segmentations are based on, I believe it's
> Duvernoy but I'm cc-ing Jean Augustinack and Brad Dickerson who know
> more about this.
>
> Hope this helps,
>
> Koen
>
>
> On Thu, Jan 26, 2012 at 9:54 AM, JOANA BRAGA PEREIRA
>  wrote:
> > Dear Koen & Freesurfers,
> >
> > I've been working with the GEMS tool for hippocampal subfields
> > segmentation and have a question I would like to ask you all.
> >
> > I've noticed that the CA1 sector appears to be quite small compared to
> > other subfields (CA2-3 seems to be the largest), while previous
> > studies suggest that it should be the largest subfield of the
> > hippocampus. Why?
> >
> > On the other hand, I have read the paper by Van Leemput et al. [2009]
> > and how the subfields were initially delineated and was wondering what
> > atlas was the manual tracing based on?
> >
> > Many thanks!
> >
> > joana
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
> >
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Re: [Freesurfer] hippocampal subfields segmentation

2012-01-26 Thread Joshua Lee

I am not an expert but I'll say this as far as compliance to Duvernoy: In
the body of the hippocampus, compliance to Duvernoy is quite strongmuch
better than any others I've seen. However, according to my reading of
Duvernoy, the positions of the subfields change in the anterior head and
posterior tail, as compared to the body. Subiculum comes farther laterally,
and CA1 is further up superior-lateral (about at 10:00 o'clock), and
proceeds superiorally of the hippocmapus almost to the most medial extent
of the hippocampus...leading me to conclude that CA3 is very small in the
head, and may be non existent in the most anterior half of the headat
least according to my reading of Duvernoy atlas.

I want to reiterate my support for this project. The hippocampal subfields
are very important to a great number of researchers, as are the other MTL
structures (i.e. perirhinal cortex, posterior parahippocampal gyrus,
entorhinal cortex). By implementing an easy to use automated technique,
Freesurfer will, in my estimation become the de-facto standard in the
field. As such, I believe the segmentation protocol will come under
increased scrutiny by the community...and I wish that an effort is made by
someone (like Duvernoy but more robustly quantified) to create a standard
that is well validated by which all researchers may begin making
comparisons of their findings. The current Freesurfer implementation does a
pretty good job...but the field needs to come to terms with the positions
of the fields, and how those might change along the long-axis of the
hippocampus.

Best,

Joshua

n Thu, Jan 26, 2012 at 8:50 AM, Joana Braga Pereira  wrote:

> Dear Koen,
>
> Thanks! I will wait for Dr. Augustinack and Dr. Dickerson's answers.
>
> joana
>
>
> 2012/1/26 Koen Van Leemput 
>
>> Hi Joana,
>>
>> The smallness of our CA1 compared to other protocols seems to be
>> caused by disagreements in the fields of where the subfield boundaries
>> should be located. I've talked to several experts on this and they all
>> are confident that their own definition is the only "right" one. :-)
>>
>> As for the atlas our manual segmentations are based on, I believe it's
>> Duvernoy but I'm cc-ing Jean Augustinack and Brad Dickerson who know
>> more about this.
>>
>> Hope this helps,
>>
>> Koen
>>
>>
>> On Thu, Jan 26, 2012 at 9:54 AM, JOANA BRAGA PEREIRA
>>  wrote:
>> > Dear Koen & Freesurfers,
>> >
>> > I've been working with the GEMS tool for hippocampal subfields
>> > segmentation and have a question I would like to ask you all.
>> >
>> > I've noticed that the CA1 sector appears to be quite small compared to
>> > other subfields (CA2-3 seems to be the largest), while previous
>> > studies suggest that it should be the largest subfield of the
>> > hippocampus. Why?
>> >
>> > On the other hand, I have read the paper by Van Leemput et al. [2009]
>> > and how the subfields were initially delineated and was wondering what
>> > atlas was the manual tracing based on?
>> >
>> > Many thanks!
>> >
>> > joana
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> > contains patient information, please contact the Partners Compliance
>> HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> > but does not contain patient information, please contact the sender and
>> properly
>> > dispose of the e-mail.
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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>
>
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread pierre deman

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some
library (libmwi18n.so for example, it was missing others before that I
added on my computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
permesh.dhil...@nottingham.ac.uk> wrote:

> Hello FreeSurfer Developers,
>
> I’m having issues with the hippocampal subfields segmentation using OS X
> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp:
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp:
> freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>
> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
> getting an error message : Error:CTF file
> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
> failed to open for 'Read' access. Error message: 'Open a zip file for
> read/modify failed.’
>
> The segmented hippocampal files as described on free surfer wiki cannot
> be found under the subject ‘mri’ folder.
> I understand other users have complained of a similar issue within the
> last week.
>
> I’d ve grateful if you could assist me with the issue above.
>
> Many thanks
> Permesh
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment.  Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
> computer system, you are advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
> permitted by UK legislation.
>
>
> ___
> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread Iglesias, Eugenio

Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library
(libmwi18n.so for example, it was missing others before that I added on my
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting
an error message : Error:CTF file
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
failed to open for 'Read' access. Error message: 'Open a zip file for
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this
message or in any attachment. Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

--
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Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread pierre deman

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
wrote:

> Hi everyone,
> you need to install the Matlab 2012b runtime as explained in the wiki:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
>
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 27 Jun 2016, at 15:16, pierre deman  wrote:
>
> Hello,
>
> I have similar problem. "
> "Error:Cannot find CTF archive
>
> /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
> the file is here but when I try to execute it, it's always missing some
> library (libmwi18n.so for example, it was missing others before that I
> added on my computer, but it never ends)
> I am on ubuntu 14.04.
> I thought that the problem is linked to the matlab runtime. I installed
> the 2012b. I tried newer version. installed again the 2012b.
>
> Regards,
> Pierre
>
>
> On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
> permesh.dhil...@nottingham.ac.uk> wrote:
>
>> Hello FreeSurfer Developers,
>>
>> I’m having issues with the hippocampal subfields segmentation using OS X
>> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject
>> Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current
>> Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>>
>> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
>> getting an error message : Error:CTF file
>> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
>> failed to open for 'Read' access. Error message: 'Open a zip file for
>> read/modify failed.’
>>
>> The segmented hippocampal files as described on free surfer wiki cannot
>> be found under the subject ‘mri’ folder.
>> I understand other users have complained of a similar issue within the
>> last week.
>>
>> I’d ve grateful if you could assist me with the issue above.
>>
>> Many thanks
>> Permesh
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete it.
>>
>> Please do not use, copy or disclose the information contained in this
>> message or in any attachment.  Any views or opinions expressed by the
>> author of this email do not necessarily reflect the views of the
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an
>> attachment may still contain software viruses which could damage your
>> computer system, you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK legislation.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94
> ___
> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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The informati

Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-27 Thread Iglesias, Eugenio

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out
what’s going on. But it definitely sounds funny that it is asking for the CTF,
since this is supposed to be embedded in the executable… I’ll get back to you
as soon as possible.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:32, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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--
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-06-29 Thread Iglesias, Eugenio

I could finally look into this. It is indeed weird. The CTF is indeed embedded
in the executable…
Zeke/Nick, can you shed some light on this?
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:43, Iglesias, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:32, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

I tried that. but didn't work.

Cheers,
Pierre

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 27 Jun 2016, at 15:16, pierre deman
mailto:deman.pie...@gmail.com>> wrote:

Hello,

Regards,
Pierre

On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon
mailto:permesh.dhil...@nottingham.ac.uk>>
wrote:
Hello FreeSurfer Developers,

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-07-05 Thread pierre deman

Hi,
I still have a problem as well with the subfields segmentation (ubuntu
14.04, with the files .ctf)

Cheers,
Pierre
Hello FreeSurfer Experts,

I’m having issues with the hippocampal subfields segmentation using OS X
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp:
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
getting an error message : Error:CTF file
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
failed to open for 'Read' access. Error message: 'Open a zip file for
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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Re: [Freesurfer] Hippocampal Subfields Segmentation

2016-07-06 Thread Iglesias, Eugenio

Dear all,

We are working on this; I'll write again when the problem is solved (hopefully 
soon!)

Cheers

Eugenio


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of pierre deman 

Sent: Tuesday, July 5, 2016 7:04:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation


Hi,
I still have a problem as well with the subfields segmentation (ubuntu 14.04, 
with the files .ctf)

Cheers,
Pierre

Hello FreeSurfer Experts,

I'm having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.'

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject 'mri' folder.
I understand other users have complained of a similar issue within the last 
week.

I'd ve grateful if you could assist me with the issue above.

Many thanks
Permesh




This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.


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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Hippocampal subfields segmentation

2018-01-22 Thread Iglesias Gonzalez, Eugenio

Hi Alexis,
Yes please send me the images!
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Alexis Guyot 

Reply-To: Freesurfer support list 
Date: Monday, 22 January 2018 at 17:49
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields segmentation

Dear Freesurfer developers,

I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the 
hippocampal subfields of two 7T MR images in NIFTI format: an isotropic 
(0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic 
(0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and centred 
on a region comprising both hippocampi.

I have followed the instructions in 
https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon to correct the bias in 
the two 7T volumes ('T1_biasCorrected.png', 'T2_biasCorrected.png'). I have run 
'recon-all -hires [...] -expert expert.txt' ('expert.txt') on my bias-corrected 
T1 volume, which produced an accurate segmentation ('aseg.png', 
'recon-all.log'). Following this, I have run 'recon-all 
-hippocampal-subfields-T2' on the bias-corrected T2 volume 
('hippocampal-subfields-T2.log').
Looking at the resulting segmentation, I am unsure the molecular layer has been 
properly delineated in the body of the hippocampus 
('right_hippocampus_body.png', 'right_hippocampus_body_seg.png'). In addition, 
it appears the convolutions in the hippocampal head have not been correctly 
segmented ('right_hippocampus_head.png', 'right_hippocampus_head_seg.png').

I am not certain this is the expected behaviour when running the hippocampal 
subfields module on high-res data. Is it possible the recon-all output is not 
accurate enough (should I adjust the mres_inflate value prior to segmenting the 
brain)? Could the high anisotropy of the T2 volume hinder the segmentation 
process?
Any thoughts on this? Screenshots/attachments are available on request, as my 
previous message was rejected for being too big.

Thanks for your help,
Alexis
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Re: [Freesurfer] Hippocampal Subfields Segmentation Error

2017-01-25 Thread Iglesias Gonzalez, Eugenio

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine 
running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu mailto:a...@live.nl>> wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation 
analysis however, I keep running into the following error. I tried to solve it 
by myself however I had no luck ( I tried by removing the exec flag from the 
files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 
/usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 
GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument

Started at Tue Jan 24 13:43:45 STD 2017
Ended   at Tue Jan 24 13:43:47 STD 2017
#@#%# recon-all-run-time-hours 0.001
recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017
done

Sincerely,
Michel


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Re: [Freesurfer] Hippocampal Subfields Segmentation Error

2017-01-25 Thread Michel Hu

Dear  Juan,

I actually followed the guide on the following website in order to make it work 
on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/

Installing and running FreeSurfer on Windows 10 - Imaging 
...<http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/>
nuclear-imaging.info
Before I get into how to install FreeSurfer, I must thank the author at K-Lab 
for the post on “How to run FSL on Windows 10“. That post describes how to 
install ...

Sincerely,
Michel hu




Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Iglesias Gonzalez, Eugenio 

Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine 
running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu mailto:a...@live.nl>> wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation 
analysis however, I keep running into the following error. I tried to solve it 
by myself however I had no luck ( I tried by removing the exec flag from the 
files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 
/usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 
GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument

Started at Tue Jan 24 13:43:45 STD 2017
Ended   at Tue Jan 24 13:43:47 STD 2017
#@#%# recon-all-run-time-hours 0.001
recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017
done

Sincerely,
Michel


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Re: [Freesurfer] Hippocampal Subfields Segmentation Error

2017-01-26 Thread Iglesias Gonzalez, Eugenio

I have never tried this. Does the rest of recon-all -all run without errors?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 25 Jan 2017, at 11:45, Michel Hu mailto:a...@live.nl>> wrote:

Dear  Juan,

I actually followed the guide on the following website in order to make it work 
on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
Installing and running FreeSurfer on Windows 10 - Imaging 
...<http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/>
nuclear-imaging.info<http://nuclear-imaging.info/>
Before I get into how to install FreeSurfer, I must thank the author at K-Lab 
for the post on “How to run FSL on Windows 10“. That post describes how to 
install ...

Sincerely,
Michel hu




Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 namens Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine 
running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu mailto:a...@live.nl>> wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation 
analysis however, I keep running into the following error. I tried to solve it 
by myself however I had no luck ( I tried by removing the exec flag from the 
files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 
/usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 
GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument

Started at Tue Jan 24 13:43:45 STD 2017
Ended   at T

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

2017-01-27 Thread Michel Hu

Dear Juan,

Yes the recon -all -all works without errors
The problem seems to only arise when trying to use the segmentation command.
I believe it might have something to do with the matlab libraries?

Sincerely,
Michel Hu

On 26 Jan 2017, at 13:17, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

I have never tried this. Does the rest of recon-all -all run without errors?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 25 Jan 2017, at 11:45, Michel Hu mailto:a...@live.nl>> wrote:

Dear  Juan,

I actually followed the guide on the following website in order to make it work 
on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
Installing and running FreeSurfer on Windows 10 - Imaging 
...<http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/>
nuclear-imaging.info<http://nuclear-imaging.info/>
Before I get into how to install FreeSurfer, I must thank the author at K-Lab 
for the post on “How to run FSL on Windows 10“. That post describes how to 
install ...

Sincerely,
Michel hu




Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 namens Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine 
running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu mailto:a...@live.nl>> wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation 
analysis however, I keep running into the following error. I tried to solve it 
by myself however I had no luck ( I tried by removing the exec flag from the 
files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 
/usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 
GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/a

Re: [Freesurfer] hippocampal subfields segmentation error

2018-07-30 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: JongHyun Lee 
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung

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Re: [Freesurfer] hippocampal subfields segmentation error

2018-07-30 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Dear Jin,
6.0 does not segment the nuclei of the amygdala; you can ignore that line, 
assuming the code runs to completion (I am assuming it does?)
If you want to segment the nuclei of the amygdala, you’ll have to download the 
development version:
http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of 오진영 

Reply-To: Freesurfer support list 
Date: Monday, 30 July 2018 at 09:29
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Dear Eugenio,

Thanks for your reply.
I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of 
freesurfer.
As the log is so long, I attached whole log as a text file and I just copied 
few lines before the error below:


WorldToImageTransform after cropping:

AffineTransform (0x128c17790)

  RTTI typeinfo:   itk::AffineTransform

  Reference Count: 1

  Modified Time: 377450804

  Debug: Off

  Object Name:

  Observers:

none

  Matrix:

-3.3 8.73125e-11 2.22045e-16

-8.4821e-14 -2.67186e-12 -3.3

5.55112e-16 3.3 1.97674e-10

  Offset: [15.4608, 101.71, 117.525]

  Center: [0, 0, 0]

  Translation: [15.4608, 101.71, 117.525]

  Inverse:

-0.3 4.85723e-17 9.7012e-12

8.32667e-17 2.19633e-11 0.3

9.42996e-15 -0.3 -2.96735e-13

  Singular: 0

I am WriteImage and I'm running!

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

numberOfLabels: 25

Rasterizing mesh...here: 25

here2: 25

done

mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest 
-odt float -rl 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from discreteLabels.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 2.84217e-14)

j_ras = (0, 6.58905e-11, -1)

k_ras = (2.91038e-11, 1, -8.90815e-13)

reading template info from volume 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...

Reslicing using nearest

writing to discreteLabelsResampledT1.mgz...

mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

Thank you so much.
Hope to hear you soon!

Jin Young

2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>>:

External Email - Use Caution
Dear Jinyoung,
Can you please send us the log, or at least the last few lines before the error?
Also, which exact version are you using? 6.0 or dev?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 오진영 mailto:jinyoung.oh...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 30 July 2018 at 06:41
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: JongHyun Lee mailto:jonghyunlee1...@gmail.com>>
Subject: [Freesurfer] hippocampal subfields segmentation error


External Email - Use Caution
Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala 
by using "segmentSF_T1.sh" command.
I have downloaded the newest development version(freesurfer v.6.0) and license, 
as well as the required matlab runtime.

However, I am getting the following error:
mv: rename volumesAmygdala.txt to 
/Users/mnd_mac/Desktop/JY_surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt:
 No such file or directory

and I have no idea how to find the text file and solve this problem out.
If you have any idea or recommends, please send me the e-mail back.

Thanks!

Jinyoung


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] hippocampal subfields segmentation error

2018-07-30 Thread 오진영

External Email - Use Caution

Dear Eugenio

Thank you for your help.
As I need to segment the nuclei of amygdala, I'll try to download the
development version.

Thanks!!

Jinyoung

2018-07-30 17:39 GMT+09:00 Iglesias Gonzalez, Eugenio 
:

> External Email - Use Caution
>
> Dear Jin,
>
> 6.0 does not segment the nuclei of the amygdala; you can ignore that line,
> assuming the code runs to completion (I am assuming it does?)
>
> If you want to segment the nuclei of the amygdala, you’ll have to download
> the development version:
>
> http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 09:29
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Dear Eugenio,
>
>
>
> Thanks for your reply.
>
> I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" of
> freesurfer.
>
> As the log is so long, I attached whole log as a text file and I just
> copied few lines before the error below:
>
>
>
> WorldToImageTransform after cropping:
>
> AffineTransform (0x128c17790)
>
>   RTTI typeinfo:   itk::AffineTransform
>
>   Reference Count: 1
>
>   Modified Time: 377450804
>
>   Debug: Off
>
>   Object Name:
>
>   Observers:
>
> none
>
>   Matrix:
>
> -3.3 8.73125e-11 2.22045e-16
>
> -8.4821e-14 -2.67186e-12 -3.3
>
> 5.55112e-16 3.3 1.97674e-10
>
>   Offset: [15.4608, 101.71, 117.525]
>
>   Center: [0, 0, 0]
>
>   Translation: [15.4608, 101.71, 117.525]
>
>   Inverse:
>
> -0.3 4.85723e-17 9.7012e-12
>
> 8.32667e-17 2.19633e-11 0.3
>
> 9.42996e-15 -0.3 -2.96735e-13
>
>   Singular: 0
>
> I am WriteImage and I'm running!
>
> Wrote image to file asmr2.mgz
>
> This file does not contain MRI parameters
>
> This file does not contain MRI parameters
>
> numberOfLabels: 25
>
> Rasterizing mesh...here: 25
>
> here2: 25
>
> done
>
> mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt
> nearest -odt float -rl /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz
>
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>
> reading from discreteLabels.mgz...
>
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 2.84217e-14)
>
> j_ras = (0, 6.58905e-11, -1)
>
> k_ras = (2.91038e-11, 1, -8.90815e-13)
>
> reading template info from volume /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/norm.mgz...
>
> Reslicing using nearest
>
> writing to discreteLabelsResampledT1.mgz...
>
> mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_
> surfer/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.
> hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory
>
>
>
> Thank you so much.
>
> Hope to hear you soon!
>
>
>
> Jin Young
>
>
>
> 2018-07-30 17:01 GMT+09:00 Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk>:
>
> *External Email - Use Caution*
>
> Dear Jinyoung,
>
> Can you please send us the log, or at least the last few lines before the
> error?
>
> Also, which exact version are you using? 6.0 or dev?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of 오진영 <
> jinyoung.oh...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, 30 July 2018 at 06:41
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Cc: *JongHyun Lee 
> *Subject: *[Freesurfer] hippocampal subfields segmentation error
>
>
>
> *External Email - Use Caution*
>
> Hello, freesurfer experts
>
>
>
> I'm trying to run segmentation of hippocampal subfields and nuclei of
> amygdala by using "segmentSF_T1.sh" command.
>
> I have downloaded the newest development version(free

Re: [Freesurfer] Hippocampal subfields segmentation template

2019-04-30 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Dear Wu,
The “templates” are probabilistic atlases with no image intensities. All you 
can look at is images like the ones in the top panel of Figure 5 in the paper.
If you want to generate these, let me know and I’ll show you instructions (it’s 
a bit tricky, because it requires  combining different versions of FreeSurfer….)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Dongsheng Wu 

Reply-To: Freesurfer support list 
Date: Tuesday, 30 April 2019 at 04:38
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields segmentation template


External Email - Use Caution
Dear FS developers,

I uesd the ''recon-all command'' to get the volumes of the hippocampal 
subfields, and we would like to perform further analysis with  these subfields 
in MNI. Could you show us the templates which are used to perform hippocampal 
segmentation (CA1, CA3, HATA, etc.)?


Best wishes,
Wu





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Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-23 Thread fsbuild

External Email - Use Caution

I”m wondering if this is an issue with the version of Java installed on the 
machine and Matlab.  I’ve seen the latest MCR Matlab installer try to make 
changes to java installed on a Mac.  So maybe updating or re-installing 
the Matlab software on your machine could force a java update.  You should 
be able to exit the installer before it makes any changes if you decide not to 
go thru with it.
- R..

On Mar 23, 2021, at 17:45, Ramtilak Gattu  
wrote:External Email - Use 
CautionExternal
 Email - Use CautionHi,I am 
also encountering the same issue as WON JONG CHWA on my macbook pro (16gb ram) 
and I even tried the same on imac (8gb ram). I ran recon-all successfully on 
both systems. Here are my system detailsHardware Overview:  Model 
Name: MacBook Pro  Model 
Identifier: MacBookPro16,1  Processor Name: 6-Core Intel 
Core i7  Processor Speed: 2.6 GHz  Number of 
Processors: 1  Total Number of Cores: 6  L2 Cache 
(per Core): 256 KB  L3 Cache: 12 
MB  Hyper-Threading 
Technology: Enabled  Memory: 16 GB  System 
Firmware Version: 1554.80.3.0.0 (iBridge: 
18.16.14347.0.0,0)  Serial Number 
(system): C02DPB3BMD6M  Hardware 
UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4  Provisioning 
UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4  Activation Lock 
Status: EnabledHere is the log for segmentation violation 
error***Fitting mesh to image 
data took 742.9022 secondsTransforming pointsTransforming pointsWrote image to 
file image.mgzConstructing image-to-world transform from header information 
(asmr1.mgz)Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)Wrote
 image to file asmr2.mgzThis file does not contain MRI parametersCaught 
unexpected exception of unknown 
type. 
      Segmentation violation detected at Tue Mar 23 15:53:07 
2021Configuration: 
 Crash Decoding     : Disabled  Current Visual     : 
Quartz  Default Encoding   : ISO-8859-1  MATLAB Architecture: 
maci64  MATLAB Root        : 
/Applications/freesurfer/7.1.1/MCRv84  MATLAB Version     : 
8.4.0.150421 (R2014b)  Operating System   : Darwin 20..3.0 Darwin 
Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; 
root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64  Processor ID     
  : x86 Family 6 Model 158 Stepping 10, GenuineIntel  Software OpenGL 
   : 0  Virtual Machine    : Java 1.7.0_55-b13 with 
Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode  Window 
System      : QuartzFault Count: 1Abnormal 
termination:Segmentation violationRegister State (from fault):  RAX = 
0003  RBX = 000102cde080  RCX = 7ff4ce00 
 RDX = 7624c180  RSP = 7ff4ce00  RBP = 
7fff2041595e  RSI = 7000  RDI = 
7fff204171f9   R8 = 660333a0   R9 = 
7624c180  R10 = 7fff20410002  R11 = 
7ff4ce05b4e0  R12 = 7624c498  R13 = 
  R14 = 00010e5fbd9b  R15 = 
0060  RIP = 7624c498  RFL = 
7624c1e0   CS = 00010e49227b   FS = 7624c1c0 
  GS = 0001Stack Trace (from fault):[  0] 
0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052[ 
 1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906[  2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119[  3] 
0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146[  4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880[  5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275[  6] 0x7fff20630d7d       
    /usr/lib/system/libsystem_platform.dylib+00015741 
_sigtramp+0029[  7] 0x         
                      
    +[  8] 0x00010e49227b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667[ 
 9] 0x00010e3eba17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119[ 10] 0x00010e49029d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509[ 11] 
0x000

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-23 Thread Ramtilak Gattu

bbP15inWorkSpace_tag+0066

[ 17] 0x00010eda72de 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+00402142
 
_Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKSbItSt11char_traitsItESaItEEPibbP15inWorkSpace_tag+0062

[ 18] 0x00010f8f593e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00227646 
_ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEP15inWorkSpace_tag+0094

[ 19] 0x00010f8f4df4 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00224756 
_ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0132

[ 20] 0x00010ec10358 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00209752 
_ZN3mcr3mvm27McrSwappingIqmPluginAdapterIN3iqm18InternalEvalPluginEE7executeEP15inWorkSpace_tagRN5boost10shared_ptrIN14cmddistributor17IIPCompletedEventEEE+0600

[ 21] 0x00010f8e5418 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00160792 
_ZNK3iqm17DefaultPacketInfo7executeEP15inWorkSpace_tag+0296

[ 22] 0x00010f8d07f1 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwiqm.dylib+00075761 
_ZN3iqm3Iqm15setupIqmFcnPtrsEv+4945

[ 23] 0x00010148e005 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+00196613 
_ZN10eventqueue18UserEventQueueImpl5flushEv+1205

[ 24] 0x00010fa83a65 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwuix.dylib+00043621 
_Z25isHandleUserEventCallbackPFvPvE+0501

[ 25] 0x00010155da45 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01047109 
_Z21svWS_ProcessCallbacksv+00016693

[ 26] 0x000101559152 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01028434 
_Z25svWS_ProcessPendingEventsiib+0834

[ 27] 0x000101558e5e 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwservices.dylib+01027678 
_Z25svWS_ProcessPendingEventsiib+0078

[ 28] 0x00010ebfa18f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119183 
_ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+0095

[ 29] 0x00010ebfa49f 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00119967 
_ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+0335

[ 30] 0x00010ebe0d1b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00015643 
_Z26run_init_and_handle_eventsPv+0059

[ 31] 0x7fff20454950
/usr/lib/system/libsystem_pthread.dylib+00026960 _pthread_start+0224

[ 32] 0x7fff2045047b
/usr/lib/system/libsystem_pthread.dylib+9339 thread_start+0015



If this problem is reproducible, please submit a Service Request via:

http://www.mathworks.com/support/contact_us/


A technical support engineer might contact you with further information.


Thank you for your help.** This crash report has been saved to disk as 
/Users/tilak/matlab_crash_dump.2179-1 **




MATLAB is exiting because of fatal error

/Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 33:  2179 Killed: 9   
/Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 Amy_Damboise /Users/tilak/Desktop/Work/CNS_cases/Hipps 
0. 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz 
/Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 
0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr 
/Applications/freesurfer/7.1.1/bin/' 0

Darwin tilak.lan 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 
2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64


T1 hippocampal subfields exited with ERRORS at Wed Mar 24 00:59:59 EDT 2021


For more details, see the log file 
/Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.log


tilak@tilak Hipps %




From: fsbuild 
Sent: Tuesday, March 23, 2021 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

[EXTERNAL]
I”m wondering if this is an issue with the version of Java installed on the 
machine and Matlab.  I’ve seen the latest MCR Matlab installer try to make 
changes to java installed on a Mac.  So maybe updating or re-installing the 
Matlab software on your machine could force a java update.  You should be able 
to exit the installer before it makes any changes if you decide not to go thru 
with it.

- R.

On Mar 23, 2021, at 17:45, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

I am also encountering the same issue as WON JONG CHWA on my

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-24 Thread fsbuild

h.harvard.edu>Cc: Ramtilak
 Gattu <rg...@med.wayne.edu>Subject: Re: [Freesurfer] Hippocampal 
Subfields Segmentation Violation-error [EXTERNAL]I”m wondering if this is 
an issue with the version of Java installed on the machine and Matlab. 
 I’ve seen the latest MCR Matlab installer try to make changes to java 
installed on a Mac.  So maybe updating or re-installing the Matlab 
software on your machine could force a java update.  You should be able to 
exit the installer before it makes any changes if you decide not to go thru 
with it.- R.On Mar 23, 2021, at 17:45, Ramtilak Gattu 
<rg...@med.wayne.edu> 
wrote:External Email - Use 
CautionExternal
 Email - Use CautionHi,I am 
also encountering the same issue as WON JONG CHWA on my macbook pro (16gb ram) 
and I even tried the same on imac (8gb ram). I ran recon-all successfully on 
both systems. Here are my system detailsHardware Overview:  Model 
Name: MacBook Pro  Model 
Identifier: MacBookPro16,1  Processor Name: 6-Core Intel 
Core i7  Processor Speed: 2.6 GHz  Number of 
Processors: 1  Total Number of Cores: 6  L2 Cache 
(per Core): 256 KB  L3 Cache: 12 
MB  Hyper-Threading 
Technology: Enabled  Memory: 16 GB  System 
Firmware Version: 1554.80.3.0.0 (iBridge: 
18.16.14347.0.0,0)  Serial Number 
(system): C02DPB3BMD6M  Hardware 
UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4  Provisioning 
UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4  Activation Lock 
Status: EnabledHere is the log for segmentation violation 
error***Fitting mesh to image 
data took 742.9022 secondsTransforming pointsTransforming pointsWrote image to 
file image.mgzConstructing image-to-world transform from header information 
(asmr1.mgz)Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)Wrote
 image to file asmr2.mgzThis file does not contain MRI parametersCaught 
unexpected exception of unknown 
type. 
      Segmentation violation detected at Tue Mar 23 15:53:07 
2021Configuration: 
 Crash Decoding     : Disabled  Current Visual     : 
Quartz  Default Encoding   : ISO-8859-1  MATLAB Architecture: 
maci64  MATLAB Root        : 
/Applications/freesurfer/7..1.1/MCRv84  MATLAB Version     : 
8.4.0.150421 (R2014b)  Operating System   : Darwin 20.3.0 Darwin 
Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; 
root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64  Processor ID     
  : x86 Family 6 Model 158 Stepping 10, GenuineIntel  Software OpenGL 
   : 0  Virtual Machine    : Java 1.7.0_55-b13 with 
Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode  Window 
System      : QuartzFault Count: 1Abnormal 
termination:Segmentation violationRegister State (from fault):  RAX = 
0003  RBX = 000102cde080  RCX = 7ff4ce00 
 RDX = 7624c180  RSP = 7ff4ce00  RBP = 
7fff2041595e  RSI = 7000  RDI = 
7fff204171f9   R8 = 660333a0   R9 = 
7624c180  R10 = 7fff20410002  R11 = 
7ff4ce05b4e0  R12 = 7624c498  R13 = 
  R14 = 00010e5fbd9b  R15 = 
0060  RIP = 7624c498  RFL = 
7624c1e0   CS = 00010e49227b   FS = 7624c1c0 
  GS = 0001Stack Trace (from fault):[  0] 
0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052[ 
 1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906[  2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119[  3] 
0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146[  4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880[  5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275[  6] 0x7fff20630d7d       
    /usr/lib/system/libsystem_platform.dylib+00015741 
_sigtramp+0029[  7] 0x         
                      
    <unknown-module>+[  8] 0x00010e49227b 
/Applications/freesurfer/7.1..1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667[ 
 9] 0x00010e3eba17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119[ 10] 0x00010e49029d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_i

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-24 Thread Ramtilak Gattu

External Email - Use Caution

Yes it says enabled.


[tilak:~] tilak% csrutil status

System Integrity Protection status: enabled.

Thanks

Regards,
Tilak

From: fsbuild 
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is 
turned on the Mac (which is the default).  The following command will report if 
it is enabled or disabled, e.g., when enabled,

$ csrutil status
System Integrity Protection status: enabled.

- R.
On Mar 24, 2021, at 01:48, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running 
"fs_install_mcr R2014b" as suggested in FSwiki.

I updated java to version "1.8.0_281" (Java(TM) SE Runtime Environment (build 
1.8.0_281-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode) 
and reinstalled or overwritten mcrv8.4 by running the same command again 
"fs_install_mcr R2014b" but still it ended after running for a whileand exited 
with errors again. But this time it says "Bus error detected instead of 
segmentation violation error.

Bus error detected at Wed Mar 24 00:59:58 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Bus error

Register State (from fault):
  RAX = 0003  RBX = 00010145d080
  RCX = 7fdc9c70  RDX = 7959f180
  RSP = 7fdc9c70  RBP = 7fff2027d95e
  RSI = 7000  RDI = 7fff2027f1f9

   R8 = 70c054b0   R9 = 7959f180
  R10 = 7fff20270002  R11 = 7fdc9c7429e0
  R12 = 7959f498  R13 = 
  R14 = 00010f061d9b  R15 = 0060

  RIP = 7959f498  RFL = 7959f1e0

   CS = 00010eef827b   FS = 7959f1c0   GS = 0001

Stack Trace (from fault):
[  0] 0x0001036a0e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001036a4a2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001036a4477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x00010ec3bb7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x00010ec3be58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x00010ec39733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff20498d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010eef827b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x00010ee51a17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
 _Z15inRunFinalizers7opcodesPS_Pi+0119
[ 10] 0x00010eef629d 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509
[ 11] 0x00010fc74c55 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469
 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645
[ 12] 0x00010ee9948b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803
 
_Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+0219
[ 13] 0x00010ee4bf4b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci6

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-24 Thread Iglesias Gonzalez, Juan E.

Thank you both! On Linux, 8GB is insufficient, and 16GB is normally 
sufficient; I wonder if the requirements are a bit higher on MAC?

Could you please try the following?

  1.  Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo)
  2.  Replace the line:
set RESOLUTION="0.";
by:
set RESOLUTION="0.5";
  3.  Rerunning the code, and see if it runs to completion?
Cheers,
/E


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Ramtilak Gattu 

Reply-To: Freesurfer support list 
Date: Tuesday, March 23, 2021 at 17:46
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal Subfields Segmentation Violation-error


External Email - Use Caution

External Email - Use Caution
Hi,

I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb 
ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully 
on both systems. Here are my system details


Hardware Overview:



  Model Name: MacBook Pro

  Model Identifier: MacBookPro16,1

  Processor Name: 6-Core Intel Core i7

  Processor Speed: 2.6 GHz

  Number of Processors: 1

  Total Number of Cores: 6

  L2 Cache (per Core): 256 KB

  L3 Cache: 12 MB

  Hyper-Threading Technology: Enabled

  Memory: 16 GB

  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

  Serial Number (system): C02DPB3BMD6M

  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4

  Activation Lock Status: Enabled



Here is the log for segmentation violation error
***
Fitting mesh to image data took 742.9022 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Users/tilak/Desktop/Work/CNS_cases/Hipps/AD/tmp/hippoSF_T1_v21_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Caught unexpected exception of unknown type.


   Segmentation violation detected at Tue Mar 23 15:53:07 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java 
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0003  RBX = 000102cde080
  RCX = 7ff4ce00  RDX = 7624c180
  RSP = 7ff4ce00  RBP = 7fff2041595e
  RSI = 7000  RDI = 7fff204171f9

   R8 = 660333a0   R9 = 7624c180
  R10 = 7fff20410002  R11 = 7ff4ce05b4e0
  R12 = 7624c498  R13 = 
  R14 = 00010e5fbd9b  R15 = 0060

  RIP = 7624c498  RFL = 7624c1e0

   CS = 00010e49227b   FS = 7624c1c0   GS = 0001

Stack Trace (from fault):
[  0] 0x0001048a9e64 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x0001048ada2a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x0001048ad477 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x000107e39b7a 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x000107e39e58 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x000107e37733 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275
[  6] 0x7fff20630d7d   
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x   
+
[  8] 0x00010e49227b 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x00010e3eba17 
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpret

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

2021-03-27 Thread Hoopes, Andrew

Matt (cc’d) has recently posted a similar error on the last. Unfortunately, 
these mac MCR errors are difficult to debug. You could wait for the python 
subfield port to get released, but that might be a few months down the line. If 
you want to get things running immediately, one thing to try is to download the 
7.1 docker container from https://hub.docker.com/r/freesurfer/freesurfer and 
run FS through that. That should fix any system-specific problems.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ramtilak Gattu 

Date: Thursday, March 25, 2021 at 7:20 PM
To: fsbuild , freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution

External Email - Use Caution
Hi 'E' / 'R',

I even tried changing the resolution to 1.0 with no success ruling put memory 
issues.

Just wondering if its time to give up and wait for your python build to 
successfully finish the job in mac. I wonder if any other user with a similar 
MacBook pro configuration as mine
Hardware Overview:

  Model Name: MacBook Pro
  Model Identifier: MacBookPro16,1
  Processor Name: 6-Core Intel Core i7
  Processor Speed: 2.6 GHz
  Number of Processors: 1
  Total Number of Cores: 6
  L2 Cache (per Core): 256 KB
  L3 Cache: 12 MB
  Hyper-Threading Technology: Enabled
  Memory: 16 GB
  System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
  Serial Number (system): C02DPB3BMD6M
  Hardware UUID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Provisioning UDID: D313516B-A3B9-500F-9303-EB0F4D4946A4
  Activation Lock Status: Enabled

had successfully finished the processing or encountered the same issue and 
later fixed it to successfully run the segmentation. Is there a way to bypass 
that step and run the program till the end?

I think some Compatability issues with 'MCR' holding back the processing at 
that stage.

Again, thanks a lot for all your help in this regards.

Regards
Tilak

From: Ramtilak Gattu 
Sent: Wednesday, March 24, 2021 8:32 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

First let me thank you 'R' and 'E' for being so patient and working with me to 
resolve this issue.

As suggested by 'R' I monitored the activity monitored but unfortunately, the 
memory pressure graph remained green throughout the process. When the program 
was running memory usage jumped from 6.25gb to 7.85 gb.

As suggeted by 'E" I even tried to run the code by changing the parameters in 
the code for


set RESOLUTION="0.".

by:

set RESOLUTION="0.5";

still, the error persists.

It works fine on my Linux centos system(8gb ram) but fails on both the macs. 
surprisingly, it's the same exact error.

Does running the routine after installing full matlab instead of just mcr8.4 
would help? just a thought.

Thanks

Regards
Tilak


From: fsbuild 
Sent: Wednesday, March 24, 2021 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Ramtilak Gattu 
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

I don’t see anything in your output showing say code 01 with Bus Error.  But 
code 01 could indicate a memory issue, e.g., not enough RAM.

You could bring up the Activity Monitor program and click on the memory tab to 
profile memory during the command run.  But the "memory pressure" graph does 
not go back very far in time, so you would need to be able to see it close to 
the time the command exits. See  
https://www.lifewire.com/use-activity-monitor-to-track-mac-memory-usage-2260880

- R.


On Mar 24, 2021, at 04:26, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Yes it says enabled.

[tilak:~] tilak% csrutil status
System Integrity Protection status: enabled.

Thanks

Regards,
Tilak

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Wednesday, March 24, 2021 4:22 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Ramtilak Gattu mailto:rg...@med.wayne.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Maybe you could let us know if the system integrity protection feature is 
turned on the Mac (which is the default).  The following command will report if 
it is enabled or disabled, e.g., when enabled,

$ csrutil status
System Integrity Protection status: enabled.
- R.

On Mar 24, 2021, at 01:48, Ramtilak Gattu  wrote:

External Email - Use Caution
External Email - Use Caution
Hi,

Earlier I didnt have a full matlab verion but I installed mcr by running 
"fs_install_mcr R2014b" as suggested in FSwiki.

I updated jav

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Matt Glasser

I would be interested to know how well 0.7mm isotropic resolution data
performs at hippocampal segmentation.  It would be better if folks could do
this then needing to acquire specialized anisotropic scans for hippocampal
segmentation.

Peace,

Matt.

From:   on behalf of Fernando
Pasquini Santos 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:23 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal
Subfield segmentation in Freesurfer 6.0 -
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the
same standard 1mm T1 image with an additional scan. However, I want to use a
0.7mm T1 image as input, with an additional T2 scan. When I run the program
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm
voxel size. So, I don't know if this happens just because of the recon-all
program or if the segmentation is being done in the downsampled T1 image or
in the original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation
using ex vivo, ultra-high resolution MRI: Application to adaptive
segmentation of in vivo MRI" I saw that, in the methods section, the
algorithm is used to segment 0.6mm T1 images. But is this possible to do in
the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm
data would be better than a downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Iglesias, Eugenio

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Iglesias, Eugenio

Hi Matt,
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:31, Matt Glasser mailto:m...@ma-tea.com>> 
wrote:

I would be interested to know how well 0.7mm isotropic resolution data performs 
at hippocampal segmentation.  It would be better if folks could do this then 
needing to acquire specialized anisotropic scans for hippocampal segmentation.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, June 9, 2016 at 1:23 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel 
size of the input?

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu
fernando.pasquini.san...@usp.br
___ Freesurfer mailing list 
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in 
this e-mail is intended only for the person to whom it is addressed. If you 
believe this e-mail was sent to you in error and the e-mail contains patient 
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but does not contain patient information, please contact the sender and 
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Matt Glasser

Hi Eugenio,

Did you already do this?  If so, a published reference would be more useful
to me than instructions for how to do it, as I¹m more interested in making
an argument for an acquisition protocol modification.

Matt.

From:   on behalf of "Iglesias,
Eugenio" 
Reply-To:  Freesurfer support list 
Date:  Thursday, June 9, 2016 at 1:37 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Hippocampal subfields segmentation - what is the
voxel size of the input?

Hi Matt, 
you can use strategy 3 of my previous email ;-)
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

> On 9 Jun 2016, at 19:31, Matt Glasser  wrote:
> 
> I would be interested to know how well 0.7mm isotropic resolution data
> performs at hippocampal segmentation.  It would be better if folks could do
> this then needing to acquire specialized anisotropic scans for hippocampal
> segmentation.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of Fernando Pasquini
> Santos 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 9, 2016 at 1:23 PM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel
> size of the input?
> 
> Dear,
> 
> I have a doubt regarding the input T1 image used for the Hippocampal Subfield
> segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
> 
> In this documentation it says that I can use a standard 1mm T1 image or the
> same standard 1mm T1 image with an additional scan. However, I want to use a
> 0.7mm T1 image as input, with an additional T2 scan. When I run the program
> with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel
> size. So, I don't know if this happens just because of the recon-all program
> or if the segmentation is being done in the downsampled T1 image or in the
> original 0.7mm.
> 
> By reading the article "A computational atlas of the hippocampal formation
> using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation
> of in vivo MRI" I saw that, in the methods section, the algorithm is used to
> segment 0.6mm T1 images. But is this possible to do in the Freesurfer package?
> Obviously, doing the segmentation directly on 0.7mm data would be better than
> a downsampled version to 1mm...
> 
> Thanks,
> 
> Fernando Pasquini Santos
> PhD student in Dynamic Systems
> fernandosan...@pitt.edu
> fernando.pasquini.san...@usp.br
> ___ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information
> in this e-mail is intended only for the person to whom it is addressed. If you
> believe this e-mail was sent to you in error and the e-mail contains patient
> information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error but does not contain patient information, please contact the sender and
> properly dispose of the e-mail.
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.

___ Freesurfer mailing list
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-09 Thread Hibert, Matthew Louis

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu<mailto:fernandosan...@pitt.edu>
fernando.pasquini.san...@usp.br<mailto:fernando.pasquini.san...@usp.br>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-10 Thread Iglesias, Eugenio

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu<mailto:fernandosan...@pitt.edu>
fernando.pasquini.san...@usp.br<mailto:fernando.pasquini.san...@usp.br>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Co

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-06-22 Thread Fernando Pasquini Santos

Hi all,

I'll give some feedback about the two methods you've mentioned. I also
tried using a 0.5 T1 image and then:

*Changing the headers of the T1 and T2 images:*
It worked for the 0.7mm T1, however, in the 0.5mm the tailarach aligment
failed.

In both cases I had the warning "MRIsetRas2VoxFromMatrix(): voxels sizes
are inconsistent"

Output:

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0434, pval=0.0034 < threshold=0.0050)

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach



*Using the -hires flag:*Although it is not sure if this is handling the
original resolution, it also worked only for the 0.7mm, and for the 0.5mm
it had a segmentation fault in the topology correction step.


Em sex, 10 de jun de 2016 às 03:37, Iglesias, Eugenio 
escreveu:

> Hi Matt,
> Bruce actually mentioned this possibility yesterday. Good to hear it
> doesn’t crash when you run it! That said, I need to go through the code,
> and make sure that data are handled the way they are supposed to: the fact
> that it doesn’t crash doesn’t directly imply that it is working properly.
> Hopefully I’ll find time to do this next week…
> Cheers,
> Eugenio
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
> wrote:
>
> Hi Eugenio,
> Would it also be possible to use the -hires flag in the initial recon-all
> command to prevent the T1 from being downsampled and maintain the voxel
> size that the T1 was acquired at, and use that resulting recon for the
> hippocampal subfield segmentation?  I've tested this with MEMPRAGE scans
> acquired at 0.75mm isotropic and coronal T2 anisotropic scans acquired at
> 0.33mm in plane with 1mm thick slices, and the results look reasonable.
> The "1mm" label files are correctly downsampled to 0.75mm instead of 1mm,
> and the higher resolution label files remain at 0.33mm resolution.
>
> Thanks,
> Matt
>
> Stufflebeam Lab
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> 149 13th Street, Room 1115S
> Charlestown, MA 02129
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio [
> e.igles...@ucl.ac.uk]
> *Sent:* Thursday, June 09, 2016 2:36 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Hippocampal subfields segmentation - what is
> the voxel size of the input?
>
> Hi Fernando,
>
> Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield
> code assumes that the T1 comes from FreeSurfer… For the paper, I hacked the
> code to take advantage of multiple images with higher resolution, but it
> hasn’t been thoroughly tested and it’s not publicly available at this
> point.
> That said, there are different things you can do at this point:
> 1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
> 2. Use only the T2.
> 3. Use only the T1. To do this, you would use the T1 as additional scan on
> its own (i.e., the main and additional scans are the same, but the
> additional one won’t be resampled).
> 4. There might be a way (hack) of using both scans at full resolution. If
> you change the header of the T1 scan and specify that the voxel size is
> 1mm, no resampling will happen; FreeSurfer will believe that you’re dealing
> with a subject with a very large head. If you do this, you’ll also have to
> enlarge the voxel size of the T2 by a factor 1/0.7. Also, the resulting
> volumes will have to be divided by (1/0.7)^3 in order to correct for the
> “wrong” voxel size.
>
> I hope this helps!
>
> Cheers,
>
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:
>
> Dear,
>
> I have a doubt regarding the input T1 image used for the Hippocampal
> Subfield segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
>
> In this documentation it says that I can use a standard 1mm T1 image or
> the same standard 1mm T1 image with an additional scan. However, I want to
> use a 0.7mm T1 image as input, with an additional T2 scan. When I run the
> program with it, the output images (nu.mgz and orig.mgz) are downsampled to
&

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-07-06 Thread Hibert, Matthew Louis

Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag 
with the hippocampal subfield segmentation?

Thanks,
Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu<mailto:fernandosan...@pitt.edu>

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

2016-07-06 Thread Iglesias, Eugenio

Not yet, sorry. But it’s on my todo list.


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 6 Jul 2016, at 14:39, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag 
with the hippocampal subfield segmentation?

Thanks,
Matt

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
mailto:mhib...@mgh.harvard.edu>> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
mailto:fernandop...@gmail.com>> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Ap

Re: [Freesurfer] hippocampal subfields segmentation

Re: [Freesurfer] hippocampal subfields segmentation

Re: [Freesurfer] hippocampal subfields segmentation

Re: [Freesurfer] Hippocampal Subfields Segmentation

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Re: [Freesurfer] Hippocampal Subfields Segmentation

Re: [Freesurfer] Hippocampal Subfields Segmentation

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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

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