Re: [Freesurfer] freesurfer 6.0 hires fix

[Greve, Douglas N.,Ph.D.]

You have to rerun from the beginning. (sorry)

On 9/9/19 3:12 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
>
> I noticed that you guys released a fix to improve the -hires option.  
> I have been processing some of our data using the hires flag. if i use 
> this fix do i need to run recon-all from the beginning or can I run 
> over the old folders?
>
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[Freesurfer] freesurfer 6.0 hires fix

[Aaron Tanenbaum]

External Email - Use Caution

I noticed that you guys released a fix to improve the -hires option.  I
have been processing some of our data using the hires flag. if i use this
fix do i need to run recon-all from the beginning or can I run over the old
folders?
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Re: [Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

[fsbuild]

External Email - Use Caution

​Hello Gonzola,
I use a CentOS7 VM image  (on virtualbox) originally downloaded from 
osboxes.org. After downloading and bringing up the image, I installed 
various packages for freesurfer. But apart from my image being CentOS7 
(and not CentOS6), I think it is currently too large for it to be practical to 
upload/download.

You can download CentOS6 images from osboxes.org, 
https://www.osboxes.org/centos/If you scroll down that page you will see the 
latest CentOS6 image is 6.10, followed by previous 6.X releases.

Some of the packages I installed are,
qt-create qt-config.x86_64
qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64
boost.x86_64 boost-devel.x86_64
tk-devel.x86_64 
opencl-filesystem.noarch opencl-headers.noarch
opencv.x86_64 opencv-devel.x86_64
git-annex

- R.
On Apr 24, 2019, at 11:21, Gonzalo Rojas Costa 
gonzalo.rojas.co...@gmail.com 
wrote:External Email - Use Caution 
Hi:Where can I find the 
FreeSurfer 6.0 disk image for VirtualBox?Sincerely,Gonzalo Rojas Costa
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[Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

[Gonzalo Rojas Costa]

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Hi:

  Where can I find the FreeSurfer 6.0 disk image for VirtualBox?

  Sincerely,


Gonzalo Rojas Costa

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Yendiki, Anastasia]

Hi Matt – If your original DWIs are also truncated (which is what it looks like 
from the screenshots you sent), then it’s not tracula that’s truncating them. 
Any tracts that go through the truncated part of the brain (like the ILF, which 
is where you were getting the error, if I remember correctly) will not be 
reconstructed. You can still run tracula but use a configuration file and 
specify the pathlist so that it doesn’t include the tracts that go through the 
truncated part of the brain.

Best,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, September 25, 2018 at 9:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

I posted a reply with the dwi_orig.nii screenshots on Friday, but they did not 
show up on the list.

Yes, the dwi_orig.nii images appear the same as the dwi.nii.gz images.

Also, I ran them through TrackVis/DTK and they came out correct, so it seems to 
be something within Tracula that is not working for me as expected.

On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Thank you. Can you also send screenshots of your original DWIs, if they don't 
look like this?


From:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Sent: Friday, September 21, 2018 10:27:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 
degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of 
an FA map that looked truncated, with slices missing from the bottom of the 
brain (which explains why the error happened for the ILF, which would go 
through that missing part of the brain). Does dmri/dwi.nii.gz look like that?


Best,

a.y


From:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the 
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't 
appear to have brain parts missing, although some appear more noisy and 
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a 
Siemens 3T.



----
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek 
mailto:m...@grecsek.com><mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.


Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Matthew Grecsek]

External Email - Use Caution

I posted a reply with the dwi_orig.nii screenshots on Friday, but they did
not show up on the list.

Yes, the dwi_orig.nii images appear the same as the dwi.nii.gz images.

Also, I ran them through TrackVis/DTK and they came out correct, so it
seems to be something within Tracula that is not working for me as expected.

On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Thank you. Can you also send screenshots of your original DWIs, if they
> don't look like this?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <
> m...@grecsek.com>
> *Sent:* Friday, September 21, 2018 10:27:37 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Please see attached screenshots from dwi.nii.gz. The first 4 are rotated
> 90 degrees around y axis and the last 2 are top and bottom.
>
> Thanks,
>
> -Matt
>
> On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Matt - I am asking about the raw diffusion images. You sent a
> screenshot of an FA map that looked truncated, with slices missing from the
> bottom of the brain (which explains why the error happened for the ILF,
> which would go through that missing part of the brain). Does
> dmri/dwi.nii.gz look like that?
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <
> m...@grecsek.com>
> *Sent:* Thursday, September 20, 2018 2:00:11 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
>
>
> External Email - Use Caution
>
> If you are referring to the T1 raw images, no they appear normal and the
> standard Freesurfer pipeline generates correct volumes.
>
> If you are referring to the DTI raw images off the scanner, they also
> don't appear to have brain parts missing, although some appear more noisy
> and pixelated than others.
>
> This is a mTBI subject with no other anatomical brain anomalies scanned
> with a Siemens 3T.
>
>
> 
> Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
> Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700
>
>
>
> Do the raw images look like that too?
>
> From:
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu
>  >>
>  on behalf of Matthew Grecsek mailto:m...@grecsek.com 
> >>
> Reply-To: Freesurfer support list
> mailto:freesurfer@nmr.mgh.harvard.edu 
> >>
> Date: Wednesday, September 19, 2018 at 4:07 PM
> To: Freesurfer support list
> mailto:freesurfer@nmr.mgh.harvard.edu 
> >>
> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
>
>     External Email - Use Caution
>
> Yes, a part of the brain appears missing. See attached screenshot.
>
> I did not use a configuration file, I simply accepted all defaults and kicked
> off the process with -s and -i flags.
>
> 
> Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
> Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700
>
> Hi Matt – It looks like some sort of registration issue. When you display the
> FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
> (label/diff/aparc+aseg), do they look fine? Is there any part of the brain 
> that
> is cut off from any of the images? Also, can you attach your config file?
> Thanks!
>
> a.y
>
> ___
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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 wh

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Yendiki, Anastasia]

Thank you. Can you also send screenshots of your original DWIs, if they don't 
look like this?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Matthew Grecsek 

Sent: Friday, September 21, 2018 10:27:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 
degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of 
an FA map that looked truncated, with slices missing from the bottom of the 
brain (which explains why the error happened for the ILF, which would go 
through that missing part of the brain). Does dmri/dwi.nii.gz look like that?


Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the 
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't 
appear to have brain parts missing, although some appear more noisy and 
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a 
Siemens 3T.



--------
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek 
mailto:m...@grecsek.com><mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.

----
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y

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

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Yendiki, Anastasia]

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of 
an FA map that looked truncated, with slices missing from the bottom of the 
brain (which explains why the error happened for the ILF, which would go 
through that missing part of the brain). Does dmri/dwi.nii.gz look like that?


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Matthew Grecsek 

Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the 
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't 
appear to have brain parts missing, although some appear more noisy and 
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a 
Siemens 3T.




Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek 
mailto:m...@grecsek.com><mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.

------------
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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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] Freesurfer 6.0 - Tracula - Segmentation fault

[Matthew Grecsek]

External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't
appear to have brain parts missing, although some appear more noisy and
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned
with a Siemens 3T.



Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu
>>
 on behalf of Matthew Grecsek
mailto:m...@grecsek.com >>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu
>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu
>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.

--------
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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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] Freesurfer 6.0 - Tracula - Segmentation fault

[Yendiki, Anastasia]

Do the raw images look like that too?

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked 
off the process with -s and -i flags.

--------
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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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] Freesurfer 6.0 - Tracula - Segmentation fault

[Matthew Grecsek]

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and
kicked off the process with -s and -i flags.


Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display
the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain
that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Yendiki, Anastasia]

Hi Matt – It looks like some sort of registration issue. When you display the 
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space 
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that 
is cut off from any of the images? Also, can you attach your config file? 
Thanks!

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, September 18, 2018 at 11:50 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


External Email - Use Caution

I ran standard recon-all on a single subject and then trac-all -prep.

The process ran for approximately 1 hour and exited with errors: Segmentation 
fault.

This is my first time testing Tracula, so user error likely.

Here are the final lines from the console and trac-all.log attached:


INFO: Distances between consecutive points in test subject's space are 9 13 13 
12

WARN: Could not find satisfactory control point fit - try 912

Finding center streamline

INFO: Step is 5 voxels

WARN: Turning off deviation check for center streamline

INFO: Step is 5 voxels

WARN: Turning off FA check for center streamline

INFO: Step is 5 voxels

WARN: Turning off overlap check for center streamline

INFO: Step is 5 voxels

INFO: Length of center streamline is 114 voxels

Selecting 5 points on center streamline

INFO: Minimum allowable distance between dominant points is 15

INFO: Minimum allowable curvature at a dominant point is 0.0447089

INFO: Points where local peeks in curvature occur are

 67 116 39 (curv = 0.0963721)

 77 75 87 (curv = 0.114559)

 75 76 95 (curv = 0.0564307)

 69 74 105 (curv = 0.126918)

 74 67 115 (curv = 0.0809615)

INFO: Intermediate dominant points are

 67 135 33

 67 116 39

 75 82 76

 69 74 105

 74 49 116

INFO: Final dominant points are

 67 135 33

 67 116 39

 77 75 88

 69 74 105

 74 49 116

WARN: Defaulting to equidistant control points

INFO: Selected control points are

 67 135 33

 68 108 46

 75 83 75

 69 74 105

 74 49 116

INFO: Distances between consecutive points are 30 39 32 28

INFO: Selected control points in test subject's space are

 56 58 -8

 56 46 -3

 58 35 9

 55 30 22

 57 19 26

INFO: Distances between consecutive points in test subject's space are 13 16 14 
12

WARN: Could not find satisfactory control point fit - try 913

Writing output files to 
/Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_*

Writing spline volume to 
/Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz

Segmentation fault

Darwin Matthews-MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 
21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Sep 17 16:26:23 EDT 2018

Thanks,

-Matt
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error

[Iglesias Gonzalez, Eugenio]

Hi Patricia,
Do you think you could send us an example? I’ve never seen the registration 
fail with good prealignment on an of my datasets, so this would be very, very 
helpful to improve the software.
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/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Patricia Linortner 
<plino...@stanford.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 31 October 2017 at 22:54
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode 
B) - Registration error

Hi all,

I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B:  
-hippocampal-subfields-T1T2).
For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial 
brain).

Segmentation works in most subjects, but in some subjects the co-registration 
of the 7T-T2 MRI scan fails.
[Despite good scan quality and pre-alignment using Freeview]

I was wondering if you had any input/suggestion(s) for fixing this error (e.g. 
using mri_register)?

Thanks,
Patricia
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dispose of the e-mail.

[Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error

[Patricia Linortner]

Hi all,

I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B:  
-hippocampal-subfields-T1T2).
For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial 
brain).

Segmentation works in most subjects, but in some subjects the co-registration 
of the 7T-T2 MRI scan fails.
[Despite good scan quality and pre-alignment using Freeview]

I was wondering if you had any input/suggestion(s) for fixing this error (e.g. 
using mri_register)?

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

[Freesurfer] Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume

[Lucette Cysique]

Hello all


FYI

I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my 
healthy young sample

It is probably due to the cerebellum computation changes (presented in released 
notes for 6.0)

Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar

(all was checked by simple correlations)


Could people who have good knowledge of cerebellum studies  comment on the 
reliability of freesurfer 5.3 in assessing size of the cerebellum versus manual 
tracing? This may need to be redone for version 6.0.


Regards

Lucette



Lucette A. Cysique, Ph.D.

NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017
NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA
Senior Lecturer SoMs, UNSW Medicine
Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied 
Medical Research Centre, Peter Duncan Neuroscience Unit

Postal Address:
Neuroscience Research Australia
PO Box 1165 (Street Address: 139 Barker Street)
Randwick NSW 2031
Australia

Office Ph: +61 2 9399 1880
Mobile Ph: (+61)  (0)431 576 710 (text preferred)

Emails:
lcysi...@unsw.edu.au (primary)
lucette.cysi...@svha.org.au (St. Vincent's Hospital Sydney, related project)
lcysi...@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project)
Twitter: @Lucette_C
http://www.neura.edu.au/research/themes/cysique-group
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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] freesurfer 6.0 with some of the analyses

[Antonin Skoch]

Dear Batool,

just small remark:

If you did not manually modified talairach registration in your v5.3 subjects, 
I think it could be maybe beneficial to add -clean-tal to reinvoke talairach 
registration. The registration atlas has been updated in V6 but without 
-clean-tal option the registration will not be run again.

And, also, if you do T2 or FLAIR adjustment of surfaces, it could be maybe 
beneficial to add -clean-T2 (-clean-FLAIR) to reinvoke T2/FLAIR registration to 
T1. There is new implementation of initial registration method (mri_coreg) for 
bbregister.

Regards,

Antonin Skoch


You are correct that the former is true.

Run recon-all -all on your existing subject directories after moving them
to a new v6 directory (with the new fsaverage, etc.) -- it will rerun all
the commands and use your brainmask.mgz deleted voxels, and your wm.mgz 255
voxels to correct the surfaces.You will still need to open your subjects up in 
tkmedit or freeview and
inspect the surfaces for errors.

On Fri, Jan 27, 2017 at 11:13 AM Rizvi, Batool <br2...@cumc.columbia.edu>
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Thanks for your responses!
>
>
>
>
>
>
> Sorry for the naive question, but I'm wondering which commands I'd use to
> re-process all the data from 5.3. Can I run recon-all -all, and it will go
> through all the steps that it would if I ran it from the start? Or would it
> skip certain steps if it finds
>
> certain files existing already. I'm pretty sure the former is true, but
> just wanted to confirm.
>
>
>
>
>
>
>
> Thanks again!
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
> --
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
> Eugenio [e.igles...@ucl.ac.uk]
>
>
> *Sent:* Thursday, January 26, 2017 11:01 AM
>
>
> *To:* Freesurfer support list
>
>
> *Subject:* Re: [Freesurfer] freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
> Dear Batool,
>
> Sorry for missing your message.
>
>
> And dear Adam:
>
>
> Thanks for covering me! That’s exactly my standard answer to that question
> ;-)
>
>
>
>
>
>
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
>
>
>
> ERC Senior Research Fellow
>
>
> Translational Imaging Group
>
>
> University College London
>
>
> http://www.jeiglesias.com
>
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 26 Jan 2017, at 15:55, Adam Martersteck <acmar...@gmail.com> wrote:
>
>
>
>
>
>
>
> I believe Dr. Iglesias previous responses on this exact question have
> been, "yes it's possible, but your results may be harder to
>
> reproduce"
>
>
> e.g. If someone wanted to replicate your study they may have a harder time
> having to download 2 different versions of freesurfer
>
> to achieve comparable results with your study.
>
>
>
>
>
>
>
> I think the general consensus is "how many subjects do you have?" -- if
> it's less than 50, you may want to just rerun
>
> v6 on your subjects as it should preserve the edits -- but it's
> recommended you still open them up and double check.
>
>
>
>
>
>
>
> -Adam
>
>
>
>
>
>
>
> On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2...@cumc.columbia.edu>
> wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
>
>
>
> Can anyone comment on my question below?
>
>
>
>
>
>
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering
>
> that I've already
>
>
>
>
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
>
>
>
>
>
>
>
>
>
> *From:* Rizvi, Batool
>
>
>
>

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

[Adam Martersteck]

You are correct that the former is true.

Run recon-all -all on your existing subject directories after moving them
to a new v6 directory (with the new fsaverage, etc.) -- it will rerun all
the commands and use your brainmask.mgz deleted voxels, and your wm.mgz 255
voxels to correct the surfaces.

You will still need to open your subjects up in tkmedit or freeview and
inspect the surfaces for errors.

On Fri, Jan 27, 2017 at 11:13 AM Rizvi, Batool <br2...@cumc.columbia.edu>
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Thanks for your responses!
>
>
>
>
>
>
> Sorry for the naive question, but I'm wondering which commands I'd use to
> re-process all the data from 5.3. Can I run recon-all -all, and it will go
> through all the steps that it would if I ran it from the start? Or would it
> skip certain steps if it finds
>
> certain files existing already. I'm pretty sure the former is true, but
> just wanted to confirm.
>
>
>
>
>
>
>
> Thanks again!
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
> --
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
> Eugenio [e.igles...@ucl.ac.uk]
>
>
> *Sent:* Thursday, January 26, 2017 11:01 AM
>
>
> *To:* Freesurfer support list
>
>
> *Subject:* Re: [Freesurfer] freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
> Dear Batool,
>
> Sorry for missing your message.
>
>
> And dear Adam:
>
>
> Thanks for covering me! That’s exactly my standard answer to that question
> ;-)
>
>
>
>
>
>
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
>
>
>
> ERC Senior Research Fellow
>
>
> Translational Imaging Group
>
>
> University College London
>
>
> http://www.jeiglesias.com
>
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 26 Jan 2017, at 15:55, Adam Martersteck <acmar...@gmail.com> wrote:
>
>
>
>
>
>
>
> I believe Dr. Iglesias previous responses on this exact question have
> been, "yes it's possible, but your results may be harder to
>
> reproduce"
>
>
> e.g. If someone wanted to replicate your study they may have a harder time
> having to download 2 different versions of freesurfer
>
> to achieve comparable results with your study.
>
>
>
>
>
>
>
> I think the general consensus is "how many subjects do you have?" -- if
> it's less than 50, you may want to just rerun
>
> v6 on your subjects as it should preserve the edits -- but it's
> recommended you still open them up and double check.
>
>
>
>
>
>
>
> -Adam
>
>
>
>
>
>
>
> On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2...@cumc.columbia.edu>
> wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
>
>
>
> Can anyone comment on my question below?
>
>
>
>
>
>
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering
>
> that I've already
>
>
>
>
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
>
>
>
>
>
>
>
>
>
> *From:* Rizvi, Batool
>
>
>
>
>
>
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
>
>
>
>
>
>
> *To:*
>
> freesurfer@nmr.mgh.harvard.edu
>
>
>
>
>
>
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

[Rizvi, Batool]

Thanks for your responses!

Sorry for the naive question, but I'm wondering which commands I'd use to 
re-process all the data from 5.3. Can I run recon-all -all, and it will go 
through all the steps that it would if I ran it from the start? Or would it 
skip certain steps if it finds certain files existing already. I'm pretty sure 
the former is true, but just wanted to confirm.

Thanks again!

Batool

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, January 26, 2017 11:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses

Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)

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


On 26 Jan 2017, at 15:55, Adam Martersteck 
<acmar...@gmail.com<mailto:acmar...@gmail.com>> wrote:

I believe Dr. Iglesias previous responses on this exact question have been, 
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time 
having to download 2 different versions of freesurfer to achieve comparable 
results with your study.

I think the general consensus is "how many subjects do you have?" -- if it's 
less than 50, you may want to just rerun v6 on your subjects as it should 
preserve the edits -- but it's recommended you still open them up and double 
check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote:












Hi,

Can anyone comment on my question below?


I think the FAQ page mentions that the same version should be used to process 
all cases within a dataset, but my question is whether I can have the same 
dataset used for two different versions for separate analyses? This is 
considering that I've already

processed all my data with 5.3, but am interested in getting hippocampal 
subfields through 6.0.












Thanks so much!


Batool







From: Rizvi, Batool


Sent: Wednesday, January 25, 2017 12:54 PM


To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>


Subject: freesurfer 6.0 with some of the analyses













Hi,


I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0?

Or do you recommend us starting over for the analyses we've already done in 5.3 
for that study?






Thank you!


Batool










___

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 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<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 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] freesurfer 6.0 with some of the analyses

[Iglesias Gonzalez, Eugenio]

Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)

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


On 26 Jan 2017, at 15:55, Adam Martersteck 
> wrote:

I believe Dr. Iglesias previous responses on this exact question have been, 
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time 
having to download 2 different versions of freesurfer to achieve comparable 
results with your study.

I think the general consensus is "how many subjects do you have?" -- if it's 
less than 50, you may want to just rerun v6 on your subjects as it should 
preserve the edits -- but it's recommended you still open them up and double 
check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
> wrote:












Hi,

Can anyone comment on my question below?


I think the FAQ page mentions that the same version should be used to process 
all cases within a dataset, but my question is whether I can have the same 
dataset used for two different versions for separate analyses? This is 
considering that I've already

processed all my data with 5.3, but am interested in getting hippocampal 
subfields through 6.0.












Thanks so much!


Batool







From: Rizvi, Batool


Sent: Wednesday, January 25, 2017 12:54 PM


To: freesurfer@nmr.mgh.harvard.edu


Subject: freesurfer 6.0 with some of the analyses













Hi,


I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0?

Or do you recommend us starting over for the analyses we've already done in 5.3 
for that study?






Thank you!


Batool










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Re: [Freesurfer] freesurfer 6.0 with some of the analyses

[Adam Martersteck]

I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results with your study.

I think the general consensus is "how many subjects do you have?" -- if
it's less than 50, you may want to just rerun v6 on your subjects as it
should preserve the edits -- but it's recommended you still open them up
and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
> Can anyone comment on my question below?
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering that I've already
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
> Batool
>
>
>
>
> --
>
>
> *From:* Rizvi, Batool
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
> *To:* freesurfer@nmr.mgh.harvard.edu
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
> I'm wondering if it's okay to run some of the analyses within one study
> on v.5.3 and the other hippocampal analyses on 6.0?
>
> Or do you recommend us starting over for the analyses we've already done
> in 5.3 for that study?
>
>
>
>
>
>
> Thank you!
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
> ___
>
> 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] freesurfer 6.0 with some of the analyses

[Rizvi, Batool]

Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process 
all cases within a dataset, but my question is whether I can have the same 
dataset used for two different versions for separate analyses? This is 
considering that I've already processed all my data with 5.3, but am interested 
in getting hippocampal subfields through 6.0.


Thanks so much!
Batool

From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some of the analyses

Hi,
I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us 
starting over for the analyses we've already done in 5.3 for that study?

Thank you!
Batool
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Re: [Freesurfer] Freesurfer 6.0 and MNI template

[Trisanna Sprung-Much]

thanks Doug!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve 
wrote:

> Still in 305
>
>
> On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> > Me again,
> >
> > Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in
> > MNI305 space or have they been updated to the MNI152 space?
> >
> > many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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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.
>
>
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Re: [Freesurfer] Freesurfer 6.0 and MNI template

[Douglas N Greve]

Still in 305


On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> Me again,
>
> Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in 
> MNI305 space or have they been updated to the MNI152 space?
>
> many thanks!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Freesurfer 6.0 and MNI template

[Trisanna Sprung-Much]

Me again,

Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305
space or have they been updated to the MNI152 space?

many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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[Freesurfer] freesurfer 6.0 with some of the analyses

[Rizvi, Batool]

Hi,
I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us 
starting over for the analyses we've already done in 5.3 for that study?

Thank you!
Batool
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Re: [Freesurfer] Freesurfer 6.0 link

[Aziz Nanthaamornphong]

Thank a lot.

Aziz.

On Wed, Jan 25, 2017 at 9:38 PM, Z K  wrote:

> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> > Hi experts,
> >
> > How can I download Freesurfer version 6.0? Is there an available URL
> link?
> >
> > Thank you,
> > Aziz
> > --
> >
> > Aziz Nanthaamornphong, Ph.D.,
> > Chair of Master of Science Program in Information Technology
> > Department of ICT
> > Faculty of Technology and Environment
> > Prince of Songkla University, Phuket Campus
> > +66 7627 6716 (v)
> > http://research.te.psu.ac.th/aziz
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
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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
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> but does not contain patient information, please contact the sender and
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>
>
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Re: [Freesurfer] Freesurfer 6.0 link

[Z K]

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science Program in Information Technology
> Department of ICT
> Faculty of Technology and Environment
> Prince of Songkla University, Phuket Campus
> +66 7627 6716 (v)
> http://research.te.psu.ac.th/aziz
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Freesurfer 6.0

[John Papatriantafyllou]

Please do not forget windows people
John

On Jan 25, 2017 12:45 PM, "Aziz Nanthaamornphong" 
wrote:

> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science Program in Information Technology
> Department of ICT
> Faculty of Technology and Environment
> Prince of Songkla University, Phuket Campus
> +66 7627 6716 (v)
> http://research.te.psu.ac.th/aziz
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> 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
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> but does not contain patient information, please contact the sender and
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[Freesurfer] Freesurfer 6.0 link

[Aziz Nanthaamornphong]

Hi experts,

How can I download Freesurfer version 6.0? Is there an available URL link?

Thank you,
Aziz
-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

[Trisanna Sprung-Much]

thanks for the quick response Bruce!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 24, 2017 at 1:18 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> it is better about handling highres data, but the ex vivo recon stream is
> still a work in progress
>
> cheers
> Bruce
> On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote:
>
> Hi there
>> I am wondering if the Freesurfer 6.0 version is more flexible with the
>> parameters used for ex-vivo scans other than what 5.3 required, as listed
>> here
>>  https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.
>>
>> We acquired some ex-vivo scans at 0.4mm iso but not with those above
>> parameters.
>>
>> many thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
> ___
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>
>
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> 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
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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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Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

[Bruce Fischl]

Hi Trisanna

it is better about handling highres data, but the ex vivo recon stream is 
still a work in progress


cheers
Bruce
On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote:


Hi there
I am wondering if the Freesurfer 6.0 version is more flexible with the
parameters used for ex-vivo scans other than what 5.3 required, as listed
here
 https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.

We acquired some ex-vivo scans at 0.4mm iso but not with those above
parameters.

many thanks!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology



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[Freesurfer] Freesurfer 6.0 and ex-vivo T1

[Trisanna Sprung-Much]

Hi there

I am wondering if the Freesurfer 6.0 version is more flexible with the
parameters used for ex-vivo scans other than what 5.3 required, as listed
here
 https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.

We acquired some ex-vivo scans at 0.4mm iso but not with those above
parameters.

many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)

[Iglesias Gonzalez, Eugenio]

Ciao Daniele,
This is weird. Would you mind verifying that file T1resampled.mgz actually 
exists in the temporary directory of the subject? You can do that by CDing to 
$SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command:
find . -name “T1resampled.mgz”
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 7 Nov 2016, at 16:39, Daniele Orlandi 
> wrote:

Dear experts,
I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for 
hippocampal subfield features extraction (always on Ubuntu 14.01 environment).

After several trial I realized that before pipeline ends I've got the following 
error:

/opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz  
hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127
Error using kvlGEMSMatlab
/cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz

Error in kvlReadCroppedImage (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 588)


Could you help me?
Best
Daniele

PS: Even though one of the last row display " finished without error", no 
output is generated in the /mri/ folder.


--
--
Daniele Orlandi, PsyD
IRCCS Fatebenefratelli
Via Pilastroni 4
25125 Brescia - Italy
tel: +39 030 35 01 563
e-mail: dorla...@fatebenefratelli.eu
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[Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)

[Daniele Orlandi]

Dear experts, 
I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for 
hippocampal subfield features extraction (always on Ubuntu 14.01 environment). 

After several trial I realized that before pipeline ends I've got the following 
error: 

/opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz 
hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127 
Error using kvlGEMSMatlab 
/cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216: 
itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz 

Error in kvlReadCroppedImage (line 11) 

Error in segmentSubjectT1_autoEstimateAlveusML (line 588) 


Could you help me? 
Best 
Daniele 

PS: Even though one of the last row display " finished without error", no 
output is generated in the /mri/ folder. 


-- 
-- 
Daniele Orlandi, PsyD 
IRCCS Fatebenefratelli 
Via Pilastroni 4 
25125 Brescia - Italy 
tel: +39 030 35 01 563 
e-mail: dorla...@fatebenefratelli.eu 
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Re: [Freesurfer] Freesurfer 6.0?

[VA Research]

Did you receive a reply/

Any news update for 6.0 release?

On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create better surfaces using
> Freesurfer 6.0 and I am wondering if it really will improve surface
> extraction that much.
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> ___
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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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Re: [Freesurfer] freesurfer 6.0 release date

[Bruce Fischl]

Hi Fengji

we have frozen the code and are going through various tests now so are 
hoping sometime in the next few weeks, but of course it's impossible to say 
as it depends on how well the tests turn out.


cheers
Bruce


On Mon, 1 
Aug 2016, Fengji Geng wrote:



Hi fs developers, 
I am wondering if you have any estimation when fs 6.0 will come out.  The
reason that I ask this is because we are running some analysis using fs 5.1
and planning to switch to a more recent version of fs. If fs 6.0 will come
out soon, we will probably hold and wait for it. If not, we will just switch
to fs 5.3. 

Thanks!

--
Fengji Geng

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[Freesurfer] freesurfer 6.0 release date

[Fengji Geng]

Hi fs developers,

I am wondering if you have any estimation when fs 6.0 will come out.  The
reason that I ask this is because we are running some analysis using fs 5.1
and planning to switch to a more recent version of fs. If fs 6.0 will come
out soon, we will probably hold and wait for it. If not, we will just
switch to fs 5.3.

Thanks!

-- 
Fengji Geng
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Re: [Freesurfer] FreeSurfer 6.0

[Del Re, Elisabetta]

Thank you,

looking forward to the 6.0!

Regards,

Elisabetta


Elisabetta C. del Re, Ph.D.
Instructor,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
Sent: Thursday, July 28, 2016 4:31 PM
To: Freesurfer support list
Cc: Anastasia Haidar
Subject: Re: [Freesurfer] FreeSurfer 6.0

Hi Elisabetta

FS 6 is not available yet. We are hoping to have a beta in a couple of
weeks and are actively working on getting it out

cheers
Bruce
On Thu, 28 Jul 2016,
elisabetta_de...@hms.harvard.edu wrote:

>
>
> Dear FreeSurfer team,
> we are trying to find a downloadable version of FS6.0 to use on our
> data.
> We can not find it on the web.
> Could you help us with that?
> Thank you,
> best regards,
> Elisabetta
>
> --
> Elisabetta C. del Re, Ph.D.
> Instructor,
> Department of Psychiatry
> Harvard Medical School
> phone 617 9675569
> mail elisabetta_de...@hms.harvard.edu
>
>
>
>
> --
> Elisabetta C. del Re, Ph.D.
> Instructor,
> Department of Psychiatry
> Harvard Medical School
> phone 617 9675569
> mail elisabetta_de...@hms.harvard.edu
>
>
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Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

Hi Elisabetta​

FS 6 is not available yet. We are hoping to have a beta in a couple of 
weeks and are actively working on getting it out


cheers
Bruce
On Thu, 28 Jul 2016, 
elisabetta_de...@hms.harvard.edu wrote:





​Dear FreeSurfer team,
we are trying to find a downloadable version of FS6.0 to use on our
data.
We can not find it on the web. 
Could you help us with that?
Thank you,
best regards,
Elisabetta​

--
Elisabetta C. del Re, Ph.D.
Instructor,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu




--
Elisabetta C. del Re, Ph.D.
Instructor,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu

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Re: [Freesurfer] FreeSurfer 6.0

[elisabetta_de...@hms.harvard.edu]

>
> ​Dear FreeSurfer team,
> we are trying to find a downloadable version of FS6.0 to use on our data.
> We can not find it on the web.
> Could you help us with that?
> Thank you,
> best regards,
> Elisabetta​
>
> --
> *Elisabetta C. del Re, Ph.D.*
>
> *Instructor,*
> *Department of Psychiatry*
> *Harvard Medical School*
> *phone 617 9675569 <617%209675569>*
> *mail elisabetta_de...@hms.harvard.edu *
>



-- 
*Elisabetta C. del Re, Ph.D.*

*Instructor,*
*Department of Psychiatry*
*Harvard Medical School*
*phone 617 9675569*
*mail elisabetta_de...@hms.harvard.edu *
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Re: [Freesurfer] Freesurfer 6.0?

[Trisanna Sprung-Much]

thanks, Doug!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve 
wrote:

> We are working pretty hard to get it out but we are still reluctant to set
> a hard date. I think we'll have a beta version in two weeks, but that's
> just a guess.
>
> doug
>
>
>
> On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:
>
>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create better surfaces using
> Freesurfer 6.0 and I am wondering if it really will improve surface
> extraction that much.
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
> ___
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>
>
>
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> 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
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
>
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Re: [Freesurfer] Freesurfer 6.0?

[Douglas Greve]

We are working pretty hard to get it out but we are still reluctant to 
set a hard date. I think we'll have a beta version in two weeks, but 
that's just a guess.


doug



On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:


Hi there

Do we have a potential date for the Freesurfer 6.0 release? I was told 
I would want to re-run all my subjects to create better surfaces using 
Freesurfer 6.0 and I am wondering if it really will improve surface 
extraction that much.


Many thanks!

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology



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[Freesurfer] Freesurfer 6.0?

[Trisanna Sprung-Much]

Hi there

Do we have a potential date for the Freesurfer 6.0 release? I was told I
would want to re-run all my subjects to create better surfaces using
Freesurfer 6.0 and I am wondering if it really will improve surface
extraction that much.

Many thanks!

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

The color still indicates the direction. If you have a signed 
hypothesis, then you can run it with pos or neg instead of abs, however, 
in this case it will change the voxel-wise cluster-forming threshold 
(make it more liberal) because the voxel-wise p-value is computed 
assuming an unsigned test.

On 05/10/2016 11:59 AM, Ajay Kurani wrote:
> Hi Doug,
>Ok this makes more sense now.  In my case if I choose abs I would 
> look at the max cdf < 0.05 for the corresponding cluster extent in the 
> TH13 folder.
>
>
> In terms of the |a-b|<0,05 does this mean that if I got results in 
> blue it just means significant but with no directionality as to if A > 
> B or B>A?  I guess with the blue and red color bars I thought 
> directionality was implied.
>
> Or would one need to do a subsequent one tailed test (Pos A>B; Neg 
> B>A)d in order to determine directionality of thickness results?
>
> Thanks,
> Ajay
>
> On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness
> files (smoothed 15mm translates to FWHM=21mm), I looked at
> fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option
> mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it
> the alpha per tail (5% A>B, 5% B>A)?  Would I look at the max cdf
> 0.05 which is a cluster size of 1302 or would I look at max cdf
> <0.1 which is 1109?  This relates to the first question of if 0.05
> relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied?  I initially thought that T
> or Z=1.3 is the threshold but in looking at tutorials I see that
> may be related to the color scale -log(0.05), so I am not sure if
> there is a minimum T/Z value to be included in the cluster or if I
> was correct at 1.3 is the threshold value (T or Z score or
> something else)?.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani
> > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my
> thickness files (smoothed 15mm translates to FWHM=21mm), I
> looked at fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3
> option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A )
> or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at
> the max cdf 0.05 which is a cluster size of 1302 or would I
> look at max cdf <0.1 which is 1109?  This relates to the first
> question of if 0.05 relates to the overall probability or per
> tail.
>
> Also is there a T/Z threshold applied to these clusters or
> just cluster-extent is used?  In looking at the tutorials I
> see that 1.3 really is -log(0.05) so I do not think this
> relates to any sort of T or Z threshold but I just wanted to
> verify.
>
> Thanks,
> Ajay
>
>
> Also, when smoothed at 15mm the estimated smoothness was
> around 21mm.  When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  > wrote:
>
> Hi Doug,
>I wanted to figure out what is the minimum cluster
> extent for a given monte carlo simulation (ie when you
> choose p=0.5/T=1.3).  I saw the following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
> and so I wanted to know if freesurfer estimates the
> smoothness for each subject's cortical thickness for a
> hemisphere and then chooses the corresponding fwhm folder
> or if by choosing lh 15mm in qdec the clusterwise values
> are taken from the 15mm folder?  Is the smoothness based
> on the smoothing kernel used or the inherent smoothness of
> that particular measure (ie measuring the smoothness of
> the input thicknesss image)?  Is there a way to see what
> cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of
> cortical thickness, qcache, mris_fwhm or mri_surf2surf
> would all do the same thing and so I should be getting
> similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared
> to mri_smooth.
>
> For mri_surf2surf I used the following command for
> smoothing LGI and cortical thickness and 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Ok this makes more sense now.  In my case if I choose abs I would look
at the max cdf < 0.05 for the corresponding cluster extent in the TH13
folder.


In terms of the |a-b|<0,05 does this mean that if I got results in blue it
just means significant but with no directionality as to if A > B or B>A?  I
guess with the blue and red color bars I thought directionality was
implied.

Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in
order to determine directionality of thickness results?

Thanks,
Ajay

On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
> file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
> overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
> (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
> of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
> first question of if 0.05 relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied?  I initially thought that T or
> Z=1.3 is the threshold but in looking at tutorials I see that may be
> related to the color scale -log(0.05), so I am not sure if there is a
> minimum T/Z value to be included in the cluster or if I was correct at 1.3
> is the threshold value (T or Z score or something else)?.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the explanation. In using p=0.05 with my thickness files
>> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
>> file.
>>
>>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean
>> the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per
>> tail (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster
>> size of 1302 or would I look at max cdf <0.1 which is 1109?  This relates
>> to the first question of if 0.05 relates to the overall probability or per
>> tail.
>>
>> Also is there a T/Z threshold applied to these clusters or just
>> cluster-extent is used?  In looking at the tutorials I see that 1.3 really
>> is -log(0.05) so I do not think this relates to any sort of T or Z
>> threshold but I just wanted to verify.
>>
>> Thanks,
>> Ajay
>>
>>
>>
>> Also, when smoothed at 15mm the estimated smoothness was around 21mm.
>> When lo
>>
>>
>> On Friday, May 6, 2016, Ajay Kurani  wrote:
>>
>>> Hi Doug,
>>>I wanted to figure out what is the minimum cluster extent for a given
>>> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
>>> following tutorial :
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so
>>> I wanted to know if freesurfer estimates the smoothness for each subject's
>>> cortical thickness for a hemisphere and then chooses the corresponding fwhm
>>> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
>>> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
>>> or the inherent smoothness of that particular measure (ie measuring the
>>> smoothness of the input thicknesss image)?  Is there a way to see what
>>> cluster minimum is used?
>>>
>>> Thanks,
>>> Ajay
>>>
>>>
>>> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Doug,
Thanks for the clarification.  So in the case of cortical thickness,
 qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
 should be getting similar results if everything is entered in the same
 fashion.  This would be the approriate choice compared to mri_smooth.

 For mri_surf2surf I used the following command for smoothing LGI and
 cortical thickness and converting to .gii files.

 mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
 rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
 mris_convert -c rh.thickness.fwhm15.mgz
 $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii


 1) For cortical thickness does it make sense to use the --cortex option
 or should I specify a mask of some type (if so which) in mris_surf2surf?

 2) For converting files to .gii should I be using rh.white as the
 option or should it be rh.pial?


 Best,
 Ajay



 On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
 wrote:

> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
> analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

On 05/09/2016 04:11 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files 
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ 
> cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean 
> the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha 
> per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a 
> cluster size of 1302 or would I look at max cdf <0.1 which is 1109?  
> This relates to the first question of if 0.05 relates to the overall 
> probability or per tail.
It is the overall alpha, but the test is unsigned, so it is 5% for |A-B|>0
>
> Also is there a T/Z threshold applied?  I initially thought that T or 
> Z=1.3 is the threshold but in looking at tutorials I see that may be 
> related to the color scale -log(0.05), so I am not sure if there is a 
> minimum T/Z value to be included in the cluster or if I was correct at 
> 1.3 is the threshold value (T or Z score or something else)?.
In the simulation, the cluster-forming threshold (eg, p<.01,sig>2) is 
converted into a z-score and used to threshold the smoothed z-map. No 
t-thresholding is done,.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness
> files (smoothed 15mm translates to FWHM=21mm), I looked at
> fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option
> mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it
> the alpha per tail (5% A>B, 5% B>A)?  Would I look at the max cdf
> 0.05 which is a cluster size of 1302 or would I look at max cdf
> <0.1 which is 1109?  This relates to the first question of if 0.05
> relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied to these clusters or just
> cluster-extent is used?  In looking at the tutorials I see that
> 1.3 really is -log(0.05) so I do not think this relates to any
> sort of T or Z threshold but I just wanted to verify.
>
> Thanks,
> Ajay
>
>
> Also, when smoothed at 15mm the estimated smoothness was around
> 21mm.  When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  > wrote:
>
> Hi Doug,
>I wanted to figure out what is the minimum cluster extent
> for a given monte carlo simulation (ie when you choose
> p=0.5/T=1.3). I saw the following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
> and so I wanted to know if freesurfer estimates the smoothness
> for each subject's cortical thickness for a hemisphere and
> then chooses the corresponding fwhm folder or if by choosing
> lh 15mm in qdec the clusterwise values are taken from the 15mm
> folder?  Is the smoothness based on the smoothing kernel used
> or the inherent smoothness of that particular measure (ie
> measuring the smoothness of the input thicknesss image)?  Is
> there a way to see what cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of
> cortical thickness, qcache, mris_fwhm or mri_surf2surf
> would all do the same thing and so I should be getting
> similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared to
> mri_smooth.
>
> For mri_surf2surf I used the following command for
> smoothing LGI and cortical thickness and converting to
> .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15
> --sval rh.thickness.fsaverage.mgh --tval
> rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white
> rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the
> --cortex option or should I specify a mask of some type
> (if so which) in mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white
> as the option or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with
> mris_smooth and mri_surf2surf 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.

 In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
(5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
first question of if 0.05 relates to the overall probability or per tail.

Also is there a T/Z threshold applied?  I initially thought that T or Z=1.3
is the threshold but in looking at tutorials I see that may be related to
the color scale -log(0.05), so I am not sure if there is a minimum T/Z
value to be included in the cluster or if I was correct at 1.3 is the
threshold value (T or Z score or something else)?.

Thanks,
Ajay

On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
> file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
> overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
> (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
> of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
> first question of if 0.05 relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied to these clusters or just
> cluster-extent is used?  In looking at the tutorials I see that 1.3 really
> is -log(0.05) so I do not think this relates to any sort of T or Z
> threshold but I just wanted to verify.
>
> Thanks,
> Ajay
>
>
>
> Also, when smoothed at 15mm the estimated smoothness was around 21mm.
> When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  wrote:
>
>> Hi Doug,
>>I wanted to figure out what is the minimum cluster extent for a given
>> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
>> following tutorial :
>> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so
>> I wanted to know if freesurfer estimates the smoothness for each subject's
>> cortical thickness for a hemisphere and then chooses the corresponding fwhm
>> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
>> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
>> or the inherent smoothness of that particular measure (ie measuring the
>> smoothness of the input thicknesss image)?  Is there a way to see what
>> cluster minimum is used?
>>
>> Thanks,
>> Ajay
>>
>>
>> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Doug,
>>>Thanks for the clarification.  So in the case of cortical thickness,
>>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
>>> should be getting similar results if everything is entered in the same
>>> fashion.  This would be the approriate choice compared to mri_smooth.
>>>
>>> For mri_surf2surf I used the following command for smoothing LGI and
>>> cortical thickness and converting to .gii files.
>>>
>>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
>>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
>>> mris_convert -c rh.thickness.fwhm15.mgz
>>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>>>
>>>
>>> 1) For cortical thickness does it make sense to use the --cortex option
>>> or should I specify a mask of some type (if so which) in mris_surf2surf?
>>>
>>> 2) For converting files to .gii should I be using rh.white as the option
>>> or should it be rh.pial?
>>>
>>>
>>> Best,
>>> Ajay
>>>
>>>
>>>
>>> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Doug,
Thanks for the quick reply.

 Is there a difference  from qcache/mris_fwhm with mris_smooth and
 mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
 analysis?

 Thanks,
 Ajay

 On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
 wrote:

> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts which
> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
> cortical thickness analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
> group analysis.  After finding regions of difference, I would then like to
> use the ROI to extract each individual's mean thickness in the ROI in 
> order
> to run a correlation with other measures.  Based on this, I assume it 
> would
> make sense to use smoothed data to identify the ROI and then use 
> unsmoothed
> data for extracting 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.

 In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
(5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
first question of if 0.05 relates to the overall probability or per tail.

Also is there a T/Z threshold applied to these clusters or just
cluster-extent is used?  In looking at the tutorials I see that 1.3 really
is -log(0.05) so I do not think this relates to any sort of T or Z
threshold but I just wanted to verify.

Thanks,
Ajay



Also, when smoothed at 15mm the estimated smoothness was around 21mm.  When
lo


On Friday, May 6, 2016, Ajay Kurani  wrote:

> Hi Doug,
>I wanted to figure out what is the minimum cluster extent for a given
> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
> following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
> wanted to know if freesurfer estimates the smoothness for each subject's
> cortical thickness for a hemisphere and then chooses the corresponding fwhm
> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
> or the inherent smoothness of that particular measure (ie measuring the
> smoothness of the input thicknesss image)?  Is there a way to see what
> cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the clarification.  So in the case of cortical thickness,
>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
>> should be getting similar results if everything is entered in the same
>> fashion.  This would be the approriate choice compared to mri_smooth.
>>
>> For mri_surf2surf I used the following command for smoothing LGI and
>> cortical thickness and converting to .gii files.
>>
>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
>> mris_convert -c rh.thickness.fwhm15.mgz
>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>>
>>
>> 1) For cortical thickness does it make sense to use the --cortex option
>> or should I specify a mask of some type (if so which) in mris_surf2surf?
>>
>> 2) For converting files to .gii should I be using rh.white as the option
>> or should it be rh.pial?
>>
>>
>> Best,
>> Ajay
>>
>>
>>
>> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Doug,
>>>Thanks for the quick reply.
>>>
>>> Is there a difference  from qcache/mris_fwhm with mris_smooth and
>>> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
>>> analysis?
>>>
>>> Thanks,
>>> Ajay
>>>
>>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Freesurfer Experts,
Just as a followup through my reading i've come across posts which
 use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
 cortical thickness analysis I would like to smooth all of my
 rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
 group analysis.  After finding regions of difference, I would then like to
 use the ROI to extract each individual's mean thickness in the ROI in order
 to run a correlation with other measures.  Based on this, I assume it would
 make sense to use smoothed data to identify the ROI and then use unsmoothed
 data for extracting actual thickness measures (does lh.thickness.fsaverage
 contain the original thickness or warped thickness values).

 I am unsure which smoothing is the most accurate or preferred.  In
 using qcache the smoothness of the images do not seem to reach the filter
 level (based on the earlier email) so I am not sure if there is a
 freesurfer tool to check the smoothness level or if the qcache smoothness
 levels make sense for cortical thickness.

 Thanks,
 Ajay

 On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
 wrote:

> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache option and
> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
> (converted) files.  I used an afni tool SurfFWHM to estimate the 
> smoothness
> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
> and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by 
computing the pearson correation coefficient of the residual error 
between adjacent vertices. This is then averaged over all vertices to 
compute a mean cor coef. A transform is then applied to compute the 
FWHM. This is consistent in that if you synthesize white gaussian noise 
on the surface, then smooth it with a given FWHM (mri_surf2surf or 
mris_fwhm), then use that data to compute the FWHM, the applied and 
estimated FWHM will be equal (or close).

If you look in a given file produced by the simulator, eg,
  
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th20/mc-z.cdf
the two relevant columns will be MaxClustBin and MaxClustCDF, eg,
# BinNo  MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin 
MaxSigPDF MaxSigCDF
   33  181.572128   0.010100 0.092500  0.132425 14.427808  
0.004600  0.593700
Means that a cluster of size 181.57 has a probability of 0.0925 under 
the null when the FWHM=10 and the threshold is p<.01 (th20)




On 05/06/2016 03:59 PM, Ajay Kurani wrote:
> Hi Doug,
>I wanted to figure out what is the minimum cluster extent for a 
> given monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw 
> the following tutorial : 
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and 
> so I wanted to know if freesurfer estimates the smoothness for each 
> subject's cortical thickness for a hemisphere and then chooses the 
> corresponding fwhm folder or if by choosing lh 15mm in qdec the 
> clusterwise values are taken from the 15mm folder?  Is the smoothness 
> based on the smoothing kernel used or the inherent smoothness of that 
> particular measure (ie measuring the smoothness of the input 
> thicknesss image)?  Is there a way to see what cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of cortical
> thickness, qcache, mris_fwhm or mri_surf2surf would all do the
> same thing and so I should be getting similar results if
> everything is entered in the same fashion. This would be the
> approriate choice compared to mri_smooth.
>
> For mri_surf2surf I used the following command for smoothing LGI
> and cortical thickness and converting to .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white
> rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the --cortex
> option or should I specify a mask of some type (if so which) in
> mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white as the
> option or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani
> > wrote:
>
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth
> and mri_surf2surf -fwhm ? If so,  which is recommended for
> cortical thickness analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani
> >
> wrote:
>
> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across
> posts which use qcache, mris_fwhm, mri_surf2surf or
> mris_smooth for smoothing.  For my cortical thickness
> analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in
> order to run a group analysis.  After finding regions of
> difference, I would then like to use the ROI to extract
> each individual's mean thickness in the ROI in order to
> run a correlation with other measures.  Based on this, I
> assume it would make sense to use smoothed data to
> identify the ROI and then use unsmoothed data for
> extracting actual thickness measures (does
> lh.thickness.fsaverage contain the original thickness or
> warped thickness values).
>
> I am unsure which smoothing is the most accurate or
> preferred.  In using qcache the smoothness of the images
> do not seem to reach the filter level (based on the
> earlier email) so I am not sure if there is a freesurfer
> tool to check the smoothness level or if the qcache
> smoothness levels make sense for cortical thickness.
>
> Thanks,
> Ajay
>
> 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   I wanted to figure out what is the minimum cluster extent for a given
monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
following tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
wanted to know if freesurfer estimates the smoothness for each subject's
cortical thickness for a hemisphere and then chooses the corresponding fwhm
folder or if by choosing lh 15mm in qdec the clusterwise values are taken
from the 15mm folder?  Is the smoothness based on the smoothing kernel used
or the inherent smoothness of that particular measure (ie measuring the
smoothness of the input thicknesss image)?  Is there a way to see what
cluster minimum is used?

Thanks,
Ajay


On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the clarification.  So in the case of cortical thickness,
> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
> should be getting similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared to mri_smooth.
>
> For mri_surf2surf I used the following command for smoothing LGI and
> cortical thickness and converting to .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the --cortex option or
> should I specify a mask of some type (if so which) in mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white as the option
> or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the quick reply.
>>
>> Is there a difference  from qcache/mris_fwhm with mris_smooth and
>> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
>> analysis?
>>
>> Thanks,
>> Ajay
>>
>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Freesurfer Experts,
>>>Just as a followup through my reading i've come across posts which
>>> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
>>> cortical thickness analysis I would like to smooth all of my
>>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
>>> group analysis.  After finding regions of difference, I would then like to
>>> use the ROI to extract each individual's mean thickness in the ROI in order
>>> to run a correlation with other measures.  Based on this, I assume it would
>>> make sense to use smoothed data to identify the ROI and then use unsmoothed
>>> data for extracting actual thickness measures (does lh.thickness.fsaverage
>>> contain the original thickness or warped thickness values).
>>>
>>> I am unsure which smoothing is the most accurate or preferred.  In using
>>> qcache the smoothness of the images do not seem to reach the filter level
>>> (based on the earlier email) so I am not sure if there is a freesurfer tool
>>> to check the smoothness level or if the qcache smoothness levels make sense
>>> for cortical thickness.
>>>
>>> Thanks,
>>> Ajay
>>>
>>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Freesurfer Experts,
I am trying to understand the difference between qcache option and
 mris_fwhm and which is appropriate for a cortical thickness analysis.  I
 processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
 (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
 of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
 and 20mm it was approximately 9.3-9.9 smoothness level.

 I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
 lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
 using SurfFWHM on the smae subject the smoothness was estimated at 11.25.


 1) I am not sure if the qcache or the mris_fwhm file is more
 appropriate to use for a cortical thickness analysis.

 2) For qdec if I select the 15mm  option does it assume the smoothness
 is 15mm when calculating monte carlo corrections?  Would there be a
 different way to estimate this since my smoothness at 15mm is closer to
 10mm?

 Thanks,
 Ajay

>>>
>>>
>>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the clarification.  So in the case of cortical thickness,
qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
should be getting similar results if everything is entered in the same
fashion.  This would be the approriate choice compared to mri_smooth.

For mri_surf2surf I used the following command for smoothing LGI and
cortical thickness and converting to .gii files.

mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
mris_convert -c rh.thickness.fwhm15.mgz
$FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii


1) For cortical thickness does it make sense to use the --cortex option or
should I specify a mask of some type (if so which) in mris_surf2surf?

2) For converting files to .gii should I be using rh.white as the option or
should it be rh.pial?


Best,
Ajay



On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
> analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>Just as a followup through my reading i've come across posts which use
>> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
>> cortical thickness analysis I would like to smooth all of my
>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
>> group analysis.  After finding regions of difference, I would then like to
>> use the ROI to extract each individual's mean thickness in the ROI in order
>> to run a correlation with other measures.  Based on this, I assume it would
>> make sense to use smoothed data to identify the ROI and then use unsmoothed
>> data for extracting actual thickness measures (does lh.thickness.fsaverage
>> contain the original thickness or warped thickness values).
>>
>> I am unsure which smoothing is the most accurate or preferred.  In using
>> qcache the smoothness of the images do not seem to reach the filter level
>> (based on the earlier email) so I am not sure if there is a freesurfer tool
>> to check the smoothness level or if the qcache smoothness levels make sense
>> for cortical thickness.
>>
>> Thanks,
>> Ajay
>>
>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Freesurfer Experts,
>>>I am trying to understand the difference between qcache option and
>>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>>
>>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>>
>>>
>>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>>> to use for a cortical thickness analysis.
>>>
>>> 2) For qdec if I select the 15mm  option does it assume the smoothness
>>> is 15mm when calculating monte carlo corrections?  Would there be a
>>> different way to estimate this since my smoothness at 15mm is closer to
>>> 10mm?
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

There is not a difference between mris_fwhm and mri_surf2surf. 
mris_smooth smoothes the xyz coordinates of the vertices of a surface 
(the others smooth an overlay).

On 05/05/2016 03:53 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and 
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical 
> thickness analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani  > wrote:
>
> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts
> which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for
> smoothing.  For my cortical thickness analysis I would like to
> smooth all of my rh/lh.thickness.fsaverage.mgh files for each
> subject in order to run a group analysis.  After finding regions
> of difference, I would then like to use the ROI to extract each
> individual's mean thickness in the ROI in order to run a
> correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use
> unsmoothed data for extracting actual thickness measures (does
> lh.thickness.fsaverage contain the original thickness or warped
> thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In
> using qcache the smoothness of the images do not seem to reach the
> filter level (based on the earlier email) so I am not sure if
> there is a freesurfer tool to check the smoothness level or if the
> qcache smoothness levels make sense for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani
> > wrote:
>
> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache
> option and mris_fwhm and which is appropriate for a cortical
> thickness analysis.  I processed my  files with qcache and
> have lh.thickness.fsaverage.fwhm15.gii (converted) files.  I
> used an afni tool SurfFWHM to estimate the smoothness of a
> subject at when looking at the fwhm0 image it iwas 5.5 and for
> 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only
> --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o
> test_15.gii  and when using SurfFWHM on the smae subject the
> smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more
> appropriate to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the
> smoothness is 15mm when calculating monte carlo corrections? 
> Would there be a different way to estimate this since my
> smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the quick reply.

Is there a difference  from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
analysis?

Thanks,
Ajay

On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts which use
> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
> cortical thickness analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
> group analysis.  After finding regions of difference, I would then like to
> use the ROI to extract each individual's mean thickness in the ROI in order
> to run a correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use unsmoothed
> data for extracting actual thickness measures (does lh.thickness.fsaverage
> contain the original thickness or warped thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In using
> qcache the smoothness of the images do not seem to reach the filter level
> (based on the earlier email) so I am not sure if there is a freesurfer tool
> to check the smoothness level or if the qcache smoothness levels make sense
> for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>I am trying to understand the difference between qcache option and
>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>
>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>
>>
>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>> to use for a cortical thickness analysis.
>>
>> 2) For qdec if I select the 15mm  option does it assume the smoothness is
>> 15mm when calculating monte carlo corrections?  Would there be a different
>> way to estimate this since my smoothness at 15mm is closer to 10mm?
>>
>> Thanks,
>> Ajay
>>
>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas Greve]

Underneath, they both use the same code, so they should give the same 
results. Are you saying they are different? I don't know what SurfFWHM 
is doing so I can't comment on what those results mean. Measuring the 
FWHM on the surface is quite tricky.

doug


On 5/4/16 6:41 PM, Ajay Kurani wrote:

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and 
mris_fwhm and which is appropriate for a cortical thickness analysis.  
I processed my  files with qcache and have 
lh.thickness.fsaverage.fwhm15.gii (converted) files.  I used an afni 
tool SurfFWHM to estimate the smoothness of a subject at when looking 
at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was 
approximately 9.3-9.9 smoothness level.


I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i 
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and 
when using SurfFWHM on the smae subject the smoothness was estimated 
at 11.25.



1) I am not sure if the qcache or the mris_fwhm file is more 
appropriate to use for a cortical thickness analysis.


2) For qdec if I select the 15mm  option does it assume the smoothness 
is 15mm when calculating monte carlo corrections?  Would there be a 
different way to estimate this since my smoothness at 15mm is closer 
to 10mm?


Thanks,
Ajay


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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   Just as a followup through my reading i've come across posts which use
qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
cortical thickness analysis I would like to smooth all of my
rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
group analysis.  After finding regions of difference, I would then like to
use the ROI to extract each individual's mean thickness in the ROI in order
to run a correlation with other measures.  Based on this, I assume it would
make sense to use smoothed data to identify the ROI and then use unsmoothed
data for extracting actual thickness measures (does lh.thickness.fsaverage
contain the original thickness or warped thickness values).

I am unsure which smoothing is the most accurate or preferred.  In using
qcache the smoothness of the images do not seem to reach the filter level
(based on the earlier email) so I am not sure if there is a freesurfer tool
to check the smoothness level or if the qcache smoothness levels make sense
for cortical thickness.

Thanks,
Ajay

On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache option and
> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
> and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
> to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the smoothness is
> 15mm when calculating monte carlo corrections?  Would there be a different
> way to estimate this since my smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
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[Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and
mris_fwhm and which is appropriate for a cortical thickness analysis.  I
processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
(converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
and 20mm it was approximately 9.3-9.9 smoothness level.

I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
using SurfFWHM on the smae subject the smoothness was estimated at 11.25.


1) I am not sure if the qcache or the mris_fwhm file is more appropriate to
use for a cortical thickness analysis.

2) For qdec if I select the 15mm  option does it assume the smoothness is
15mm when calculating monte carlo corrections?  Would there be a different
way to estimate this since my smoothness at 15mm is closer to 10mm?

Thanks,
Ajay
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Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

yes, although the hippocampal stuff hasn't changed I don't think 
(Eugenio: is that correct)?


On Wed, 16 Mar 2016, Alan Francis wrote:


Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
ran the HSF method successfully. Have they retracted that version?

best,

Alan

On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
wrote:
  actually there is no beta yet, but hopefully within a week or so
  On Wed, 16 Mar 2016, Alan Francis wrote:

Hi Elizabeth:

I ran the Hippocampal subfields on 6.0 beta. The
parcellation looks great.
Beta is available for download. Here is the URL:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best,

Alan

On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
 wrote:
      Dear ladies and gentlemen,

for a research project I need to measure the volume
of the different
hippocampus subregions. I want to use FreeSurfer 6.0
for that but I
can only find FreeSurfer 5.3 online. Is FreeSurfer
6.0 not yet
released and if so, when will it be released? If it
is already
released, could you tell me where to find it?

Thank you very much in advance.

Kind regards,

Elisabeth Paul

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Alan N. Francis PhD
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Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                            
                             
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Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

Hi Elisabeth

we don't have an exact date yet, but have finished our code modifications 
(hopefully!) and are in the process of freezing a version after which we 
will run a set of tests and hopefully release it

cheers
Bruce


On Wed, 16 Mar 
2016, Elisabeth Paul wrote:

> Dear ladies and gentlemen,
> 
> for a research project I need to measure the volume of the different
> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can only
> find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if so,
> when will it be released? If it is already released, could you tell me where
> to find it?
> 
> Thank you very much in advance.
> 
> Kind regards,
> 
> Elisabeth Paul
> 
>
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FreeSurfer 6.0

[Martin Reuter]

Although it should be mentioned that outputs (even of subfields) are 
going to change due to differences in the regular freesurfer processing, 
as the subfields stream builds upon the regular FS stream.

Best, Martin


On 03/16/2016 10:52 AM, Eugenio Iglesias wrote:
> I only changed some details (e.g., temporary directories) that do not affect 
> the output.
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original Message -
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Wednesday, March 16, 2016 3:49:31 PM
> Subject: Re: [Freesurfer] FreeSurfer 6.0
>
> yes, although the hippocampal stuff hasn't changed I don't think
> (Eugenio: is that correct)?
>
> On Wed, 16 Mar 2016, Alan Francis wrote:
>
>> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
>> ran the HSF method successfully. Have they retracted that version?
>>
>> best,
>>
>> Alan
>>
>> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>>actually there is no beta yet, but hopefully within a week or so
>>On Wed, 16 Mar 2016, Alan Francis wrote:
>>
>>  Hi Elizabeth:
>>
>>  I ran the Hippocampal subfields on 6.0 beta. The
>>  parcellation looks great.
>>  Beta is available for download. Here is the URL:
>>
>>  https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>>  best,
>>
>>  Alan
>>
>>  On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>  <elisabeth.p...@student.uva.nl> wrote:
>>Dear ladies and gentlemen,
>>
>>  for a research project I need to measure the volume
>>  of the different
>>  hippocampus subregions. I want to use FreeSurfer 6.0
>>  for that but I
>>  can only find FreeSurfer 5.3 online. Is FreeSurfer
>>  6.0 not yet
>>  released and if so, when will it be released? If it
>>  is already
>>  released, could you tell me where to find it?
>>
>>  Thank you very much in advance.
>>
>>  Kind regards,
>>
>>  Elisabeth Paul
>>
>>  ___
>>  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.
>>
>>
>>
>>
>>  --
>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>  Alan N. Francis PhD
>>  NIDA T32  Fellow in Computational Neuroscience
>>  Brain Imaging Center
>>  McLean Hospital
>>  Harvard Medical School
>>  115 Mill Street, Belmont, MA 02478
>>  al...@bwh.harvard.edu
>>  afran...@mclean.harvard.edu
>>  
>> 
>>   
>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
>> ___
>> 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
>> addr

Re: [Freesurfer] FreeSurfer 6.0

[Eugenio Iglesias]

I only changed some details (e.g., temporary directories) that do not affect 
the output.


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 16, 2016 3:49:31 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0

yes, although the hippocampal stuff hasn't changed I don't think 
(Eugenio: is that correct)?

On Wed, 16 Mar 2016, Alan Francis wrote:

> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
> ran the HSF method successfully. Have they retracted that version?
> 
> best,
> 
> Alan
> 
> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>   actually there is no beta yet, but hopefully within a week or so
>   On Wed, 16 Mar 2016, Alan Francis wrote:
>
> Hi Elizabeth:
>
> I ran the Hippocampal subfields on 6.0 beta. The
> parcellation looks great.
> Beta is available for download. Here is the URL:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> best,
>
> Alan
>
> On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
> <elisabeth.p...@student.uva.nl> wrote:
>       Dear ladies and gentlemen,
>
> for a research project I need to measure the volume
> of the different
> hippocampus subregions. I want to use FreeSurfer 6.0
> for that but I
> can only find FreeSurfer 5.3 online. Is FreeSurfer
> 6.0 not yet
> released and if so, when will it be released? If it
> is already
> released, could you tell me where to find it?
>
> Thank you very much in advance.
>
> Kind regards,
>
> Elisabeth Paul
>
> ___
> 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.
> 
> 
> 
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> Alan N. Francis PhD
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu
> afran...@mclean.harvard.edu
>                                                     
>                        
>                              
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> 
> ___
> 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.
> 
> 
> 
> 
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> Alan N. Francis PhD
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu
> afran...@mclean.harvard.edu
>                                                                             
>                              
&

Re: [Freesurfer] FreeSurfer 6.0

[Alan Francis]

Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
ran the HSF method successfully. Have they retracted that version?

best,

Alan

On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
wrote:

> actually there is no beta yet, but hopefully within a week or so
>
> On Wed, 16 Mar 2016, Alan Francis wrote:
>
> Hi Elizabeth:
>>
>> I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
>> Beta is available for download. Here is the URL:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>> best,
>>
>> Alan
>>
>> On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>  wrote:
>>   Dear ladies and gentlemen,
>>
>> for a research project I need to measure the volume of the different
>> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I
>> can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet
>> released and if so, when will it be released? If it is already
>> released, could you tell me where to find it?
>>
>> Thank you very much in advance.
>>
>> Kind regards,
>>
>> Elisabeth Paul
>>
>> ___
>> 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.
>>
>>
>>
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
> ___
> 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.
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
___
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.

Re: [Freesurfer] FreeSurfer 6.0

[Alan Francis]

Hi Elizabeth:

I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best,

Alan

On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul <
elisabeth.p...@student.uva.nl> wrote:

> Dear ladies and gentlemen,
>
> for a research project I need to measure the volume of the different
> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can
> only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if
> so, when will it be released? If it is already released, could you tell me
> where to find it?
>
> Thank you very much in advance.
>
> Kind regards,
>
> Elisabeth Paul
>
> ___
> 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.
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
___
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.

Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

that's a good point
On Wed, 16 Mar 2016, Martin Reuter wrote:

>
> Although it should be mentioned that outputs (even of subfields) are
> going to change due to differences in the regular freesurfer processing,
> as the subfields stream builds upon the regular FS stream.
>
> Best, Martin
>
>
> On 03/16/2016 10:52 AM, Eugenio Iglesias wrote:
>> I only changed some details (e.g., temporary directories) that do not affect 
>> the output.
>>
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
>> Sent: Wednesday, March 16, 2016 3:49:31 PM
>> Subject: Re: [Freesurfer] FreeSurfer 6.0
>>
>> yes, although the hippocampal stuff hasn't changed I don't think
>> (Eugenio: is that correct)?
>>
>> On Wed, 16 Mar 2016, Alan Francis wrote:
>>
>>> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
>>> ran the HSF method successfully. Have they retracted that version?
>>>
>>> best,
>>>
>>> Alan
>>>
>>> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>actually there is no beta yet, but hopefully within a week or so
>>>On Wed, 16 Mar 2016, Alan Francis wrote:
>>>
>>>  Hi Elizabeth:
>>>
>>>  I ran the Hippocampal subfields on 6.0 beta. The
>>>  parcellation looks great.
>>>  Beta is available for download. Here is the URL:
>>>
>>>  https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>>
>>>  best,
>>>
>>>  Alan
>>>
>>>  On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>>  <elisabeth.p...@student.uva.nl> wrote:
>>>Dear ladies and gentlemen,
>>>
>>>  for a research project I need to measure the volume
>>>  of the different
>>>  hippocampus subregions. I want to use FreeSurfer 6.0
>>>  for that but I
>>>  can only find FreeSurfer 5.3 online. Is FreeSurfer
>>>  6.0 not yet
>>>  released and if so, when will it be released? If it
>>>  is already
>>>  released, could you tell me where to find it?
>>>
>>>  Thank you very much in advance.
>>>
>>>  Kind regards,
>>>
>>>  Elisabeth Paul
>>>
>>>  ___
>>>  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.
>>>
>>>
>>>
>>>
>>>  --
>>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>>
>>>  Alan N. Francis PhD
>>>  NIDA T32  Fellow in Computational Neuroscience
>>>  Brain Imaging Center
>>>  McLean Hospital
>>>  Harvard Medical School
>>>  115 Mill Street, Belmont, MA 02478
>>>  al...@bwh.harvard.edu
>>>  afran...@mclean.harvard.edu
>>>
>>>
>>>
>>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>

Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

actually there is no beta yet, but hopefully within a week or so
On Wed, 16 
Mar 2016, Alan Francis wrote:



Hi Elizabeth:

I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best,

Alan

On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
 wrote:
  Dear ladies and gentlemen,

for a research project I need to measure the volume of the different
hippocampus subregions. I want to use FreeSurfer 6.0 for that but I
can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet
released and if so, when will it be released? If it is already
released, could you tell me where to find it?

Thank you very much in advance.

Kind regards,

Elisabeth Paul

___
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.




--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                            
                             
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

___
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 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] FreeSurfer 6.0

[Alan Francis]

Thanks for that.

On Wed, Mar 16, 2016 at 11:37 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> that's a good point
> On Wed, 16 Mar 2016, Martin Reuter wrote:
>
> >
> > Although it should be mentioned that outputs (even of subfields) are
> > going to change due to differences in the regular freesurfer processing,
> > as the subfields stream builds upon the regular FS stream.
> >
> > Best, Martin
> >
> >
> > On 03/16/2016 10:52 AM, Eugenio Iglesias wrote:
> >> I only changed some details (e.g., temporary directories) that do not
> affect the output.
> >>
> >>
> >> Juan Eugenio Iglesias
> >> Postdoctoral researcher BCBL
> >> www.jeiglesias.com
> >> www.bcbl.eu
> >>
> >> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> >>
> >> - Original Message -
> >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> >> Sent: Wednesday, March 16, 2016 3:49:31 PM
> >> Subject: Re: [Freesurfer] FreeSurfer 6.0
> >>
> >> yes, although the hippocampal stuff hasn't changed I don't think
> >> (Eugenio: is that correct)?
> >>
> >> On Wed, 16 Mar 2016, Alan Francis wrote:
> >>
> >>> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago
> and
> >>> ran the HSF method successfully. Have they retracted that version?
> >>>
> >>> best,
> >>>
> >>> Alan
> >>>
> >>> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> >>> wrote:
> >>>actually there is no beta yet, but hopefully within a week or so
> >>>On Wed, 16 Mar 2016, Alan Francis wrote:
> >>>
> >>>  Hi Elizabeth:
> >>>
> >>>  I ran the Hippocampal subfields on 6.0 beta. The
> >>>  parcellation looks great.
> >>>  Beta is available for download. Here is the URL:
> >>>
> >>>  https://surfer.nmr.mgh.harvard.edu/fswiki/Download
> >>>
> >>>  best,
> >>>
> >>>  Alan
> >>>
> >>>  On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
> >>>  <elisabeth.p...@student.uva.nl> wrote:
> >>>Dear ladies and gentlemen,
> >>>
> >>>  for a research project I need to measure the volume
> >>>  of the different
> >>>  hippocampus subregions. I want to use FreeSurfer 6.0
> >>>  for that but I
> >>>  can only find FreeSurfer 5.3 online. Is FreeSurfer
> >>>  6.0 not yet
> >>>  released and if so, when will it be released? If it
> >>>  is already
> >>>  released, could you tell me where to find it?
> >>>
> >>>  Thank you very much in advance.
> >>>
> >>>  Kind regards,
> >>>
> >>>  Elisabeth Paul
> >>>
> >>>  ___
> >>>  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] FreeSurfer 6.0

[Elisabeth Paul]

Dear ladies and gentlemen,

for a research project I need to measure the volume of the different
hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can
only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if
so, when will it be released? If it is already released, could you tell me
where to find it?

Thank you very much in advance.

Kind regards,

Elisabeth Paul
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[Freesurfer] FreeSurfer 6.0 hippocampal subfields error

[Rosanna Olsen]

Dear Eugenio,

I am writing because I am getting a mkdir error when I try to run the
FreeSurfer 6.0 hippocampal subfields segmentation.  I tried moving my
installation of freesurfer to a local directory where I have write
permission and I also made sure I had write permission in my subject's
directory. Do you have any idea what might be causing the error?   Thanks
in advance!

Command and error pasted below:
recon-all -s 1001 -sd . -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015
INFO: SUBJECTS_DIR is
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0
Actual FREESURFER_HOME /opt/freesurfer6
-rw-rw-r-- 1 rolsen buchsbaum_lab 549732 Feb  3 09:35
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/recon-all.log
Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25
21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
#
#@# Hippocampal Subfields processing (T1 only) left Wed Feb  3 09:35:59 EST
2016

 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80
/opt/freesurfer6 1001
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 left

See log file:
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported
Warning: application is running on a locale different from the original
platform locale.
Error using mkdir
Permission denied

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)



MATLAB:MKDIR:OSError
#
#@# Hippocampal Subfields processing (T1 only) right Wed Feb  3 09:36:07
EST 2016

 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80
/opt/freesurfer6 1001
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 right

See log file:
/scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported
Warning: application is running on a locale different from the original
platform locale.
Error using mkdir
Permission denied

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)



MATLAB:MKDIR:OSError

#--

Started at Wed Feb 3 09:35:56 EST 2016
Ended   at Wed Feb 3 09:36:14 EST 2016
#@#%# recon-all-run-time-hours 0.005
recon-all -s 1001 finished without error at Wed Feb  3 09:36:15 EST 2016
done


-- 
Rosanna Olsen, Ph.D.
Scientist, Rotman Research Institute, Baycrest
rol...@research.baycrest.org
http://research.baycrest.org/rolsen
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Re: [Freesurfer] Freesurfer 6.0 -hires mri_segment potential issue

[Bruce Fischl]

Hi Ajay

it's kind of dicey to use an arbitrary nightly build as we have no idea 
what was in that that might have been fixed the next day. I would wait 
for a beta, or at the very least try a new version as I don't think our 
current version exhibits the behavior you are experiencing.


cheers
Bruce
On Tue, 29 Dec 
2015, Ajay Kurani wrote:



Hello Freesurfer experts,

   I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu
14.04 with a high resolution image (0.5mm isotropic).  I set
OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags
in my autorecon 2 line command.  Autorecon1 and the beginning parts of
Autorecon2 ran in a reasonable amount of time. 

Currently the program is running the mri_segment -keep -mprage brain.mgz
wm.seg.mgz line command however it has been at this step for approximately 5
days!  I used top line command to verify that the program is still running
and it seems to be still running.  I wasn't sure if this time for this step
is typical for a high-res image (as this is my first time processing data
higher than 1mm iso), or if there is a potential bug.

I ran this same subject on another computer using the same version of
Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been
running for over a day so far.  Any feedback would be appreciated as to if
this amount of processing time is typical for this type of resolution, or if
it could be a potential bug and that I should wait for a new beta release?

Thanks,
Ajay

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[Freesurfer] Freesurfer 6.0 -hires mri_segment potential issue

[Ajay Kurani]

Hello Freesurfer experts,

   I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu
14.04 with a high resolution image (0.5mm isotropic).  I set
OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags
in my autorecon 2 line command.  Autorecon1 and the beginning parts of
Autorecon2 ran in a reasonable amount of time.

Currently the program is running the mri_segment -keep -mprage brain.mgz
wm.seg.mgz line command however it has been at this step for approximately
5 days!  I used top line command to verify that the program is still
running and it seems to be still running.  I wasn't sure if this time for
this step is typical for a high-res image (as this is my first time
processing data higher than 1mm iso), or if there is a potential bug.

I ran this same subject on another computer using the same version of
Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been
running for over a day so far.  Any feedback would be appreciated as to if
this amount of processing time is typical for this type of resolution, or
if it could be a potential bug and that I should wait for a new beta
release?

Thanks,
Ajay
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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Ajay

I have found the problem that messed up the surfaces and fixed it. We can 
get you an updated mris_fix_topology that will not generate corrupted 
surfaces. However, the underlying problem is huge topological defects 
caused by low gray/white contrast in this data. For example in the left 
hemi, there is on in the insula (e.g. voxels around 362, 213, 200 and 364, 
229, 207 and in the temporal lobe (351, 286, 282, 283, 309, 258).



Basically the gray/white contrast isn't high enough for us to accurately 
segment the wm with our default procedures. Control points may help a bit, 
but you may also need to manually edit the wm.mgz to remove the largest 
defects. The easiest way to do this is to visualize them on the 
lh.inflated.nofix surface with the lh.defect_labels overlaid to show you 
where the defects are, then go into the volume in the wm.mgz and either add 
control points or erase wm to fix things.


Let us know if you want a new mris_fix_topology. I'm not sure it is worth 
the trouble since while it will now generate topologically correct surfaces 
for this dataset, they will not be geometrically acccurate in the vicinity 
of the huge (>200,000 vertices!) defects.


cheers
Bruce


On Wed, 2 Dec 2015, Ajay Kurani wrote:


Hi Bruce,

  The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which I 
downloaded from the
McGills site (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  
The template has a
range of values from 0-100.  Then I combined the csf/wm/gm masks (derived from 
the 2009c template
which is 1mm isotropic) and resampled to 0.5 mm to mask the brain.  
Subsequently I rescaled the
data to have a range of 0-255 and used this output as my input T1 for 
Freesurfer.  Thank you very
much for looking into this matter, it is much appreciated!  I will look at the 
file as you
suggested.

Sincerely,
Ajay

On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
  Hi Ajay

  can you explain your entire processing stream, including the details of 
the
  acquisition? What sequence/coil/scanner was used? You could fix your 
problem by looking
  at the defects on the inflated.nofix, overlaying
  lh.defect_labels on it to see where they are, then figuring out what 
caused them in the
  volume. However, there is a bug in mris_fix_topology that only comes up 
when it
  encounters a large enough defect (with nvertices>200,000). The code tries 
to avoid
  running it's normal genetic algorithm as it would take days (or weeks) to 
finish, since
  it scales with the square of the number of vertices. I haven't figured 
out what is
  going wrong yet, but hopefully will have a code fix soon.

  cheers
  Bruce


  On Tue, 1 Dec 2015, Ajay Kurani wrote:

Hi Bruce,  When looking at my top slices in brain ask I noticed 
that the
gray/white matter shows but the darker areas surrounding it are not 
present
(this usually goes to the edge of the brain).  Could the large 
defects be a
result of having masked this out on the input file?  I multiplied 
the
template with the GM/WM/CSF masks they provided to get the brain 
extracted
so I only see this missing in the very top few slices of the brain.

Thanks,
Ajay

On Tuesday, December 1, 2015, Bruce Fischl 
<fis...@nmr.mgh.harvard.edu>
wrote:
      Hi Falk

      I don't think you need to rerun the qsphere. I'm pretty sure
      this is a bug in mris_fix_topology for giant defects, but
      haven't finished tracking it down yet

      cheers
      Bruce


      On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


            Hi Ajay,

             

            you should

             

            cp ?h.orig.nofix ?h.orig

            cp ?h.inflated.nofix ?h.inflated

             

            with ? being l or r depending your hemisphere.
            After the fixing stage the
            surfaces got damaged somehow, therefore you have to
            recreate it them. I’m
            not entirely sure about the qsphere. Probably you
            have to run the -qsphere
            stage again also.

             

            Best,

            Falk

             

             

            Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
            Gesendet: Montag, 30. November 2015 21:50
            An: Falk Lüsebrink
            Cc: Freesurfer support list; Bruce Fischl
            Betreff: Re: [Freesurfer] Freesurfer 6.0 -
            

[Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

   On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
>>
>>
>> Hi Ajay,
>>
>>
>>
>> you should
>>
>>
>>
>> cp ?h.orig.nofix ?h.orig
>>
>> cp ?h.inflated.nofix ?h.inflated
>>
>>
>>
>> with ? being l or r depending your hemisphere.
>> After the fixing stage the
>>         surfaces got damaged somehow, therefore you have
>> to
>> recreate it them. I’m
>> not entirely sure about the qsphere. Probably you
>> have to run the -qsphere
>> stage again also.
>>
>>
>>
>> Best,
>>
>> Falk
>>
>>
>>
>>
>>
>> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com
>> ]
>> Gesendet: Montag, 30. November 2015 21:50
>> An: Falk Lüsebrink
>> Cc: Freesurfer support list; Bruce Fischl
>> Betreff: Re: [Freesurfer] Freesurfer 6.0 -
>> Autorecon2 failure
>> (mris_euler_number) using high res (0.5mm
>> isotropic) T1 image
>>
>>
>>
>> Hi Falk,
>>
>>I used the command and got the following error:
>>
>> Command: ris_topo_fixer -mgz -warning -seed 1234
>> ICBM lh
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading
>>
>> inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
>> lin_sym
>> _09b/ICBM/surf/lh.orig...
>>
>> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
>> i_icbm152_nlin_sym
>> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
>> but face 46196 not in
>> vertex 24215 face list
>>
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading
>>
>> inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
>> lin_sym
>> _09b/ICBM/surf/rh.orig...
>>
>> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
>> i_icbm152_nlin_sym
>> _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903,
>> but face 35822 not in
>> vertex 18903 face list
>>
>> Any suggestions would be appreciated.
>>
>> Thanks,
>>
>> Ajay
>>
>>
>>
>>     On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
>> <falk.luesebr...@ovgu.de>
>> wrote:
>>
>> Hi Ajay,
>>
>> I ran into the same error processing hires data a
>> while ago using a nightly
>> build of centos 6 with the hires flag only. Disk
>> space or alike wasn't an
>> issue. I ran mris_topo_fixer instead of
>> mris_fix_topology to get working
>> surfaces.
>>
>> Best,
>> Falk
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
>> Im
>> Auftrag von Bruce Fischl
>> Gesendet: Sonntag, 29. November 2015 22:48
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer]

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

pretty
sure
                  this is a bug in mris_fix_topology for giant 
defects, but
                  haven't finished tracking it down yet

                  cheers
                  Bruce


                  On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


                        Hi Ajay,

                         

                        you should

                         

                        cp ?h.orig.nofix ?h.orig

                        cp ?h.inflated.nofix ?h.inflated

                         

                        with ? being l or r depending your 
hemisphere.
                        After the fixing stage the
                        surfaces got damaged somehow, therefore you 
have to
                        recreate it them. I’m
                        not entirely sure about the qsphere. 
Probably you
                        have to run the -qsphere
                        stage again also.

                         

                        Best,

                        Falk

                         

                         

                        Von: Ajay Kurani 
[mailto:dr.ajay.kur...@gmail.com]
                        Gesendet: Montag, 30. November 2015 21:50
                        An: Falk Lüsebrink
                        Cc: Freesurfer support list; Bruce Fischl
                        Betreff: Re: [Freesurfer] Freesurfer 6.0 -
                        Autorecon2 failure
                        (mris_euler_number) using high res (0.5mm
                        isotropic) T1 image

                         

                        Hi Falk,

                           I used the command and got the following 
error:

                        Command: ris_topo_fixer -mgz -warning -seed 
1234
                        ICBM lh
                        mris_topo_fixer -mgz -warning -seed 1234 
ICBM lh
                        INFO: assuming .mgz format
                        setting seed for random number genererator 
to 1234
                        reading
           

inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                        lin_sym
                        _09b/ICBM/surf/lh.orig...
           

mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                        i_icbm152_nlin_sym
                        _09b/ICBM/surf/lh.orig: face[46196].v[0] = 
24215,
                        but face 46196 not in
                        vertex 24215 face list

                        mris_topo_fixer -mgz -warning -seed 1234 
ICBM rh
                        INFO: assuming .mgz format
                        setting seed for random number genererator 
to 1234
                        reading
           

inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
                        lin_sym
                        _09b/ICBM/surf/rh.orig...
           

mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
                        i_icbm152_nlin_sym
                        _09b/ICBM/surf/rh.orig: face[35822].v[2] = 
18903,
                        but face 35822 not in
                        vertex 18903 face list

                        Any suggestions would be appreciated.

                        Thanks,

                        Ajay

                         

                        On Mon, Nov 30, 2015 at 2:41 AM, Falk 
Lüsebrink
                        <falk.luesebr...@ovgu.de>
                        wrote:

                        Hi Ajay,

                        I ran into the same error processing hires 
data a
                        while ago using a nightly
                        build of centos 6 with the hires flag only. 
Disk
                        space or alike wasn't an
                        issue. I ran mris_topo_fixer instead of
                        mris_fix_topology to get working
                        surfaces.

                        Best,
  

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hi Bruce,

  The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which
I downloaded from the McGills site (
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  The
template has a range of values from 0-100.  Then I combined the csf/wm/gm
masks (derived from the 2009c template which is 1mm isotropic) and
resampled to 0.5 mm to mask the brain.  Subsequently I rescaled the data to
have a range of 0-255 and used this output as my input T1 for Freesurfer.
Thank you very much for looking into this matter, it is much appreciated!
I will look at the file as you suggested.

Sincerely,
Ajay

On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Ajay
>
> can you explain your entire processing stream, including the details of
> the acquisition? What sequence/coil/scanner was used? You could fix your
> problem by looking at the defects on the inflated.nofix, overlaying
> lh.defect_labels on it to see where they are, then figuring out what
> caused them in the volume. However, there is a bug in mris_fix_topology
> that only comes up when it encounters a large enough defect (with
> nvertices>200,000). The code tries to avoid running it's normal genetic
> algorithm as it would take days (or weeks) to finish, since it scales with
> the square of the number of vertices. I haven't figured out what is going
> wrong yet, but hopefully will have a code fix soon.
>
> cheers
> Bruce
>
>
>
> On Tue, 1 Dec 2015, Ajay Kurani wrote:
>
> Hi Bruce,  When looking at my top slices in brain ask I noticed that the
>> gray/white matter shows but the darker areas surrounding it are not
>> present
>> (this usually goes to the edge of the brain).  Could the large defects be
>> a
>> result of having masked this out on the input file?  I multiplied the
>> template with the GM/WM/CSF masks they provided to get the brain extracted
>> so I only see this missing in the very top few slices of the brain.
>>
>> Thanks,
>> Ajay
>>
>> On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Falk
>>
>>   I don't think you need to rerun the qsphere. I'm pretty sure
>>   this is a bug in mris_fix_topology for giant defects, but
>>   haven't finished tracking it down yet
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
>>
>>
>> Hi Ajay,
>>
>>
>>
>> you should
>>
>>
>>
>> cp ?h.orig.nofix ?h.orig
>>
>> cp ?h.inflated.nofix ?h.inflated
>>
>>
>>
>> with ? being l or r depending your hemisphere.
>> After the fixing stage the
>> surfaces got damaged somehow, therefore you have to
>> recreate it them. I’m
>> not entirely sure about the qsphere. Probably you
>> have to run the -qsphere
>>     stage again also.
>>
>>
>>
>> Best,
>>
>> Falk
>>
>>
>>
>>
>>
>> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
>> Gesendet: Montag, 30. November 2015 21:50
>> An: Falk Lüsebrink
>> Cc: Freesurfer support list; Bruce Fischl
>> Betreff: Re: [Freesurfer] Freesurfer 6.0 -
>> Autorecon2 failure
>> (mris_euler_number) using high res (0.5mm
>> isotropic) T1 image
>>
>>
>>
>> Hi Falk,
>>
>>I used the command and got the following error:
>>
>> Command: ris_topo_fixer -mgz -warning -seed 1234
>> ICBM lh
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading
>> inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
>> lin_sym
>> _09b/ICBM/surf/lh.orig...
>> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
>> i_icbm152_nlin_sym
>> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
>> but face 46196 not in
>> vertex 24215 face list
>>
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading
>> inputsurface/home/imuser/

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Falk Lüsebrink]

Hi Ajay,

you should

cp ?h.orig.nofix ?h.orig
cp ?h.inflated.nofix ?h.inflated

with ? being l or r depending your hemisphere. After the fixing stage the 
surfaces got damaged somehow, therefore you have to recreate it them. I’m not 
entirely sure about the qsphere. Probably you have to run the -qsphere stage 
again also.

Best,
Falk


Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure 
(mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Falk,
   I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface 
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig...
mrisFindNeighbors: 
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig:
 face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface 
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig...
mrisFindNeighbors: 
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig:
 face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list
Any suggestions would be appreciated.
Thanks,
Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink 
<falk.luesebr...@ovgu.de<mailto:falk.luesebr...@ovgu.de>> wrote:
Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly 
build of centos 6 with the hires flag only. Disk space or alike wasn't an 
issue. I ran mris_topo_fixer instead of mris_fix_topology to get working 
surfaces.

Best,
Falk

-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure 
(mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on 
the surfaces that should never occur

cheers
Bruce
On Sun, 29 Nov 2015, Ajay
Kurani wrote:

> Hello Freesurfer experts,
>I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
> version) with the -hires flag to process an MNI template image which
> is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
> during
> pocessing:
>
> Command run:
> recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
>
> I supplied a skull stripped brain which was nu corrected and so I used
> the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
> stage.  I then ran autorecon2 and it was working well until I was at
> the -fix stage and ran into the following error:
>
>
> Error:
> mris_euler_number ./surf/lh.orig
> mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face
> 46196 not in vertex 24215 face list
>
>
>
> I am not sure if this is due to the fact that we have a very high
> resolution image (template) and if there are any modifications needed
> aside from the hires flag.  Are there any suggestions you have?
>
> Thanks,
> Ajay
>
>

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

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Falk

I don't think you need to rerun the qsphere. I'm pretty sure this is a bug 
in mris_fix_topology for giant defects, but haven't finished tracking it 
down yet


cheers
Bruce


On Tue, 1 Dec 2015, Falk Lüsebrink wrote:



Hi Ajay,

 

you should

 

cp ?h.orig.nofix ?h.orig

cp ?h.inflated.nofix ?h.inflated

 

with ? being l or r depending your hemisphere. After the fixing stage the
surfaces got damaged somehow, therefore you have to recreate it them. I’m
not entirely sure about the qsphere. Probably you have to run the -qsphere
stage again also.

 

Best,

Falk

 

 

Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm isotropic) T1 image

 

Hi Falk,

   I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input 
surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
_09b/ICBM/surf/lh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in
vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input 
surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
_09b/ICBM/surf/rh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in
vertex 18903 face list

Any suggestions would be appreciated.

Thanks,

Ajay

 

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
wrote:

Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly
build of centos 6 with the hires flag only. Disk space or alike wasn't an
issue. I ran mris_topo_fixer instead of mris_fix_topology to get working
surfaces.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
(mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check
on the surfaces that should never occur

cheers
Bruce

On Sun, 29 Nov 2015, Ajay
Kurani wrote:

> Hello Freesurfer experts,
>    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
> version) with the -hires flag to process an MNI template image which
> is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
> during
> pocessing:
>
> Command run:
> recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
>
> I supplied a skull stripped brain which was nu corrected and so I used
> the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
> stage.  I then ran autorecon2 and it was working well until I was at
> the -fix stage and ran into the following error:
>
>
> Error:
> mris_euler_number ./surf/lh.orig
> mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face
> 46196 not in vertex 24215 face list
>
>
>
> I am not sure if this is due to the fact that we have a very high
> resolution image (template) and if there are any modifications needed
> aside from the hires flag.  Are there any suggestions you have?
>
> Thanks,
> Ajay
>
>

 


___
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.

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hi Bruce,
  When looking at my top slices in brain ask I noticed that the gray/white
matter shows but the darker areas surrounding it are not present (this
usually goes to the edge of the brain).  Could the large defects be a
result of having masked this out on the input file?  I multiplied the
template with the GM/WM/CSF masks they provided to get the brain extracted
so I only see this missing in the very top few slices of the brain.

Thanks,
Ajay

On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Falk
>
> I don't think you need to rerun the qsphere. I'm pretty sure this is a bug
> in mris_fix_topology for giant defects, but haven't finished tracking it
> down yet
>
> cheers
> Bruce
>
>
> On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
>
>
>> Hi Ajay,
>>
>>
>>
>> you should
>>
>>
>>
>> cp ?h.orig.nofix ?h.orig
>>
>> cp ?h.inflated.nofix ?h.inflated
>>
>>
>>
>> with ? being l or r depending your hemisphere. After the fixing stage the
>> surfaces got damaged somehow, therefore you have to recreate it them. I’m
>> not entirely sure about the qsphere. Probably you have to run the -qsphere
>> stage again also.
>>
>>
>>
>> Best,
>>
>> Falk
>>
>>
>>
>>
>>
>> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
>> Gesendet: Montag, 30. November 2015 21:50
>> An: Falk Lüsebrink
>> Cc: Freesurfer support list; Bruce Fischl
>> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
>> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>>
>>
>>
>> Hi Falk,
>>
>>I used the command and got the following error:
>>
>> Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading input
>> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
>> _09b/ICBM/surf/lh.orig...
>>
>> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
>> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in
>> vertex 24215 face list
>>
>> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
>> INFO: assuming .mgz format
>> setting seed for random number genererator to 1234
>> reading input
>> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
>> _09b/ICBM/surf/rh.orig...
>>
>> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym
>> _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in
>> vertex 18903 face list
>>
>> Any suggestions would be appreciated.
>>
>> Thanks,
>>
>> Ajay
>>
>>
>>
>> On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
>> wrote:
>>
>> Hi Ajay,
>>
>> I ran into the same error processing hires data a while ago using a
>> nightly
>> build of centos 6 with the hires flag only. Disk space or alike wasn't an
>> issue. I ran mris_topo_fixer instead of mris_fix_topology to get working
>> surfaces.
>>
>> Best,
>> Falk
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
>> Fischl
>> Gesendet: Sonntag, 29. November 2015 22:48
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
>> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>>
>> Hi Ajay
>>
>> are you sure you didn't run out of disk space? That error is a sanity
>> check
>> on the surfaces that should never occur
>>
>> cheers
>> Bruce
>>
>> On Sun, 29 Nov 2015, Ajay
>> Kurani wrote:
>>
>> > Hello Freesurfer experts,
>> >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
>> > version) with the -hires flag to process an MNI template image which
>> > is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
>> > during
>> > pocessing:
>> >
>> > Command run:
>> > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
>> >
>> > I supplied a skull stripped brain which was nu corrected and so I used
>> > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
>> > stage.  I then ran autore

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Ajay

can you explain your entire processing stream, including the details of 
the acquisition? What sequence/coil/scanner was used? You could fix your 
problem by looking at the defects on the inflated.nofix, overlaying
lh.defect_labels on it to see where they are, then figuring out what caused 
them in the volume. However, there is a bug in mris_fix_topology that only 
comes up when it encounters a large enough defect (with nvertices>200,000). 
The code tries to avoid running it's normal genetic algorithm as it would 
take days (or weeks) to finish, since it scales with the square of the 
number of vertices. I haven't figured out what is going wrong yet, but 
hopefully will have a code fix soon.


cheers
Bruce


On Tue, 1 
Dec 2015, Ajay Kurani wrote:



Hi Bruce,  When looking at my top slices in brain ask I noticed that the
gray/white matter shows but the darker areas surrounding it are not present
(this usually goes to the edge of the brain).  Could the large defects be a
result of having masked this out on the input file?  I multiplied the
template with the GM/WM/CSF masks they provided to get the brain extracted
so I only see this missing in the very top few slices of the brain.

Thanks,
Ajay

On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
  Hi Falk

  I don't think you need to rerun the qsphere. I'm pretty sure
  this is a bug in mris_fix_topology for giant defects, but
  haven't finished tracking it down yet

  cheers
  Bruce


  On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


Hi Ajay,

 

you should

 

cp ?h.orig.nofix ?h.orig

cp ?h.inflated.nofix ?h.inflated

 

with ? being l or r depending your hemisphere.
After the fixing stage the
surfaces got damaged somehow, therefore you have to
recreate it them. I’m
not entirely sure about the qsphere. Probably you
have to run the -qsphere
stage again also.

 

Best,

Falk

 

 

Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
Gesendet: Montag, 30. November 2015 21:50
An: Falk Lüsebrink
Cc: Freesurfer support list; Bruce Fischl
Betreff: Re: [Freesurfer] Freesurfer 6.0 -
Autorecon2 failure
(mris_euler_number) using high res (0.5mm
isotropic) T1 image

 

Hi Falk,

   I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234
ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading 
inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
lin_sym
_09b/ICBM/surf/lh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
i_icbm152_nlin_sym
_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215,
but face 46196 not in
vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading 
inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n
lin_sym
_09b/ICBM/surf/rh.orig...
mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn
i_icbm152_nlin_sym
_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903,
but face 35822 not in
vertex 18903 face list

Any suggestions would be appreciated.

Thanks,

Ajay

 

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink
<falk.luesebr...@ovgu.de>
wrote:

Hi Ajay,

I ran into the same error processing hires data a
while ago using a nightly
build of centos 6 with the hires flag only. Disk
space or alike wasn't an
issue. I ran mris_topo_fixer instead of
mris_fix_topology to get working
surfaces.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im
Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
    Betreff: Re: [Freesurfer] Freesurfer 6.0 -
Autorecon2 failure
(mris_euler_number) using high res (0.5mm
isotropic) T1 image

Hi Ajay

are you sure you didn't run ou

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Falk Lüsebrink]

Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly 
build of centos 6 with the hires flag only. Disk space or alike wasn't an 
issue. I ran mris_topo_fixer instead of mris_fix_topology to get working 
surfaces.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure 
(mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on 
the surfaces that should never occur

cheers
Bruce
On Sun, 29 Nov 2015, Ajay
Kurani wrote:

> Hello Freesurfer experts,
>    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 
> version) with the -hires flag to process an MNI template image which 
> is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error 
> during
> pocessing:
> 
> Command run:
> recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
> 
> I supplied a skull stripped brain which was nu corrected and so I used 
> the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 
> stage.  I then ran autorecon2 and it was working well until I was at 
> the -fix stage and ran into the following error:
> 
> 
> Error:
> mris_euler_number ./surf/lh.orig
> mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 
> 46196 not in vertex 24215 face list
> 
> 
> 
> I am not sure if this is due to the fact that we have a very high 
> resolution image (template) and if there are any modifications needed 
> aside from the hires flag.  Are there any suggestions you have?
> 
> Thanks,
> Ajay
> 
>

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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hi Falk,
   Thank you very much for the suggestion! I will give it a try.

Also Bruce I sent a separate email with a link to the original image for
you to download.  I can also move all of my processed files for that
template there if you would like so you do not have to restart from
scratch?

Thanks,
Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
wrote:

> Hi Ajay,
>
> I ran into the same error processing hires data a while ago using a
> nightly build of centos 6 with the hires flag only. Disk space or alike
> wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get
> working surfaces.
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
> Gesendet: Sonntag, 29. November 2015 22:48
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>
> Hi Ajay
>
> are you sure you didn't run out of disk space? That error is a sanity
> check on the surfaces that should never occur
>
> cheers
> Bruce
> On Sun, 29 Nov 2015, Ajay
> Kurani wrote:
>
> > Hello Freesurfer experts,
> >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
> > version) with the -hires flag to process an MNI template image which
> > is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
> > during
> > pocessing:
> >
> > Command run:
> > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
> >
> > I supplied a skull stripped brain which was nu corrected and so I used
> > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
> > stage.  I then ran autorecon2 and it was working well until I was at
> > the -fix stage and ran into the following error:
> >
> >
> > Error:
> > mris_euler_number ./surf/lh.orig
> > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face
> > 46196 not in vertex 24215 face list
> >
> >
> >
> > I am not sure if this is due to the fact that we have a very high
> > resolution image (template) and if there are any modifications needed
> > aside from the hires flag.  Are there any suggestions you have?
> >
> > Thanks,
> > Ajay
> >
> >
>
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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Ajay

if you can use our ftp or file drop, both linked at:

https://surfer.nmr.mgh.harvard.edu/fswiki

then I'll take a look. And yes, uploading the entire subject dir will make 
it easier.


cheers
Bruce


On Mon, 30 Nov 
2015, 
Ajay Kurani wrote:



Hi Falk,
   Thank you very much for the suggestion! I will give it a try.

Also Bruce I sent a separate email with a link to the original image for you
to download.  I can also move all of my processed files for that template
there if you would like so you do not have to restart from scratch? 

Thanks,
Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
wrote:
  Hi Ajay,

  I ran into the same error processing hires data a while ago
  using a nightly build of centos 6 with the hires flag only. Disk
  space or alike wasn't an issue. I ran mris_topo_fixer instead of
  mris_fix_topology to get working surfaces.

  Best,
  Falk

  -Ursprüngliche Nachricht-
  Von: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
  Bruce Fischl
  Gesendet: Sonntag, 29. November 2015 22:48
  An: Freesurfer support list
  Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
  (mris_euler_number) using high res (0.5mm isotropic) T1 image

  Hi Ajay

  are you sure you didn't run out of disk space? That error is a
  sanity check on the surfaces that should never occur

  cheers
  Bruce
  On Sun, 29 Nov 2015, Ajay
  Kurani wrote:

  > Hello Freesurfer experts,
  >    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
  > version) with the -hires flag to process an MNI template image
  which
  > is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is
  an error
  > during
  > pocessing:
  >
  > Command run:
  > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert
  expert.opts
  >
  > I supplied a skull stripped brain which was nu corrected and
  so I used
  > the T1.mgz and copied it to brainmask.mgz and nu.mgz in
  autorecon1
  > stage.  I then ran autorecon2 and it was working well until I
  was at
  > the -fix stage and ran into the following error:
  >
  >
  > Error:
  > mris_euler_number ./surf/lh.orig
  > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215,
  but face
  > 46196 not in vertex 24215 face list
  >
  >
  >
  > I am not sure if this is due to the fact that we have a very
  high
  > resolution image (template) and if there are any modifications
  needed
  > aside from the hires flag.  Are there any suggestions you
  have?
  >
  > Thanks,
  > Ajay
  >
  >



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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hi Falk,
   I used the command and got the following error:

Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh
mris_topo_fixer -mgz -warning -seed 1234 ICBM lh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig...
mrisFindNeighbors:
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig:
face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list

mris_topo_fixer -mgz -warning -seed 1234 ICBM rh
INFO: assuming .mgz format
setting seed for random number genererator to 1234
reading input surface
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig...
mrisFindNeighbors:
/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig:
face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list

Any suggestions would be appreciated.

Thanks,
Ajay

On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de>
wrote:

> Hi Ajay,
>
> I ran into the same error processing hires data a while ago using a
> nightly build of centos 6 with the hires flag only. Disk space or alike
> wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get
> working surfaces.
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
> Gesendet: Sonntag, 29. November 2015 22:48
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>
> Hi Ajay
>
> are you sure you didn't run out of disk space? That error is a sanity
> check on the surfaces that should never occur
>
> cheers
> Bruce
> On Sun, 29 Nov 2015, Ajay
> Kurani wrote:
>
> > Hello Freesurfer experts,
> >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
> > version) with the -hires flag to process an MNI template image which
> > is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
> > during
> > pocessing:
> >
> > Command run:
> > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts
> >
> > I supplied a skull stripped brain which was nu corrected and so I used
> > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
> > stage.  I then ran autorecon2 and it was working well until I was at
> > the -fix stage and ran into the following error:
> >
> >
> > Error:
> > mris_euler_number ./surf/lh.orig
> > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face
> > 46196 not in vertex 24215 face list
> >
> >
> >
> > I am not sure if this is due to the fact that we have a very high
> > resolution image (template) and if there are any modifications needed
> > aside from the hires flag.  Are there any suggestions you have?
> >
> > Thanks,
> > Ajay
> >
> >
>
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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

hmmm, if either of you wants to upload a subject that is an example of 
this we will track it down and fix it.


cheers
Bruce
On Mon, 30 Nov 2015, Falk Lüsebrink 
wrote:



Hi Ajay,

I ran into the same error processing hires data a while ago using a nightly 
build of centos 6 with the hires flag only. Disk space or alike wasn't an 
issue. I ran mris_topo_fixer instead of mris_fix_topology to get working 
surfaces.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 29. November 2015 22:48
An: Freesurfer support list
Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure 
(mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity check on 
the surfaces that should never occur

cheers
Bruce
On Sun, 29 Nov 2015, Ajay
Kurani wrote:


Hello Freesurfer experts,
   I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15
version) with the -hires flag to process an MNI template image which
is 0.5mm isotropic.  Stage 1 ran well and on stage 2 there is an error
during
pocessing:

Command run:
recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used
the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1
stage.  I then ran autorecon2 and it was working well until I was at
the -fix stage and ran into the following error:


Error:
mris_euler_number ./surf/lh.orig
mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face
46196 not in vertex 24215 face list



I am not sure if this is due to the fact that we have a very high
resolution image (template) and if there are any modifications needed
aside from the hires flag.  Are there any suggestions you have?

Thanks,
Ajay





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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
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[Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hello Freesurfer experts,
   I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version)
with the -hires flag to process an MNI template image which is 0.5mm
isotropic.  Stage 1 ran well and on stage 2 there is an error during
pocessing:

Command run:
recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the
T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage.  I
then ran autorecon2 and it was working well until I was at the -fix stage
and ran into the following error:


Error:
mris_euler_number ./surf/lh.orig
mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196
not in vertex 24215 face list



I am not sure if this is due to the fact that we have a very high
resolution image (template) and if there are any modifications needed aside
from the hires flag.  Are there any suggestions you have?

Thanks,
Ajay
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Ajay

are you sure you didn't run out of disk space? That error is a sanity 
check on the surfaces that should never occur


cheers
Bruce
On Sun, 29 Nov 2015, Ajay 
Kurani wrote:



Hello Freesurfer experts,
   I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version)
with the -hires flag to process an MNI template image which is 0.5mm
isotropic.  Stage 1 ran well and on stage 2 there is an error during
pocessing:

Command run:
recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts

I supplied a skull stripped brain which was nu corrected and so I used the
T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage.  I
then ran autorecon2 and it was working well until I was at the -fix stage
and ran into the following error:


Error:
mris_euler_number ./surf/lh.orig
mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196
not in vertex 24215 face list



I am not sure if this is due to the fact that we have a very high
resolution image (template) and if there are any modifications needed aside
from the hires flag.  Are there any suggestions you have?

Thanks,
Ajay

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Re: [Freesurfer] Freesurfer 6.0

[Bruce Fischl]

Hi Matt
this would be a beta - the new version isn't ready to be distributed yet 
(although we are getting closer)

Bruce
On Tue, 3 Nov 2015, Hoptman, Matthew wrote:



Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it
to download, it just blinks at me.  I also tried to ftp to your ftp site,
and unfortunately, I got the message

421 Proxy is closed (unknown user location). 

 

Could you please tell me how I could get the new version of Freesurfer?

Thanks,

Matt

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Re: [Freesurfer] Freesurfer 6.0

[Z K]

It must be an issue with your browser. Try using either of the following 
commands (depending on your platform) in a terminal window.

Linux:
wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz

Mac OSX:
curl -O 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg

-Zeke

On 11/03/2015 03:44 PM, Hoptman, Matthew wrote:
> Hi all,
> I can see a link for Freesurfer 6.0 on the website, but when I click on
> it to download, it just blinks at me.  I also tried to ftp to your ftp
> site, and unfortunately, I got the message
>
> 421 Proxy is closed (unknown user location).
>
> Could you please tell me how I could get the new version of Freesurfer?
>
> Thanks,
>
> Matt
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
> recipient. It may contain confidential information which is legally
> privileged or otherwise protected by law. If you received this e-mail in
> error or from someone who is not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing
> or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
> RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
> your cooperation.
>
>
> ___
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[Freesurfer] Freesurfer 6.0

[Hoptman, Matthew]

Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it to 
download, it just blinks at me.  I also tried to ftp to your ftp site, and 
unfortunately, I got the message
421 Proxy is closed (unknown user location).

Could you please tell me how I could get the new version of Freesurfer?
Thanks,
Matt
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail. 
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Eugenio Iglesias]

Hi Priyanka,
in the mri directory of each subject, you will find a file named:
[lr]h.hippoSfLabels--.v10.1mm.mgz
which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel 
space of that subject. 
Kind regards,
Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Priyanka Mehta" <priyankamehta0...@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Sunday, September 13, 2015 10:14:34 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Hi again 

I want to use my hippocampal segmentation for masking 2380 brain volumes. Is 
there a way to find out using Freesurfer if the hippocampal subfields and the 
2380 volumes are in the same space? The mean of the 2380 volumes and the 
hippocampal subfields align correctly when I use Freesurfer's freeview to view 
them. But does that also mean they are in the same voxel space? 

And if they aren't in the same space, is there any way using Freesurfer that I 
can have the two in the same space? 

I really appreciate any suggestions! 

Thanks, 
Priyanka Mehta 

On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > 
wrote: 


of course 
On Tue, 25 Aug 2015, Priyanka wrote: 

> Thanks Bruce. Just wanted to make sure I've got the correct output. 
> 
> Really appreciate the help. 
> 
> Thanks again, 
> Priyanka Mehta 
> 
>> On Aug 25, 2015, at 4:44 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > 
>> wrote: 
>> 
>> Hi Priyanka 
>> 
>> that is what mri_extract_label is designed to do. This facilitates making 
>> density maps in a common space. If you want to get the original label # back 
>> you can use something like: 
>> 
>> mri_binarize --match 128 --binval  or something like that 
>> 
>> cheers 
>> Bruce 
>> 
>> 
>>> On Tue, 25 Aug 2015, Priyanka Mehta wrote: 
>>> 
>>> Reposting my question: 
>>> This happens for all the segments that I've tried to extract using 
>>> mri_extract_label. They all show up as 128 nerve after mri_extract_label. 
>>> Is 
>>> this a bug in the dev version? 
>>> Any help is greatly appreciated! 
>>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka < priyankamehta0...@gmail.com > 
>>> wrote: 
>>> This happens for all the segments that I've tried to extract 
>>> using mri_extract_label. They all show up as 128 nerve after 
>>> mri_extract_label. Is this a bug in the dev version? 
>>> 
>>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell 
>>> < ltirr...@nmr.mgh.harvard.edu > wrote: 
>>> > 
>>> > It seems that the command: 
>>> > 
>>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii 
>>> > 
>>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 
>>> in lh.hippoSfLabels-T1.v10.mgz. You can run: 
>>> > 
>>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii 
>>> > 
>>> > and then the correct label names from the Lookup Table will 
>>> show up. 
>>> > 
>>> > Best, 
>>> > Lee 
>>> > 
>>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: 
>>> >> 
>>> >> Hi Eugenio 
>>> >> Thank you for the explanation, it makes sense to me now. 
>>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it 
>>> aligns correctly. However, when I view the segmentation 
>>> >> with color map set to Lookup Table and 'show existing labels 
>>> only' checked, the lh.CA1.nii segment shows as 128 Nerve 
>>> >> label. Shouldn't it still be showing up as 206 CA1 label? I 
>>> am confused. 
>>> >> 
>>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias 
>>> < e.igles...@bcbl.eu > wrote: 
>>> >> Hi Prya, 
>>> >> that is because MriCron is not that great at overlaying 
>>> images that are in the same physical space but not 
>>> >> in the same voxel space. You have two options here: 
>>> >> 1. Use FreeSurfer's Freeview rather than MriCron to 
>>> visualize the output. FreeView will correctly overlay 
>>> >> the segmentation. 
>>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than 
>>> lh.hippoSfLabels-T1.v10.mgz) when you call 
>>> >> mri_extract_label. That volume lives in the same voxel 
>>> space as T1.nii, and should be prope

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Hi again

I want to use my hippocampal segmentation for masking 2380 brain volumes.
Is there a way to find out using Freesurfer if the hippocampal subfields
and the 2380 volumes are in the same space? The mean of the 2380 volumes
and the hippocampal subfields align correctly when I use Freesurfer's
freeview to view them. But does that also mean they are in the same voxel
space?

And if they aren't in the same space, is there any way using Freesurfer
that I can have the two in the same space?

I really appreciate any suggestions!

Thanks,
Priyanka Mehta

On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> of course
> On Tue, 25 Aug 2015, Priyanka wrote:
>
> > Thanks Bruce. Just wanted to make sure I've got the correct output.
> >
> > Really appreciate the help.
> >
> > Thanks again,
> > Priyanka Mehta
> >
> >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
> >>
> >> Hi Priyanka
> >>
> >> that is what mri_extract_label is designed to do. This facilitates
> making density maps in a common space. If you want to get the original
> label # back you can use something like:
> >>
> >> mri_binarize --match 128 --binval  or something like
> that
> >>
> >> cheers
> >> Bruce
> >>
> >>
> >>> On Tue, 25 Aug 2015, Priyanka Mehta wrote:
> >>>
> >>> Reposting my question:
> >>> This happens for all the segments that I've tried to extract using
> >>> mri_extract_label. They all show up as 128 nerve after
> mri_extract_label. Is
> >>> this a bug in the dev version?
> >>> Any help is greatly appreciated!
> >>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka <priyankamehta0...@gmail.com
> >
> >>> wrote:
> >>>  This happens for all the segments that I've tried to extract
> >>>  using mri_extract_label. They all show up as 128 nerve after
> >>>  mri_extract_label. Is this a bug in the dev version?
> >>>
> >>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell
> >>>  <ltirr...@nmr.mgh.harvard.edu> wrote:
> >>> >
> >>> > It seems that the command:
> >>> >
> >>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
> >>> >
> >>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206
> >>>  in lh.hippoSfLabels-T1.v10.mgz. You can run:
> >>> >
> >>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
> >>> >
> >>> > and then the correct label names from the Lookup Table will
> >>>  show up.
> >>> >
> >>> > Best,
> >>> > Lee
> >>> >
> >>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote:
> >>> >>
> >>> >> Hi Eugenio
> >>> >> Thank you for the explanation, it makes sense to me now.
> >>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
> >>>  aligns correctly. However, when I view the segmentation
> >>> >> with color map set to Lookup Table and 'show existing labels
> >>>  only' checked, the lh.CA1.nii segment shows as 128 Nerve
> >>> >> label. Shouldn't it still be showing up as 206 CA1 label? I
> >>>  am confused.
> >>> >>
> >>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
> >>>  <e.igles...@bcbl.eu> wrote:
> >>> >>  Hi Prya,
> >>> >>  that is because MriCron is not that great at overlaying
> >>>  images that are in the same physical space but not
> >>> >>  in the same voxel space. You have two options here:
> >>> >>  1. Use FreeSurfer's Freeview rather than MriCron to
> >>>  visualize the output. FreeView will correctly overlay
> >>> >>  the segmentation.
> >>> >>  2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
> >>>  lh.hippoSfLabels-T1.v10.mgz) when you call
> >>> >>  mri_extract_label. That volume lives in the same voxel
> >>>  space as T1.nii, and should be properly overlayed
> >>> >>  by MriCron. However, the resolution of the segmentation
> >>>  will be 1 mm, rather than the 0.333 mm t

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Bruce Fischl]

Hi Priyanka

that is what mri_extract_label is designed to do. This facilitates making 
density maps in a common space. If you want to get the original label # 
back you can use something like:


mri_binarize --match 128 --binval output label # or something like that

cheers
Bruce


On Tue, 25 Aug 2015, Priyanka Mehta wrote:


Reposting my question:

This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?


Any help is greatly appreciated!

On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:
  This happens for all the segments that I've tried to extract
  using mri_extract_label. They all show up as 128 nerve after
  mri_extract_label. Is this a bug in the dev version?


   On Aug 20, 2015, at 3:20 PM, Lee Tirrell
  ltirr...@nmr.mgh.harvard.edu wrote:
  
   It seems that the command:
  
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
  
   put a value of 128 in lh.CA1.nii for the voxels labeled as 206
  in lh.hippoSfLabels-T1.v10.mgz. You can run:
  
   mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
  
   and then the correct label names from the Lookup Table will
  show up.
  
   Best,
   Lee
  
   On Thu, 20 Aug 2015, Priyanka Mehta wrote:
  
   Hi Eugenio
   Thank you for the explanation, it makes sense to me now.
   When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
  aligns correctly. However, when I view the segmentation
   with color map set to Lookup Table and 'show existing labels
  only' checked, the lh.CA1.nii segment shows as 128 Nerve
   label. Shouldn't it still be showing up as 206 CA1 label? I
  am confused.
  
   On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
  e.igles...@bcbl.eu wrote:
        Hi Prya,
        that is because MriCron is not that great at overlaying
  images that are in the same physical space but not
        in the same voxel space. You have two options here:
        1. Use FreeSurfer's Freeview rather than MriCron to
  visualize the output. FreeView will correctly overlay
        the segmentation.
        2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
  lh.hippoSfLabels-T1.v10.mgz) when you call
        mri_extract_label. That volume lives in the same voxel
  space as T1.nii, and should be properly overlayed
        by MriCron. However, the resolution of the segmentation
  will be 1 mm, rather than the 0.333 mm that you'd
        get in option 1.
        Cheers,
        Eugenio
  
        Juan Eugenio Iglesias
        Postdoctoral researcher BCBL
        www.jeiglesias.com
        www.bcbl.eu
  
        Legal disclaimer/Aviso legal/Lege-oharra:
  www.bcbl.eu/legal-disclaimer
  
        - Original Message -
        From: Priyanka Mehta priyankamehta0...@gmail.com
        To: Freesurfer support list
  freesurfer@nmr.mgh.harvard.edu
        Sent: Wednesday, August 19, 2015 7:50:12 PM
        Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
  Output
  
        Hi
  
        This is a follow-up question to my previous problem.
        After I run recon-all -all -i ${subject}.nii -subject
  ${subject} -hippocampal-subfields-T1, I extracted
        the left CA1 using mri_extract_label
  lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
        I used MRICro to overlay this lh.CA1.nii on my T1.nii,
  however the alignment is not correct (see attached
        picture).
  
        I wonder what is causing this issue? Since the CA1 was
  extracted from the same T1 image, they should
        technically be in the same space and therefore should
  align correctly.
  
        Please advise.
  
        Thank you,
        Priyanka
  
        On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta 
  priyankamehta0...@gmail.com  wrote:
  
        Worked! Thank you so much. Really appreciate the prompt
  response.
  
        Best,
        Priyanka
  
        On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias 
  e.igles...@bcbl.eu  wrote:
  
        Hi again,
        instead of:
        mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.mgz
        your can run:
        mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.nii
        Cheers,
        /E
  
        Juan Eugenio Iglesias
        Postdoctoral researcher BCBL
        www.jeiglesias.com
        www.bcbl.eu
  
        Legal disclaimer/Aviso legal/Lege-oharra:
  www.bcbl.eu/legal-disclaimer
  
        - Original Message -
        From: Priyanka Mehta

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka]

Thanks Bruce. Just wanted to make sure I've got the correct output. 

Really appreciate the help. 

Thanks again,
Priyanka Mehta 

 On Aug 25, 2015, at 4:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Priyanka
 
 that is what mri_extract_label is designed to do. This facilitates making 
 density maps in a common space. If you want to get the original label # back 
 you can use something like:
 
 mri_binarize --match 128 --binval output label # or something like that
 
 cheers
 Bruce
 
 
 On Tue, 25 Aug 2015, Priyanka Mehta wrote:
 
 Reposting my question:
 This happens for all the segments that I've tried to extract using
 mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
 this a bug in the dev version?
 Any help is greatly appreciated!
 On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
 wrote:
  This happens for all the segments that I've tried to extract
  using mri_extract_label. They all show up as 128 nerve after
  mri_extract_label. Is this a bug in the dev version?
 
   On Aug 20, 2015, at 3:20 PM, Lee Tirrell
  ltirr...@nmr.mgh.harvard.edu wrote:
  
   It seems that the command:
  
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
  
   put a value of 128 in lh.CA1.nii for the voxels labeled as 206
  in lh.hippoSfLabels-T1.v10.mgz. You can run:
  
   mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
  
   and then the correct label names from the Lookup Table will
  show up.
  
   Best,
   Lee
  
   On Thu, 20 Aug 2015, Priyanka Mehta wrote:
  
   Hi Eugenio
   Thank you for the explanation, it makes sense to me now.
   When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
  aligns correctly. However, when I view the segmentation
   with color map set to Lookup Table and 'show existing labels
  only' checked, the lh.CA1.nii segment shows as 128 Nerve
   label. Shouldn't it still be showing up as 206 CA1 label? I
  am confused.
  
   On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
  e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying
  images that are in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to
  visualize the output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
  lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel
  space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation
  will be 1 mm, rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
  
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
  
Legal disclaimer/Aviso legal/Lege-oharra:
  www.bcbl.eu/legal-disclaimer
  
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list
  freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
  Output
  
Hi
  
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject
  ${subject} -hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label
  lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii,
  however the alignment is not correct (see attached
picture).
  
I wonder what is causing this issue? Since the CA1 was
  extracted from the same T1 image, they should
technically be in the same space and therefore should
  align correctly.
  
Please advise.
  
Thank you,
Priyanka
  
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta 
  priyankamehta0...@gmail.com  wrote:
  
Worked! Thank you so much. Really appreciate the prompt
  response.
  
Best,
Priyanka
  
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias 
  e.igles...@bcbl.eu  wrote:
  
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.nii
Cheers,
/E
  
Juan Eugenio Iglesias
Postdoctoral researcher BCBL

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Reposting my question:

This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label.
Is this a bug in the dev version?


Any help is greatly appreciated!

On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:

 This happens for all the segments that I've tried to extract using
 mri_extract_label. They all show up as 128 nerve after mri_extract_label.
 Is this a bug in the dev version?


  On Aug 20, 2015, at 3:20 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu
 wrote:
 
  It seems that the command:
 
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
 
  put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
 lh.hippoSfLabels-T1.v10.mgz. You can run:
 
  mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
 
  and then the correct label names from the Lookup Table will show up.
 
  Best,
  Lee
 
  On Thu, 20 Aug 2015, Priyanka Mehta wrote:
 
  Hi Eugenio
  Thank you for the explanation, it makes sense to me now.
  When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
 correctly. However, when I view the segmentation
  with color map set to Lookup Table and 'show existing labels only'
 checked, the lh.CA1.nii segment shows as 128 Nerve
  label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
 
  On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu
 wrote:
   Hi Prya,
   that is because MriCron is not that great at overlaying images
 that are in the same physical space but not
   in the same voxel space. You have two options here:
   1. Use FreeSurfer's Freeview rather than MriCron to visualize the
 output. FreeView will correctly overlay
   the segmentation.
   2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
 lh.hippoSfLabels-T1.v10.mgz) when you call
   mri_extract_label. That volume lives in the same voxel space as
 T1.nii, and should be properly overlayed
   by MriCron. However, the resolution of the segmentation will be 1
 mm, rather than the 0.333 mm that you'd
   get in option 1.
   Cheers,
   Eugenio
 
   Juan Eugenio Iglesias
   Postdoctoral researcher BCBL
   www.jeiglesias.com
   www.bcbl.eu
 
   Legal disclaimer/Aviso legal/Lege-oharra:
 www.bcbl.eu/legal-disclaimer
 
   - Original Message -
   From: Priyanka Mehta priyankamehta0...@gmail.com
   To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
   Sent: Wednesday, August 19, 2015 7:50:12 PM
   Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
 
   Hi
 
   This is a follow-up question to my previous problem.
   After I run recon-all -all -i ${subject}.nii -subject ${subject}
 -hippocampal-subfields-T1, I extracted
   the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz
 206 lh.CA1.nii.
   I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
 alignment is not correct (see attached
   picture).
 
   I wonder what is causing this issue? Since the CA1 was extracted
 from the same T1 image, they should
   technically be in the same space and therefore should align
 correctly.
 
   Please advise.
 
   Thank you,
   Priyanka
 
   On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta 
 priyankamehta0...@gmail.com  wrote:
 
   Worked! Thank you so much. Really appreciate the prompt response.
 
   Best,
   Priyanka
 
   On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias 
 e.igles...@bcbl.eu  wrote:
 
   Hi again,
   instead of:
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
   your can run:
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
   Cheers,
   /E
 
   Juan Eugenio Iglesias
   Postdoctoral researcher BCBL
   www.jeiglesias.com
   www.bcbl.eu
 
   Legal disclaimer/Aviso legal/Lege-oharra:
 www.bcbl.eu/legal-disclaimer
 
   - Original Message -
   From: Priyanka Mehta  priyankamehta0...@gmail.com 
   To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu 
   Sent: Wednesday, July 29, 2015 11:26:04 AM
   Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
 
   Thanks Eugenio! Thats worked!
   One more question- how would I convert the lh.CA1.mgz that I get
 from the previous step to .nii format?
 
   Best,
   Priyanka
 
   On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias 
 e.igles...@bcbl.eu  wrote:
 
   Hi Priyanka,
 
   you can use mri_extract_label for that. For example, if you are
 interested in CA1 (label 206), you can
   run:
 
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
 
   Cheers,
 
   Eugenio
 
   Juan Eugenio Iglesias
   Postdoctoral researcher BCBL
   www.jeiglesias.com
   www.bcbl.eu
 
   Legal disclaimer/Aviso legal/Lege-oharra:
 www.bcbl.eu/legal-disclaimer

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Bruce Fischl]

of course
On Tue, 25 Aug 2015, Priyanka wrote:

 Thanks Bruce. Just wanted to make sure I've got the correct output.

 Really appreciate the help.

 Thanks again,
 Priyanka Mehta

 On Aug 25, 2015, at 4:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Priyanka

 that is what mri_extract_label is designed to do. This facilitates making 
 density maps in a common space. If you want to get the original label # back 
 you can use something like:

 mri_binarize --match 128 --binval output label # or something like that

 cheers
 Bruce


 On Tue, 25 Aug 2015, Priyanka Mehta wrote:

 Reposting my question:
 This happens for all the segments that I've tried to extract using
 mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
 this a bug in the dev version?
 Any help is greatly appreciated!
 On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
 wrote:
  This happens for all the segments that I've tried to extract
  using mri_extract_label. They all show up as 128 nerve after
  mri_extract_label. Is this a bug in the dev version?

  On Aug 20, 2015, at 3:20 PM, Lee Tirrell
  ltirr...@nmr.mgh.harvard.edu wrote:
 
  It seems that the command:
 
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
 
  put a value of 128 in lh.CA1.nii for the voxels labeled as 206
  in lh.hippoSfLabels-T1.v10.mgz. You can run:
 
  mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
 
  and then the correct label names from the Lookup Table will
  show up.
 
  Best,
  Lee
 
  On Thu, 20 Aug 2015, Priyanka Mehta wrote:
 
  Hi Eugenio
  Thank you for the explanation, it makes sense to me now.
  When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
  aligns correctly. However, when I view the segmentation
  with color map set to Lookup Table and 'show existing labels
  only' checked, the lh.CA1.nii segment shows as 128 Nerve
  label. Shouldn't it still be showing up as 206 CA1 label? I
  am confused.
 
  On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
  e.igles...@bcbl.eu wrote:
   Hi Prya,
   that is because MriCron is not that great at overlaying
  images that are in the same physical space but not
   in the same voxel space. You have two options here:
   1. Use FreeSurfer's Freeview rather than MriCron to
  visualize the output. FreeView will correctly overlay
   the segmentation.
   2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
  lh.hippoSfLabels-T1.v10.mgz) when you call
   mri_extract_label. That volume lives in the same voxel
  space as T1.nii, and should be properly overlayed
   by MriCron. However, the resolution of the segmentation
  will be 1 mm, rather than the 0.333 mm that you'd
   get in option 1.
   Cheers,
   Eugenio
 
   Juan Eugenio Iglesias
   Postdoctoral researcher BCBL
   www.jeiglesias.com
   www.bcbl.eu
 
   Legal disclaimer/Aviso legal/Lege-oharra:
  www.bcbl.eu/legal-disclaimer
 
   - Original Message -
   From: Priyanka Mehta priyankamehta0...@gmail.com
   To: Freesurfer support list
  freesurfer@nmr.mgh.harvard.edu
   Sent: Wednesday, August 19, 2015 7:50:12 PM
   Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
  Output
 
   Hi
 
   This is a follow-up question to my previous problem.
   After I run recon-all -all -i ${subject}.nii -subject
  ${subject} -hippocampal-subfields-T1, I extracted
   the left CA1 using mri_extract_label
  lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
   I used MRICro to overlay this lh.CA1.nii on my T1.nii,
  however the alignment is not correct (see attached
   picture).
 
   I wonder what is causing this issue? Since the CA1 was
  extracted from the same T1 image, they should
   technically be in the same space and therefore should
  align correctly.
 
   Please advise.
 
   Thank you,
   Priyanka
 
   On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta 
  priyankamehta0...@gmail.com  wrote:
 
   Worked! Thank you so much. Really appreciate the prompt
  response.
 
   Best,
   Priyanka
 
   On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias 
  e.igles...@bcbl.eu  wrote:
 
   Hi again,
   instead of:
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.mgz
   your can run:
   mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
  lh.CA1.nii
   Cheers,
   /E
 
   Juan Eugenio Iglesias
   Postdoctoral researcher BCBL
   www.jeiglesias.com

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka]

This happens for all the segments that I've tried to extract using 
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is 
this a bug in the dev version? 


 On Aug 20, 2015, at 3:20 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote:
 
 It seems that the command:
 
 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
 
 put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in 
 lh.hippoSfLabels-T1.v10.mgz. You can run:
 
 mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
 
 and then the correct label names from the Lookup Table will show up.
 
 Best,
 Lee
 
 On Thu, 20 Aug 2015, Priyanka Mehta wrote:
 
 Hi Eugenio
 Thank you for the explanation, it makes sense to me now.
 When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly. 
 However, when I view the segmentation
 with color map set to Lookup Table and 'show existing labels only' checked, 
 the lh.CA1.nii segment shows as 128 Nerve
 label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
  
 On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
  Hi Prya,
  that is because MriCron is not that great at overlaying images that are 
 in the same physical space but not
  in the same voxel space. You have two options here:
  1. Use FreeSurfer's Freeview rather than MriCron to visualize the 
 output. FreeView will correctly overlay
  the segmentation.
  2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than 
 lh.hippoSfLabels-T1.v10.mgz) when you call
  mri_extract_label. That volume lives in the same voxel space as T1.nii, 
 and should be properly overlayed
  by MriCron. However, the resolution of the segmentation will be 1 mm, 
 rather than the 0.333 mm that you'd
  get in option 1.
  Cheers,
  Eugenio
 
  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu
 
  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
 
  - Original Message -
  From: Priyanka Mehta priyankamehta0...@gmail.com
  To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
  Sent: Wednesday, August 19, 2015 7:50:12 PM
  Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
 
  Hi
 
  This is a follow-up question to my previous problem.
  After I run recon-all -all -i ${subject}.nii -subject ${subject} 
 -hippocampal-subfields-T1, I extracted
  the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 
 lh.CA1.nii.
  I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the 
 alignment is not correct (see attached
  picture).
 
  I wonder what is causing this issue? Since the CA1 was extracted from 
 the same T1 image, they should
  technically be in the same space and therefore should align correctly.
 
  Please advise.
 
  Thank you,
  Priyanka
 
  On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta  
 priyankamehta0...@gmail.com  wrote:
 
  Worked! Thank you so much. Really appreciate the prompt response.
 
  Best,
  Priyanka
 
  On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias  e.igles...@bcbl.eu 
  wrote:
 
  Hi again,
  instead of:
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
  your can run:
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
  Cheers,
  /E
 
  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu
 
  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
 
  - Original Message -
  From: Priyanka Mehta  priyankamehta0...@gmail.com 
  To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu 
  Sent: Wednesday, July 29, 2015 11:26:04 AM
  Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
 
  Thanks Eugenio! Thats worked!
  One more question- how would I convert the lh.CA1.mgz that I get from 
 the previous step to .nii format?
 
  Best,
  Priyanka
 
  On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu 
  wrote:
 
  Hi Priyanka,
 
  you can use mri_extract_label for that. For example, if you are 
 interested in CA1 (label 206), you can
  run:
 
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
 
  Cheers,
 
  Eugenio
 
  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu
 
  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
 
  - Original Message -
  From: Priyanka  priyankamehta0...@gmail.com 
  To: freesurfer@nmr.mgh.harvard.edu
  Sent: Wednesday, July 29, 2015 7:59:37 AM
  Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
 
  Hi,
 
  I am new to FreeSurfer and need help with hippocampal segmentation in 
 the 6.0 dev version.
  I used the following command: recon

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Lee Tirrell]

It seems that the command:

mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii

put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in 
lh.hippoSfLabels-T1.v10.mgz. You can run:


mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii

and then the correct label names from the Lookup Table will show up.

Best,
Lee

On Thu, 20 Aug 2015, Priyanka Mehta wrote:


Hi Eugenio

Thank you for the explanation, it makes sense to me now.

When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly. 
However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only' checked, the 
lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.

 

On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
  Hi Prya,
  that is because MriCron is not that great at overlaying images that are 
in the same physical space but not
  in the same voxel space. You have two options here:
  1. Use FreeSurfer's Freeview rather than MriCron to visualize the output. 
FreeView will correctly overlay
  the segmentation.
  2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than 
lh.hippoSfLabels-T1.v10.mgz) when you call
  mri_extract_label. That volume lives in the same voxel space as T1.nii, 
and should be properly overlayed
  by MriCron. However, the resolution of the segmentation will be 1 mm, 
rather than the 0.333 mm that you'd
  get in option 1.
  Cheers,
  Eugenio

  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu

  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


  - Original Message -
  From: Priyanka Mehta priyankamehta0...@gmail.com
  To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
  Sent: Wednesday, August 19, 2015 7:50:12 PM
  Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output



  Hi


  This is a follow-up question to my previous problem.
  After I run recon-all -all -i ${subject}.nii -subject ${subject} 
-hippocampal-subfields-T1, I extracted
  the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 
lh.CA1.nii.
  I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the 
alignment is not correct (see attached
  picture).


  I wonder what is causing this issue? Since the CA1 was extracted from the 
same T1 image, they should
  technically be in the same space and therefore should align correctly.


  Please advise.


  Thank you,
  Priyanka


  On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta  
priyankamehta0...@gmail.com  wrote:





  Worked! Thank you so much. Really appreciate the prompt response.

  Best,
  Priyanka





  On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias  e.igles...@bcbl.eu  
wrote:


  Hi again,
  instead of:
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
  your can run:
  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
  Cheers,
  /E

  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu

  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


  - Original Message -
  From: Priyanka Mehta  priyankamehta0...@gmail.com 
  To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu 
  Sent: Wednesday, July 29, 2015 11:26:04 AM
  Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output







  Thanks Eugenio! Thats worked!
  One more question- how would I convert the lh.CA1.mgz that I get from the 
previous step to .nii format?

  Best,
  Priyanka



  On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu  
wrote:


  Hi Priyanka,

  you can use mri_extract_label for that. For example, if you are 
interested in CA1 (label 206), you can
  run:

  mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz

  Cheers,

  Eugenio

  Juan Eugenio Iglesias
  Postdoctoral researcher BCBL
  www.jeiglesias.com
  www.bcbl.eu

  Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer




  - Original Message -
  From: Priyanka  priyankamehta0...@gmail.com 
  To: freesurfer@nmr.mgh.harvard.edu
  Sent: Wednesday, July 29, 2015 7:59:37 AM
  Subject: [Freesurfer] FreeSurfer 6.0 dev version Output

  Hi,

  I am new to FreeSurfer and need help with hippocampal segmentation in the 
6.0 dev version.
  I used the following command: recon-all -i ${subject}.nii -subject 
${subject} -all
  -hippocampal-subfields-T1.
  I can also view the segmented hippocampal regions using the command: 
freeview -v nu.mgz -v
  lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v 
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.

  However

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Hi Eugenio

Thank you for the explanation, it makes sense to me now.

When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
correctly. However, when I view the segmentation with color map set to
Lookup Table and 'show existing labels only' checked, the lh.CA1.nii
segment shows as 128 Nerve label. Shouldn't it still be showing up as 206
CA1 label? I am confused.



On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:

 Hi Prya,
 that is because MriCron is not that great at overlaying images that are in
 the same physical space but not in the same voxel space. You have two
 options here:
 1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
 FreeView will correctly overlay the segmentation.
 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
 lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume
 lives in the same voxel space as T1.nii, and should be properly overlayed
 by MriCron. However, the resolution of the segmentation will be 1 mm,
 rather than the 0.333 mm that you'd get in option 1.
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Priyanka Mehta priyankamehta0...@gmail.com
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, August 19, 2015 7:50:12 PM
 Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output



 Hi


 This is a follow-up question to my previous problem.
 After I run recon-all -all -i ${subject}.nii -subject ${subject}
 -hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
 lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
 I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
 alignment is not correct (see attached picture).


 I wonder what is causing this issue? Since the CA1 was extracted from the
 same T1 image, they should technically be in the same space and therefore
 should align correctly.


 Please advise.


 Thank you,
 Priyanka


 On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta 
 priyankamehta0...@gmail.com  wrote:





 Worked! Thank you so much. Really appreciate the prompt response.

 Best,
 Priyanka





 On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias  e.igles...@bcbl.eu 
 wrote:


 Hi again,
 instead of:
 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
 your can run:
 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
 Cheers,
 /E

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Priyanka Mehta  priyankamehta0...@gmail.com 
 To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu 
 Sent: Wednesday, July 29, 2015 11:26:04 AM
 Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output







 Thanks Eugenio! Thats worked!
 One more question- how would I convert the lh.CA1.mgz that I get from the
 previous step to .nii format?

 Best,
 Priyanka



 On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu 
 wrote:


 Hi Priyanka,

 you can use mri_extract_label for that. For example, if you are interested
 in CA1 (label 206), you can run:

 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz

 Cheers,

 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer




 - Original Message -
 From: Priyanka  priyankamehta0...@gmail.com 
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, July 29, 2015 7:59:37 AM
 Subject: [Freesurfer] FreeSurfer 6.0 dev version Output

 Hi,

 I am new to FreeSurfer and need help with hippocampal segmentation in the
 6.0 dev version.
 I used the following command: recon-all -i ${subject}.nii -subject
 ${subject} -all -hippocampal-subfields-T1.
 I can also view the segmented hippocampal regions using the command:
 freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
 rh.hippoSfLabels-T1.v10.mgz:colormap=lut.

 However, is there a way I can get a separate .nii file for each of my
 hippocampal subregion?

 I would really appreciate any help in the matter.

 Best,
 Priyanka Mehta


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 The information in this e-mail is intended only for the person to whom it
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Eugenio Iglesias]

Hi Prya,
that is because MriCron is not that great at overlaying images that are in the 
same physical space but not in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output. 
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than 
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume lives 
in the same voxel space as T1.nii, and should be properly overlayed by MriCron. 
However, the resolution of the segmentation will be 1 mm, rather than the 0.333 
mm that you'd get in option 1.
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output



Hi 


This is a follow-up question to my previous problem. 
After I run recon-all -all -i ${subject}.nii -subject ${subject} 
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label 
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii. 
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the alignment is 
not correct (see attached picture). 


I wonder what is causing this issue? Since the CA1 was extracted from the same 
T1 image, they should technically be in the same space and therefore should 
align correctly. 


Please advise. 


Thank you, 
Priyanka 


On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta  priyankamehta0...@gmail.com 
 wrote: 





Worked! Thank you so much. Really appreciate the prompt response. 

Best, 
Priyanka 





On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias  e.igles...@bcbl.eu  
wrote: 


Hi again, 
instead of: 
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz 
your can run: 
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii 
Cheers, 
/E 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


- Original Message - 
From: Priyanka Mehta  priyankamehta0...@gmail.com  
To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu  
Sent: Wednesday, July 29, 2015 11:26:04 AM 
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output 







Thanks Eugenio! Thats worked! 
One more question- how would I convert the lh.CA1.mgz that I get from the 
previous step to .nii format? 

Best, 
Priyanka 



On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu  wrote: 


Hi Priyanka, 

you can use mri_extract_label for that. For example, if you are interested in 
CA1 (label 206), you can run: 

mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz 

Cheers, 

Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 




- Original Message - 
From: Priyanka  priyankamehta0...@gmail.com  
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Wednesday, July 29, 2015 7:59:37 AM 
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output 

Hi, 

I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0 
dev version. 
I used the following command: recon-all -i ${subject}.nii -subject ${subject} 
-all -hippocampal-subfields-T1. 
I can also view the segmented hippocampal regions using the command: freeview 
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v 
rh.hippoSfLabels-T1.v10.mgz:colormap=lut. 

However, is there a way I can get a separate .nii file for each of my 
hippocampal subregion? 

I would really appreciate any help in the matter. 

Best, 
Priyanka Mehta 


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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Worked! Thank you so much. Really appreciate the prompt response.

Best,
Priyanka

On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:

 Hi again,
 instead of:
 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
 your can run:
 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
 Cheers,
 /E

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Priyanka Mehta priyankamehta0...@gmail.com
 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, July 29, 2015 11:26:04 AM
 Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output







 Thanks Eugenio! Thats worked!
 One more question- how would I convert the lh.CA1.mgz that I get from the
 previous step to .nii format?

 Best,
 Priyanka



 On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu 
 wrote:


 Hi Priyanka,

 you can use mri_extract_label for that. For example, if you are interested
 in CA1 (label 206), you can run:

 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz

 Cheers,

 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer




 - Original Message -
 From: Priyanka  priyankamehta0...@gmail.com 
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, July 29, 2015 7:59:37 AM
 Subject: [Freesurfer] FreeSurfer 6.0 dev version Output

 Hi,

 I am new to FreeSurfer and need help with hippocampal segmentation in the
 6.0 dev version.
 I used the following command: recon-all -i ${subject}.nii -subject
 ${subject} -all -hippocampal-subfields-T1.
 I can also view the segmented hippocampal regions using the command:
 freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
 rh.hippoSfLabels-T1.v10.mgz:colormap=lut.

 However, is there a way I can get a separate .nii file for each of my
 hippocampal subregion?

 I would really appreciate any help in the matter.

 Best,
 Priyanka Mehta


 ___
 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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 The information in this e-mail is intended only for the person to whom it
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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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 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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Eugenio Iglesias]

Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output







Thanks Eugenio! Thats worked! 
One more question- how would I convert the lh.CA1.mgz that I get from the 
previous step to .nii format? 

Best, 
Priyanka 



On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias  e.igles...@bcbl.eu  wrote: 


Hi Priyanka, 

you can use mri_extract_label for that. For example, if you are interested in 
CA1 (label 206), you can run: 

mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz 

Cheers, 

Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 




- Original Message - 
From: Priyanka  priyankamehta0...@gmail.com  
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Wednesday, July 29, 2015 7:59:37 AM 
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output 

Hi, 

I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0 
dev version. 
I used the following command: recon-all -i ${subject}.nii -subject ${subject} 
-all -hippocampal-subfields-T1. 
I can also view the segmented hippocampal regions using the command: freeview 
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v 
rh.hippoSfLabels-T1.v10.mgz:colormap=lut. 

However, is there a way I can get a separate .nii file for each of my 
hippocampal subregion? 

I would really appreciate any help in the matter. 

Best, 
Priyanka Mehta 


___ 
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 
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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
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output

[Priyanka Mehta]

Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?

Best,
Priyanka

On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:

 Hi Priyanka,

 you can use mri_extract_label for that. For example, if you are interested
 in CA1 (label 206), you can run:

 mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz

 Cheers,

 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Priyanka priyankamehta0...@gmail.com
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Wednesday, July 29, 2015 7:59:37 AM
 Subject: [Freesurfer] FreeSurfer 6.0 dev version Output

 Hi,

 I am new to FreeSurfer and need help with hippocampal segmentation in the
 6.0 dev version.
 I used the following command: recon-all -i ${subject}.nii -subject
 ${subject} -all -hippocampal-subfields-T1.
 I can also view the segmented hippocampal regions using the command:
 freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
 rh.hippoSfLabels-T1.v10.mgz:colormap=lut.

 However, is there a way I can get a separate .nii file for each of my
 hippocampal subregion?

 I would really appreciate any help in the matter.

 Best,
 Priyanka Mehta


 ___
 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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The information in this e-mail is intended only for the person to whom it is
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