Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-13 Thread Emil H.J. Nijhuis
Dear Bruce  Matt,

thank you for your help.

@Bruce: I would be happy to send you the data, just let me know by
e-mail which files you would need.

@Matt: Could you please specify the commands for the flags
-nsigma_above and -nsigma_below and how you would rerun the pipeline?
Also what values would be recommended?

I did not find any manual/help files regarding the flags, so it would
be helpful to document it.

NB. I found another thread in the maillist which probably relates to
the issue: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html
. However I could not verify this, due to expired dropbox files.

Yours,

 Emil


Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9
May 2014, Matt Glasser wrote:

 Hi Bruce,

 For whatever reason, sometimes the T2w surface adjustment will be way
off.
  Adjusting the -nsigma_above # -nsigma_below # even a little bit up
and
 down can get it out of the minimum and make it work, so there might be a
 bug.

 Peace,

 Matt.

 From: Emil H.J. Nijhuis emil.nijh...@gmail.com
 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date: Friday, May 9, 2014 at 4:53 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] problem with pial surface reconstruction
using T1
 (MPRAGE) and T2 (SPACE) weighted images

 Dear Bruce,

 thank you for your help.

 attached I have put an fslview, tkmedit screen-shot of the T2 image and
a tk
 surfer image of lh.woT2.pial.

 It appears that without consideration of the T2 this effect does not
happen.

 What would be your recommendation if I would like to keep using the T2
weigh
 ted image?

 Yours,
  Emil

 Hi Emil

 how do the surfaces look before you apply the T2 deformation? And how do
 they look visualized over the T2 instead of the T1?

 cheers
 Bruce

 On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:

 Hi,

 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
Trio
 scanner with a 32-channel head coil. Unfortunately for half of my
subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces
do
 not suffer from the same issue.

 The command line I have used was:

 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
-T2pial
 -3T

 Are you familiar with this issue and do you have some advice for me?

 Thank you very much for your help.

 Yours sincerely,

  Emil

 --
 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland



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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-13 Thread Bruce Fischl

Hi Emil

I would need the entire subject dir plus the T2-space volume

cheers
Bruce
On Tue, 13 May 
2014, Emil H.J. Nijhuis wrote:




Dear Bruce  Matt,
thank you for your help.

@Bruce: I would be happy to send you the data, just let me know by e-mail which 
files you wo
uld need.

@Matt: Could you please specify the commands for the flags -nsigma_above and 
-nsigma_below a
nd how you would rerun the pipeline? Also what values would be recommended?

I did not find any manual/help files regarding the flags, so it would be 
helpful to document
 it.

NB. I found another thread in the maillist which probably relates to the issue: 
https://mail
.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . However I could not 
verify this, due to expired dropbox files.


Yours,

 Emil

Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9 
May 2014, Matt Glasser wrote:


 Hi Bruce,
 
 For whatever reason, sometimes the T2w surface adjustment will be way

off.
  Adjusting the -nsigma_above # -nsigma_below # even a little bit up
and
 down can get it out of the minimum and make it work, so there might be a
 bug. 
 
 Peace,
 
 Matt.
 
 From: Emil H.J. Nijhuis emil.nijh...@gmail.com

 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date: Friday, May 9, 2014 at 4:53 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] problem with pial surface reconstruction
using T1
 (MPRAGE) and T2 (SPACE) weighted images
 
 Dear Bruce,
 
 thank you for your help.
 
 attached I have put an fslview, tkmedit screen-shot of the T2 image and

a tk
 surfer image of lh.woT2.pial.
 
 It appears that without consideration of the T2 this effect does not

happen.
 
 What would be your recommendation if I would like to keep using the T2

weigh
 ted image?
 
 Yours,

  Emil
 
 Hi Emil
 
 how do the surfaces look before you apply the T2 deformation? And how do

 they look visualized over the T2 instead of the T1?
 
 cheers

 Bruce
 
 On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
 
 Hi,
 
 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm

 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
Trio
 scanner with a 32-channel head coil. Unfortunately for half of my
subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces
do
 not suffer from the same issue.
 
 The command line I have used was:
 
 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz

-T2pial
 -3T
 
 Are you familiar with this issue and do you have some advice for me?
 
 Thank you very much for your help.
 
 Yours sincerely,
 
  Emil
 
 --

 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland
 
 
 
 ___

 Freesurfer mailing list
 
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sti
 nfo/freesurfer
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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
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-13 Thread Matt Glasser
I don’t know if recon-all will pass those flags in or not.  Probably best
to let Bruce take a look.

Peace,

Matt.

On 5/13/14, 7:36 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Emil

I would need the entire subject dir plus the T2-space volume

cheers
Bruce
On Tue, 13 May 
2014, Emil H.J. Nijhuis wrote:

 
 Dear Bruce  Matt,
 thank you for your help.
 
 @Bruce: I would be happy to send you the data, just let me know by
e-mail which files you wo
 uld need.
 
 @Matt: Could you please specify the commands for the flags
-nsigma_above and -nsigma_below a
 nd how you would rerun the pipeline? Also what values would be
recommended?
 
 I did not find any manual/help files regarding the flags, so it would
be helpful to document
  it.
 
 NB. I found another thread in the maillist which probably relates to
the issue: https://mail
 .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html .
However I could not
 verify this, due to expired dropbox files.
 
 Yours,

  Emil
 
 Probably Emil¹s current example would be best because it is failing in
 your recon-all setup.
 
 Matt.
 
 On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Matt
 
 if you can send me an example I'll try to find time to take a look
 Bruce
 On Fri, 9 
 May 2014, Matt Glasser wrote:
 
  Hi Bruce,
  
  For whatever reason, sometimes the T2w surface adjustment will be way
 off.
   Adjusting the -nsigma_above # -nsigma_below # even a little bit
up
 and
  down can get it out of the minimum and make it work, so there might
be a
  bug. 
  
  Peace,
  
  Matt.
  
  From: Emil H.J. Nijhuis emil.nijh...@gmail.com
  Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
  Date: Friday, May 9, 2014 at 4:53 AM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] problem with pial surface reconstruction
 using T1
  (MPRAGE) and T2 (SPACE) weighted images
  
  Dear Bruce,
  
  thank you for your help.
  
  attached I have put an fslview, tkmedit screen-shot of the T2 image
and
 a tk
  surfer image of lh.woT2.pial.
  
  It appears that without consideration of the T2 this effect does not
 happen.
  
  What would be your recommendation if I would like to keep using the
T2
 weigh
  ted image?
  
  Yours,
   Emil
  
  Hi Emil
  
  how do the surfaces look before you apply the T2 deformation? And
how do
  they look visualized over the T2 instead of the T1?
  
  cheers
  Bruce
  
  On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
  
  Hi,
  
  I have been using Freesurfer v5.3 to perform surface reconstruct for
1mm
  isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens
3T
 Trio
  scanner with a 32-channel head coil. Unfortunately for half of my
 subjects I
  receive an rather odd pial surface artefact, while the 'white'
surfaces
 do
  not suffer from the same issue.
  
  The command line I have used was:
  
  recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
 -T2pial
  -3T
  
  Are you familiar with this issue and do you have some advice for me?
  
  Thank you very much for your help.
  
  Yours sincerely,
  
   Emil
  
  --
  --
  Emil H.J. Nijhuis, PhD
  Researcher - Division of Diagnostic and Interventional Neuroradiology
  University Hospital Basel
  Petersgraben 4
  CH 4031 Basel Switzerland
  
  
  
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  nfo/freesurfer
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 information
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contains
  patient information, please contact the Partners Compliance HelpLine
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  http://www.partners.org/complianceline . If the e-mail was sent to
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 in
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 sender
  and properly dispose of the e-mail.
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 is
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 e-mail
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 HelpLine at
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-09 Thread Bruce Fischl

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9 
May 2014, Matt Glasser wrote:



Hi Bruce,

For whatever reason, sometimes the T2w surface adjustment will be way off.
 Adjusting the -nsigma_above # -nsigma_below # even a little bit up and
down can get it out of the minimum and make it work, so there might be a
bug.  

Peace,

Matt.

From: Emil H.J. Nijhuis emil.nijh...@gmail.com
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date: Friday, May 9, 2014 at 4:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with pial surface reconstruction using T1
(MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and a tk
surfer image of lh.woT2.pial.

It appears that without consideration of the T2 this effect does not happen.

What would be your recommendation if I would like to keep using the T2 weigh
ted image?

Yours,
 Emil

Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do
they look visualized over the T2 instead of the T1?

cheers
Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:

Hi,

I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
scanner with a 32-channel head coil. Unfortunately for half of my subjects I
receive an rather odd pial surface artefact, while the 'white' surfaces do
not suffer from the same issue.

The command line I have used was:

recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz -T2pial
-3T

Are you familiar with this issue and do you have some advice for me?

Thank you very much for your help.

Yours sincerely,

 Emil

--
--
Emil H.J. Nijhuis, PhD
Researcher - Division of Diagnostic and Interventional Neuroradiology
University Hospital Basel
Petersgraben 4
CH 4031 Basel Switzerland



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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-09 Thread Matt Glasser
Hi Bruce,

For whatever reason, sometimes the T2w surface adjustment will be way off.
Adjusting the -nsigma_above # -nsigma_below # even a little bit up and
down can get it out of the minimum and make it work, so there might be a
bug.  

Peace,

Matt.

From:  Emil H.J. Nijhuis emil.nijh...@gmail.com
Reply-To:  Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date:  Friday, May 9, 2014 at 4:53 AM
To:  freesurfer@nmr.mgh.harvard.edu
Subject:  Re: [Freesurfer] problem with pial surface reconstruction using T1
(MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and a
tksurfer image of lh.woT2.pial.

It appears that without consideration of the T2 this effect does not happen.

What would be your recommendation if I would like to keep using the T2
weighted image?

Yours,

 Emil



Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do
they look visualized over the T2 instead of the T1?
cheers
Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
 Hi,
 
 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
 scanner with a 32-channel head coil. Unfortunately for half of my subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces do
 not suffer from the same issue.
 
 The command line I have used was:
 
 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz -T2pial
 -3T
 
 Are you familiar with this issue and do you have some advice for me?
 
 Thank you very much for your help.
 
 Yours sincerely,
 
  Emil
 
 --
 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland
 
 
 
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-09 Thread Matt Glasser
Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9 
May 2014, Matt Glasser wrote:

 Hi Bruce,
 
 For whatever reason, sometimes the T2w surface adjustment will be way
off.
  Adjusting the -nsigma_above # -nsigma_below # even a little bit up
and
 down can get it out of the minimum and make it work, so there might be a
 bug.  
 
 Peace,
 
 Matt.
 
 From: Emil H.J. Nijhuis emil.nijh...@gmail.com
 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
 Date: Friday, May 9, 2014 at 4:53 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] problem with pial surface reconstruction
using T1
 (MPRAGE) and T2 (SPACE) weighted images
 
 Dear Bruce,
 
 thank you for your help.
 
 attached I have put an fslview, tkmedit screen-shot of the T2 image and
a tk
 surfer image of lh.woT2.pial.
 
 It appears that without consideration of the T2 this effect does not
happen.
 
 What would be your recommendation if I would like to keep using the T2
weigh
 ted image?
 
 Yours,
  Emil
 
 Hi Emil
 
 how do the surfaces look before you apply the T2 deformation? And how do
 they look visualized over the T2 instead of the T1?
 
 cheers
 Bruce
 
 On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
 
 Hi,
 
 I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
 isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
Trio
 scanner with a 32-channel head coil. Unfortunately for half of my
subjects I
 receive an rather odd pial surface artefact, while the 'white' surfaces
do
 not suffer from the same issue.
 
 The command line I have used was:
 
 recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
-T2pial
 -3T
 
 Are you familiar with this issue and do you have some advice for me?
 
 Thank you very much for your help.
 
 Yours sincerely,
 
  Emil
 
 --
 --
 Emil H.J. Nijhuis, PhD
 Researcher - Division of Diagnostic and Interventional Neuroradiology
 University Hospital Basel
 Petersgraben 4
 CH 4031 Basel Switzerland
 
 
 
 ___
 Freesurfer mailing list
 
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/li
sti
 nfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you
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 and properly dispose of the e-mail.
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-08 Thread Bruce Fischl

Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do 
they look visualized over the T2 instead of the T1?


cheers
Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis 
wrote:



Hi,

I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T Trio
scanner with a 32-channel head coil. Unfortunately for half of my subjects I
receive an rather odd pial surface artefact, while the 'white' surfaces do
not suffer from the same issue.

The command line I have used was:

recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz -T2pial
-3T

Are you familiar with this issue and do you have some advice for me?

Thank you very much for your help.

Yours sincerely,

 Emil

--
--
Emil H.J. Nijhuis, PhD
Researcher - Division of Diagnostic and Interventional Neuroradiology
University Hospital Basel
Petersgraben 4
CH 4031 Basel Switzerland



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