Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl 
you shouldn't be running the initial recon with a flair volume though, 
are you? That would utterly fail I would think
Bruce
On Tue, 16 Apr 2013, Watson, 
Christopher wrote:

 Hi Veronica,
 Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
 And then, when you do the remaining recon-all steps:

 recon-all -autorecon3 -s $SUBJECT -FLAIRpial

 It has worked for me. (And worked very well! No edits necessary for the pial 
 surface!)
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, April 15, 2013 12:31 PM
 To: Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: Re: [Freesurfer] pial surface with FLAIR

 Hi Veronica,

 we haven't seen that before. Can you upload your subject including the
 FLAIR and we'll take a look?

 thanks
 Bruce

 On Mon, 15 Apr 2013, Popescu, Veronica wrote:


 Dear all,

 I have already run the FreeSurfer 5.2 -all, and I would like to improve the
 pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
 have also placed the FLAIR file) I use the following syntax:

 recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

 It starts running but then it hangs, I never get an output. The FLAIR file
 is in nifti format.

 I am not sure what I am doing wrong: it is the syntax? Should I first
 convert the FLAIR file to .mgz?

 Thank you in advance for the help!

 Veronica Popescu, MD, MSc
 Department of Radiology  Nuclear Medicine
 VU University Medical Center
 Amsterdam, The Netherlands





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Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl 
Hi Veronica

what recon-all command lines did you run? You did run it with a T1 first, 
right?

Bruce
On Tue, 16 Apr 2013, Popescu, Veronica wrote:

 Hi, Christopher!
 Best of luck to you all in these difficult times!
 Thank you very much for your advice. I'll try this as well.
 Best wishes,
 Veronica

 -Original Message-
 From: Watson, Christopher [mailto:christopher.wat...@childrens.harvard.edu]
 Sent: Tuesday, 16 April, 2013 07:15
 To: Bruce Fischl; Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: RE: [Freesurfer] pial surface with FLAIR

 Hi Veronica,
 Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
 And then, when you do the remaining recon-all steps:

 recon-all -autorecon3 -s $SUBJECT -FLAIRpial

 It has worked for me. (And worked very well! No edits necessary for the pial 
 surface!) 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, April 15, 2013 12:31 PM
 To: Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: Re: [Freesurfer] pial surface with FLAIR

 Hi Veronica,

 we haven't seen that before. Can you upload your subject including the FLAIR 
 and we'll take a look?

 thanks
 Bruce

 On Mon, 15 Apr 2013, Popescu, Veronica wrote:


 Dear all,

 I have already run the FreeSurfer 5.2 -all, and I would like to
 improve the pial surface recongition using the FLAIR. From the
 $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
 syntax:

 recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

 It starts running but then it hangs, I never get an output. The FLAIR
 file is in nifti format.

 I am not sure what I am doing wrong: it is the syntax? Should I first
 convert the FLAIR file to .mgz?

 Thank you in advance for the help!

 Veronica Popescu, MD, MSc
 Department of Radiology  Nuclear Medicine VU University Medical
 Center Amsterdam, The Netherlands





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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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Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Popescu, Veronica 

Dear Bruce,
I ran the follwing: 
autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all. 
And my file was indeed a 3D T1 scan. 
Thank you very much!
Best wishes,
Veronica

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Tuesday, 16 April, 2013 15:02
To: Popescu, Veronica
Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] pial surface with FLAIR

Hi Veronica

what recon-all command lines did you run? You did run it with a T1 first, right?

Bruce
On Tue, 16 Apr 2013, Popescu, Veronica wrote:

 Hi, Christopher!
 Best of luck to you all in these difficult times!
 Thank you very much for your advice. I'll try this as well.
 Best wishes,
 Veronica

 -Original Message-
 From: Watson, Christopher 
 [mailto:christopher.wat...@childrens.harvard.edu]
 Sent: Tuesday, 16 April, 2013 07:15
 To: Bruce Fischl; Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: RE: [Freesurfer] pial surface with FLAIR

 Hi Veronica,
 Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
 And then, when you do the remaining recon-all steps:

 recon-all -autorecon3 -s $SUBJECT -FLAIRpial

 It has worked for me. (And worked very well! No edits necessary for 
 the pial surface!) 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, April 15, 2013 12:31 PM
 To: Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: Re: [Freesurfer] pial surface with FLAIR

 Hi Veronica,

 we haven't seen that before. Can you upload your subject including the FLAIR 
 and we'll take a look?

 thanks
 Bruce

 On Mon, 15 Apr 2013, Popescu, Veronica wrote:


 Dear all,

 I have already run the FreeSurfer 5.2 -all, and I would like to 
 improve the pial surface recongition using the FLAIR. From the 
 $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
 syntax:

 recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

 It starts running but then it hangs, I never get an output. The FLAIR 
 file is in nifti format.

 I am not sure what I am doing wrong: it is the syntax? Should I first 
 convert the FLAIR file to .mgz?

 Thank you in advance for the help!

 Veronica Popescu, MD, MSc
 Department of Radiology  Nuclear Medicine VU University Medical 
 Center Amsterdam, The Netherlands







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] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl 
ok, then I don't see what's going wrong. Nick: any thoughts?

On Tue, 16 Apr 
2013, Popescu, Veronica wrote:


 Dear Bruce,
 I ran the follwing:
 autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
 And my file was indeed a 3D T1 scan.
 Thank you very much!
 Best wishes,
 Veronica

 -Original Message-
 From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
 Sent: Tuesday, 16 April, 2013 15:02
 To: Popescu, Veronica
 Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
 Subject: RE: [Freesurfer] pial surface with FLAIR

 Hi Veronica

 what recon-all command lines did you run? You did run it with a T1 first, 
 right?

 Bruce
 On Tue, 16 Apr 2013, Popescu, Veronica wrote:

 Hi, Christopher!
 Best of luck to you all in these difficult times!
 Thank you very much for your advice. I'll try this as well.
 Best wishes,
 Veronica

 -Original Message-
 From: Watson, Christopher
 [mailto:christopher.wat...@childrens.harvard.edu]
 Sent: Tuesday, 16 April, 2013 07:15
 To: Bruce Fischl; Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: RE: [Freesurfer] pial surface with FLAIR

 Hi Veronica,
 Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
 And then, when you do the remaining recon-all steps:

 recon-all -autorecon3 -s $SUBJECT -FLAIRpial

 It has worked for me. (And worked very well! No edits necessary for
 the pial surface!) 
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, April 15, 2013 12:31 PM
 To: Popescu, Veronica
 Cc: 'freesurfer@nmr.mgh.harvard.edu'
 Subject: Re: [Freesurfer] pial surface with FLAIR

 Hi Veronica,

 we haven't seen that before. Can you upload your subject including the FLAIR 
 and we'll take a look?

 thanks
 Bruce

 On Mon, 15 Apr 2013, Popescu, Veronica wrote:


 Dear all,

 I have already run the FreeSurfer 5.2 -all, and I would like to
 improve the pial surface recongition using the FLAIR. From the
 $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
 syntax:

 recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

 It starts running but then it hangs, I never get an output. The FLAIR
 file is in nifti format.

 I am not sure what I am doing wrong: it is the syntax? Should I first
 convert the FLAIR file to .mgz?

 Thank you in advance for the help!

 Veronica Popescu, MD, MSc
 Department of Radiology  Nuclear Medicine VU University Medical
 Center Amsterdam, The Netherlands







 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] pial surface with FLAIR

2013-04-16 Thread Nick Schmansky 
Veronica,

Can you send me the recon-all.log?  The one where it is getting hung
when you run this:

recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

this should work, by importing the flair and then re-running the surface
creation code, but perhaps there is a dependency bug that was missed.

Nick


On Tue, 2013-04-16 at 09:27 -0400, Bruce Fischl wrote:
 ok, then I don't see what's going wrong. Nick: any thoughts?
 
 On Tue, 16 Apr 
 2013, Popescu, Veronica wrote:
 
 
  Dear Bruce,
  I ran the follwing:
  autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
  And my file was indeed a 3D T1 scan.
  Thank you very much!
  Best wishes,
  Veronica
 
  -Original Message-
  From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
  Sent: Tuesday, 16 April, 2013 15:02
  To: Popescu, Veronica
  Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
  Subject: RE: [Freesurfer] pial surface with FLAIR
 
  Hi Veronica
 
  what recon-all command lines did you run? You did run it with a T1 first, 
  right?
 
  Bruce
  On Tue, 16 Apr 2013, Popescu, Veronica wrote:
 
  Hi, Christopher!
  Best of luck to you all in these difficult times!
  Thank you very much for your advice. I'll try this as well.
  Best wishes,
  Veronica
 
  -Original Message-
  From: Watson, Christopher
  [mailto:christopher.wat...@childrens.harvard.edu]
  Sent: Tuesday, 16 April, 2013 07:15
  To: Bruce Fischl; Popescu, Veronica
  Cc: 'freesurfer@nmr.mgh.harvard.edu'
  Subject: RE: [Freesurfer] pial surface with FLAIR
 
  Hi Veronica,
  Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
  And then, when you do the remaining recon-all steps:
 
  recon-all -autorecon3 -s $SUBJECT -FLAIRpial
 
  It has worked for me. (And worked very well! No edits necessary for
  the pial surface!) 
  From: freesurfer-boun...@nmr.mgh.harvard.edu
  [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
  [fis...@nmr.mgh.harvard.edu]
  Sent: Monday, April 15, 2013 12:31 PM
  To: Popescu, Veronica
  Cc: 'freesurfer@nmr.mgh.harvard.edu'
  Subject: Re: [Freesurfer] pial surface with FLAIR
 
  Hi Veronica,
 
  we haven't seen that before. Can you upload your subject including the 
  FLAIR and we'll take a look?
 
  thanks
  Bruce
 
  On Mon, 15 Apr 2013, Popescu, Veronica wrote:
 
 
  Dear all,
 
  I have already run the FreeSurfer 5.2 -all, and I would like to
  improve the pial surface recongition using the FLAIR. From the
  $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the 
  following syntax:
 
  recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
 
  It starts running but then it hangs, I never get an output. The FLAIR
  file is in nifti format.
 
  I am not sure what I am doing wrong: it is the syntax? Should I first
  convert the FLAIR file to .mgz?
 
  Thank you in advance for the help!
 
  Veronica Popescu, MD, MSc
  Department of Radiology  Nuclear Medicine VU University Medical
  Center Amsterdam, The Netherlands
 
 
 
 
 
 
 
  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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 Freesurfer mailing list
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Re: [Freesurfer] pial surface with FLAIR

2013-04-15 Thread Bruce Fischl 

Hi Veronica,

we haven't seen that before. Can you upload your subject including the 
FLAIR and we'll take a look?


thanks
Bruce

On Mon, 15 Apr 2013, Popescu, Veronica wrote:



Dear all,

I have already run the FreeSurfer 5.2 -all, and I would like to improve the
pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
have also placed the FLAIR file) I use the following syntax: 

recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

It starts running but then it hangs, I never get an output. The FLAIR file
is in nifti format.

I am not sure what I am doing wrong: it is the syntax? Should I first
convert the FLAIR file to .mgz?

Thank you in advance for the help!
 
Veronica Popescu, MD, MSc
Department of Radiology  Nuclear Medicine
VU University Medical Center
Amsterdam, The Netherlands

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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] pial surface with FLAIR

2013-04-15 Thread Nick Schmansky 
Veronica,

Hi, can you copy me on the subject data upload?  You can upload data
here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick


On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote:
 Hi Veronica,
 
 we haven't seen that before. Can you upload your subject including the 
 FLAIR and we'll take a look?
 
 thanks
 Bruce
 
 On Mon, 15 Apr 2013, Popescu, Veronica wrote:
 
  
  Dear all,
  
  I have already run the FreeSurfer 5.2 -all, and I would like to improve the
  pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
  have also placed the FLAIR file) I use the following syntax: 
  
  recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
  
  It starts running but then it hangs, I never get an output. The FLAIR file
  is in nifti format.
  
  I am not sure what I am doing wrong: it is the syntax? Should I first
  convert the FLAIR file to .mgz?
  
  Thank you in advance for the help!
   
  Veronica Popescu, MD, MSc
  Department of Radiology  Nuclear Medicine
  VU University Medical Center
  Amsterdam, The Netherlands
  
 
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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] pial surface with FLAIR

2013-04-15 Thread Watson, Christopher 
Hi Veronica,
Did you try initially doing recon-all -i $FLAIR -s $SUBJECT?
And then, when you do the remaining recon-all steps:

recon-all -autorecon3 -s $SUBJECT -FLAIRpial

It has worked for me. (And worked very well! No edits necessary for the pial 
surface!)

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 15, 2013 12:31 PM
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] pial surface with FLAIR

Hi Veronica,

we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?

thanks
Bruce

On Mon, 15 Apr 2013, Popescu, Veronica wrote:


 Dear all,

 I have already run the FreeSurfer 5.2 -all, and I would like to improve the
 pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
 have also placed the FLAIR file) I use the following syntax:

 recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

 It starts running but then it hangs, I never get an output. The FLAIR file
 is in nifti format.

 I am not sure what I am doing wrong: it is the syntax? Should I first
 convert the FLAIR file to .mgz?

 Thank you in advance for the help!

 Veronica Popescu, MD, MSc
 Department of Radiology  Nuclear Medicine
 VU University Medical Center
 Amsterdam, The Netherlands



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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.