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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.Watson@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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

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:fischl@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.Watson@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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.

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:fischl@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.Watson@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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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