Re: [Freesurfer] recon-all with FLAIR error no FSL installed
Dear all, How "fatal" is the FSL environment not being initialized for FreeSurfer 5.3 with FLAIR refinement? I do get results (which look good). Should I rerun them with FSL installed? Thank you very much in advance! Sincerely, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: maandag 27 mei 2013 14:19 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: > Dear Bruce, > They look good to me. Should I upload a couple of them, so you can have a > look? They're about 230MB each. > My question is: how serious is the BBR not initializing? Should I run > everything again with FSL installed? > Best wishes, > Veronica > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: vrijdag 24 mei 2013 15:59 > To: Popescu, Veronica > Cc: 'freesurfer@nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed > > Hi Veronica > > BBR can use FSL or SPM to initialize, although we'll probably add an option > in the future to use some things that Martin Reuter and Christian Wachinger > are working on. How did the refinement work? We've only run it on a handful > of cases, so it's pretty bleeding edge and I'm interested in feedback. > > cheers > Bruce > > > On Fri, 24 May 2013, Popescu, Veronica > wrote: > >> Dear all, >> I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL >> installed. I do get results but there's an >> error message in the log file (attached) about the FSL installation missing. >> >> How bad is it? Do I have to rerun everything with FSL installed? And if so, >> is there any version that is >> preferable? >> Thank you very much in advance! >> Best wishes, >> Veronica >> >> >> > > > 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
Re: [Freesurfer] recon-all with FLAIR error no FSL installed
Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: > Dear all, > I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL > installed. I do get results but there's an > error message in the log file (attached) about the FSL installation missing. > How bad is it? Do I have to rerun everything with FSL installed? And if so, > is there any version that is > preferable? > Thank you very much in advance! > Best wishes, > Veronica > > > 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
Re: [Freesurfer] pial surface with FLAIR
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
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Re: [Freesurfer] pial surface with FLAIR
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
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] pial surface with FLAIR
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
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.
