Re: [Freesurfer] Running recon-all with FLAIR

[Douglas N. Greve]

Copy the lta to subject/mri/transforms/FLAIRraw.lta (there should be one 
there already, just copy over it)



On 4/16/2021 12:19 PM, Edina Szabó wrote:
 > External Email - Use Caution > > Hi Douglas, > > Thank you for your 
response! I really appreciate it. > > I ran the command – it works if I 
replace --i with --mov. > > How can I use the new FLAIRraw.lta to create 
a new FLAIR-based pial > surface? For example, should I run recon-all 
-autorecon2 or some > later step? > > Also, we were assuming that 
registration of the FLAIR to the T1 was > the problem (underestimated 
pial surface), since the FLAIR.mgz > produced by Freesurfer was not well 
registered to the T1.mgz. So, if > that's the case, and I have another 
well-registered FLAIR (using FSL > or SPM), is there a way to skip the 
Freesurfer registration and use > that FLAIR to create the FLAIR pial 
surface? > > Thank you for your help in advance! > > All the best, Edina 
Szabo > > __ Edina Szabo, PhD Research Fellow Department of 
Anesthesiology, > Critical Care and Pain Medicine Boston Children's 
Hospital | Harvard > Medical School > > - > > Try this 
cd subject/mri mri_coreg --i orig/T2raw.mgz --targ orig.mgz > --reg 
transforms/T2raw.lta You can run with multiple threads by > adding 
--threads N where N is the number of threads On 3/29/2021 5:18 > PM, 
Edina Szabó wrote: > > External Email - Use Caution > > Dear All, > > We 
are running recon-all on the latest version of FreeSurfer > (v7.1.1). We 
are using both T1 and FLAIR images to better define the > pial surfaces, 
but when we run the recommended command line > (recon-all -subject 
subjectname -i /path/to/input_volume -FLAIR > /path/to/FLAIR_volume 
-FLAIRpial -all) the pial surface is very > underestimated (?.pial.FLAIR 
– and the aseg volume is based on these > surfaces), and we get better 
results without the FLAIR. It seems that > FreeSurfer mis-registers the 
FLAIR to the T1 during the process. Is > there a separate step we should 
do to register FLAIR to T1? > > Thank you, Edina > > 
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t
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Re: [Freesurfer] Running recon-all with FLAIR

[Edina Szabó]

External Email - Use Caution

Hi Douglas,

Thank you for your response! I really appreciate it.

I ran the command – it works if I replace  --i with --mov.

How can I use the new FLAIRraw.lta to create a new FLAIR-based pial
surface? For example, should I run recon-all -autorecon2 or some later step?

Also, we were assuming that registration of the FLAIR to the T1 was the
problem (underestimated pial surface), since the FLAIR.mgz produced by
Freesurfer was not well registered to the T1.mgz. So, if that's the case,
and I have another well-registered FLAIR (using FSL or SPM), is there a way
to skip the Freesurfer registration and use that FLAIR to create the FLAIR
pial surface?

Thank you for your help in advance!

All the best,
Edina Szabo

__
Edina Szabo, PhD
Research Fellow
Department of Anesthesiology, Critical Care and Pain Medicine
Boston Children's Hospital | Harvard Medical School

-

Try this
cd subject/mri
mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta
You can run with multiple threads by adding --threads N
where N is the number of threads

On 3/29/2021 5:18 PM, Edina Szabó wrote:


External Email - Use Caution

Dear All,


We are running recon-all on the latest version of FreeSurfer (v7.1.1). We
are using both T1 and FLAIR images to better define the pial surfaces, but
when we run the recommended command line (recon-all -subject subjectname -i
/path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the
pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is
based on these surfaces), and we get better results without the FLAIR. It
seems that FreeSurfer mis-registers the FLAIR to the T1 during the process.
Is there a separate step we should do to register FLAIR to T1?

Thank you,
Edina

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Re: [Freesurfer] Running recon-all with FLAIR

[Douglas N. Greve]

Try this
cd subject/mri
mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta
You can run with multiple threads by adding --threads N
where N is the number of threads


On 3/29/2021 5:18 PM, Edina Szabó wrote:


External Email - Use Caution

Dear All,

We are running recon-all on the latest version of FreeSurfer (v7.1.1). 
We are using both T1 and FLAIR images to better define the pial 
surfaces, but when we run the recommended command line (recon-all 
-subject subjectname -i /path/to/input_volume -FLAIR 
/path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very 
underestimated (?.pial.FLAIR – and the aseg volume is based on these 
surfaces), and we get better results without the FLAIR.
It seems that FreeSurfer mis-registers the FLAIR to the T1 during the 
process. Is there a separate step we should do to register FLAIR to T1?


Thank you,
Edina

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[Freesurfer] Running recon-all with FLAIR

[Edina Szabó]

External Email - Use Caution

Dear All,

We are running recon-all on the latest version of FreeSurfer (v7.1.1). We
are using both T1 and FLAIR images to better define the pial surfaces, but
when we run the recommended command line (recon-all -subject subjectname -i
/path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the
pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is
based on these surfaces), and we get better results without the FLAIR.
It seems that FreeSurfer mis-registers the FLAIR to the T1 during the
process. Is there a separate step we should do to register FLAIR to T1?

Thank you,
Edina
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Re: [Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

[Bruce Fischl]

Hi Veronica

it's because you are mixing versions. Can you rerun your subject with 
6.0 from scratch?


cheers
Bruce
On Tue, 21 Mar 2017, Veronica Munoz wrote:


Dear all,

I'm trying to add FLAIR data to a subject. I did the first ("classic")
recon-all on a platform so I get the following warnings:

INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /home/munoz/Documents/freesurfer
    
Previous:/tmp/wrk/DIRAC_piXnbapilot/50587390/recon-all.sh-445574845579047/freesurfer


Then recon all exits with the following error:

#@# Jacobian white lh Tue Mar 21 12:25:24 CET 2017
/media/sf_C_DRIVE/Users/munoz/Documents/Stage_FLI/results/FLAIRtest/AC_005/
scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg
../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc...
MRISread(../surf/lh.white.preaparc): could not open file
No such file or directory
mris_jacobian: could not read surface file ../surf/lh.white.preaparc
No such file or directory
Linux iu-dv-464-vm.creatis.insa-lyon.fr 4.9.7-201.fc25.x86_64 #1 SMP Thu Feb
2 23:32:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Does this have something to do with my current Freesurfer version ? I don't
really know what information does "preaparc" contain.

Thank you for your help.

Best regards,

Veronica
veronica.mu...@creatis.insa-lyon.fr



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[Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

[Veronica Munoz]

Dear all,

I'm trying to add FLAIR data to a subject. I did the first ("classic") 
recon-all on a platform so I get the following warnings:


INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/munoz/Documents/freesurfer
Previous: 
/tmp/wrk/DIRAC_piXnbapilot/50587390/recon-all.sh-445574845579047/freesurfer


Then recon all exits with the following error:

#@# Jacobian white lh Tue Mar 21 12:25:24 CET 2017
/media/sf_C_DRIVE/Users/munoz/Documents/Stage_FLI/results/FLAIRtest/AC_005/scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg 
../surf/lh.jacobian_white


reading surface from ../surf/lh.white.preaparc...
MRISread(../surf/lh.white.preaparc): could not open file
No such file or directory
mris_jacobian: could not read surface file ../surf/lh.white.preaparc
No such file or directory
Linux iu-dv-464-vm.creatis.insa-lyon.fr 4.9.7-201.fc25.x86_64 #1 SMP Thu 
Feb 2 23:32:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Does this have something to do with my current Freesurfer version ? I 
don't really know what information does "preaparc" contain.


Thank you for your help.

Best regards,

Veronica
veronica.mu...@creatis.insa-lyon.fr 


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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
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