Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgz as their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).
In addition to bbr-init-header I independently tried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spm resulting in non-empty and properly registered FLAIR.prenorm.mgz and non-empty FLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successful for others as well.
Do you suggest I run them with bbr-init-spm or registering with FLAIRraw to the orig as you suggested. If bbr-init-spm is fine then with which step of recon should I run? I tried running it with autorecon3 step with bbr-init-spm and FLAIRpial flags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgz volumes.
Thanks, Sneha ________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, January 24, 2017 12:20:03 PM To: Freesurfer support list; Sneha Pandya Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Sneha,
I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:
cd 1_S_5002_snp_bbr-init-header/mri/orig mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit cp FLAIRraw.mgz FLAIRcopy.mgz mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample
This should do the trick.
best, Andrew
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Thursday, January 19, 2017 1:42:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Wednesday, January 18, 2017 2:43:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
Thanks, Sneha ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 1:58:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi Bruce,
Total is 231111108 kB from /proc/meminfo and flair vozel size is 1.0000, 0.9766, 0.9766.
I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run recon-all -autorecon3 with -bbr-init-header flag.
Thanks, Sneha
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 11:09:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Hi Sneha
how much RAM do you have in your machine? And what is the resolution of your data?
cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple T1s. We
want
to use flair to refine pial surfaces as for all the subjects pial
surfaces
are messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running
following
command to incorporate flair:
recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache
When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory"
Can someone guide what is happening? Is it that there are large
topological
error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage?
Thanks,
Sneha
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.
Ah great! If the registration is accurate with bbr-init-spm, I suggest just using that. I would only use the mri_robust_register technique if none of the bbr initialization options produce a precise alignment. To overwrite the FLAIR volumes, I'm pretty sure including the "-clean-FLAIR" flag in your autorecon3 command will do the job.
best,
Andrew
________________________________ From: Sneha Pandya snp2003@med.cornell.edu Sent: Tuesday, January 24, 2017 12:49:31 PM To: Hoopes, Andrew; Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgz as their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).
In addition to bbr-init-header I independently tried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spm resulting in non-empty and properly registered FLAIR.prenorm.mgz and non-empty FLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successful for others as well.
Do you suggest I run them with bbr-init-spm or registering with FLAIRraw to the orig as you suggested. If bbr-init-spm is fine then with which step of recon should I run? I tried running it with autorecon3 step with bbr-init-spm and FLAIRpial flags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgz volumes.
Thanks, Sneha ________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, January 24, 2017 12:20:03 PM To: Freesurfer support list; Sneha Pandya Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Sneha,
I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:
cd 1_S_5002_snp_bbr-init-header/mri/orig mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit cp FLAIRraw.mgz FLAIRcopy.mgz mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample
This should do the trick.
best, Andrew
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Thursday, January 19, 2017 1:42:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Wednesday, January 18, 2017 2:43:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
Thanks, Sneha ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 1:58:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi Bruce,
Total is 231111108 kB from /proc/meminfo and flair vozel size is 1.0000, 0.9766, 0.9766.
I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run recon-all -autorecon3 with -bbr-init-header flag.
Thanks, Sneha
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 11:09:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Hi Sneha
how much RAM do you have in your machine? And what is the resolution of your data?
cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple T1s. We
want
to use flair to refine pial surfaces as for all the subjects pial
surfaces
are messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running
following
command to incorporate flair:
recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache
When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory"
Can someone guide what is happening? Is it that there are large
topological
error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage?
Thanks,
Sneha
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.
Perfect, shall go ahead with bbr-init-spm and will try running it with "-clean-FLAIR" flag.
Thanks again!
Sneha
________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, January 24, 2017 2:15:31 PM To: Sneha Pandya; Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Ah great! If the registration is accurate with bbr-init-spm, I suggest just using that. I would only use the mri_robust_register technique if none of the bbr initialization options produce a precise alignment. To overwrite the FLAIR volumes, I'm pretty sure including the "-clean-FLAIR" flag in your autorecon3 command will do the job.
best,
Andrew
________________________________ From: Sneha Pandya snp2003@med.cornell.edu Sent: Tuesday, January 24, 2017 12:49:31 PM To: Hoopes, Andrew; Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgz as their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).
In addition to bbr-init-header I independently tried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spm resulting in non-empty and properly registered FLAIR.prenorm.mgz and non-empty FLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successful for others as well.
Do you suggest I run them with bbr-init-spm or registering with FLAIRraw to the orig as you suggested. If bbr-init-spm is fine then with which step of recon should I run? I tried running it with autorecon3 step with bbr-init-spm and FLAIRpial flags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgz volumes.
Thanks, Sneha ________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, January 24, 2017 12:20:03 PM To: Freesurfer support list; Sneha Pandya Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Sneha,
I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:
cd 1_S_5002_snp_bbr-init-header/mri/orig mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit cp FLAIRraw.mgz FLAIRcopy.mgz mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample
This should do the trick.
best, Andrew
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Thursday, January 19, 2017 1:42:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu Sent: Wednesday, January 18, 2017 2:43:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
Thanks, Sneha ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 1:58:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi Bruce,
Total is 231111108 kB from /proc/meminfo and flair vozel size is 1.0000, 0.9766, 0.9766.
I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run recon-all -autorecon3 with -bbr-init-header flag.
Thanks, Sneha
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 11:09:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Hi Sneha
how much RAM do you have in your machine? And what is the resolution of your data?
cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple T1s. We
want
to use flair to refine pial surfaces as for all the subjects pial
surfaces
are messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running
following
command to incorporate flair:
recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache
When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory"
Can someone guide what is happening? Is it that there are large
topological
error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage?
Thanks,
Sneha
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.
The -spm will work well, but it does require matlab (and spm). Note that in version 6 we use mri_coreg which is our implementation of spmreg.
On 01/24/2017 02:15 PM, Hoopes, Andrew wrote:
Ah great! If the registration is accurate with bbr-init-spm, I suggest just using that. I would only use the mri_robust_register technique if none of the bbr initialization options produce a precise alignment. To overwrite the FLAIR volumes, I'm pretty sure including the "-clean-FLAIR" flag in your autorecon3 command will do the job.
best,
Andrew
*From:* Sneha Pandya snp2003@med.cornell.edu *Sent:* Tuesday, January 24, 2017 12:49:31 PM *To:* Hoopes, Andrew; Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgzas their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).
In addition to bbr-init-headerI independentlytried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spmresulting innon-empty and properly registered FLAIR.prenorm.mgzand non-emptyFLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successfulfor others as well.
Do you suggest I run them with bbr-init-spmor registering with FLAIRraw to the origas you suggested. Ifbbr-init-spmis fine then withwhich step of recon should I run? I tried running it with autorecon3step with bbr-init-spmand FLAIRpialflags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgzvolumes.
Thanks, Sneha
*From:* Hoopes, Andrew AHOOPES@mgh.harvard.edu *Sent:* Tuesday, January 24, 2017 12:20:03 PM *To:* Freesurfer support list; Sneha Pandya *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Hi Sneha,
I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:
cd 1_S_5002_snp_bbr-init-header/mri/orig mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit cp FLAIRraw.mgz FLAIRcopy.mgz mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample
This should do the trick.
best, Andrew
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu *Sent:* Thursday, January 19, 2017 1:42:06 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu *Sent:* Wednesday, January 18, 2017 2:43:01 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
Thanks, Sneha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Wednesday, January 18, 2017 1:58:11 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi Bruce,
Total is 231111108 kB from /proc/meminfo and flair vozel size is
1.0000,
0.9766, 0.9766.
I ran quite a few recon-all after this one failed and it did not
complain.
It just fails when I run recon-all -autorecon3 with
-bbr-init-header flag.
Thanks, Sneha
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 11:09:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with
bbr-init-header
Hi Sneha
how much RAM do you have in your machine? And what is the
resolution of
your data?
cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple
T1s. We
want
to use flair to refine pial surfaces as for all the subjects pial
surfaces
are messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running
following
command to incorporate flair:
recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache
When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory"
Can someone guide what is happening? Is it that there are large
topological
error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage?
Thanks,
Sneha
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
Thank you Dough, yes I believe so, we have matlab and spm installed as well.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, January 24, 2017 5:00:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
The -spm will work well, but it does require matlab (and spm). Note that in version 6 we use mri_coreg which is our implementation of spmreg.
On 01/24/2017 02:15 PM, Hoopes, Andrew wrote:
Ah great! If the registration is accurate with bbr-init-spm, I suggest just using that. I would only use the mri_robust_register technique if none of the bbr initialization options produce a precise alignment. To overwrite the FLAIR volumes, I'm pretty sure including the "-clean-FLAIR" flag in your autorecon3 command will do the job.
best,
Andrew
*From:* Sneha Pandya snp2003@med.cornell.edu *Sent:* Tuesday, January 24, 2017 12:49:31 PM *To:* Hoopes, Andrew; Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Thank you so much Andrew, I indeed looked into that. FLAIR volume used were acquired in the same session, however not sure of different geometry. I had to also fix the origins for FLAIRraw.mgzas their origins were outside the brain (not sure if that would be contributing to different geometry, I guess not so much).
In addition to bbr-init-headerI independentlytried bbregister with bbr-init-fsl and bbr-init-spm. bbregister only worked with bbr-init-spmresulting innon-empty and properly registered FLAIR.prenorm.mgzand non-emptyFLAIR.mgz volume in the mri_normalize step. I tried this with only one case, so not sure if it will be successfulfor others as well.
Do you suggest I run them with bbr-init-spmor registering with FLAIRraw to the origas you suggested. Ifbbr-init-spmis fine then withwhich step of recon should I run? I tried running it with autorecon3step with bbr-init-spmand FLAIRpialflags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgzvolumes.
Thanks, Sneha
*From:* Hoopes, Andrew AHOOPES@mgh.harvard.edu *Sent:* Tuesday, January 24, 2017 12:20:03 PM *To:* Freesurfer support list; Sneha Pandya *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header Hi Sneha,
I took a look at your issue. Was the FLAIR volume acquired in a different scan session than the other volumes? FLAIRraw.mgz has a much different geometry than 001.mgz and 002.mgz, and so bbregister (the first step of -FLAIRpial) could not register the FLAIRraw to the orig volume, resulting in empty FLAIR.prenorm.mgz and FLAIR.mgz files. Before rerunning autorecon3, I suggest registering the FLAIRraw to the orig, and then applying the resulting transform so that the FLAIRraw geometry is initially in alignment with the other volumes:
cd 1_S_5002_snp_bbr-init-header/mri/orig mri_robust_register --mov FLAIRraw.mgz --dst ../orig.mgz --lta FLAIRorig.lta --satit cp FLAIRraw.mgz FLAIRcopy.mgz mri_vol2vol --mov FLAIRraw.mgz --lta FLAIRorig.lta --targ ../orig.mgz --o FLAIRraw.mgz --no-resample
This should do the trick.
best, Andrew
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu *Sent:* Thursday, January 19, 2017 1:42:06 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@med.cornell.edu *Sent:* Wednesday, January 18, 2017 2:43:01 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
I transferred file using ftp transfer.
Thanks, Sneha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Wednesday, January 18, 2017 1:58:11 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_make_surfaces error with bbr-init-header oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Sure, please find it attached.
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 12:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi Bruce,
Total is 231111108 kB from /proc/meminfo and flair vozel size is
1.0000,
0.9766, 0.9766.
I ran quite a few recon-all after this one failed and it did not
complain.
It just fails when I run recon-all -autorecon3 with
-bbr-init-header flag.
Thanks, Sneha
_
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2017 11:09:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with
bbr-init-header
Hi Sneha
how much RAM do you have in your machine? And what is the
resolution of
your data?
cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple
T1s. We
want
to use flair to refine pial surfaces as for all the subjects pial
surfaces
are messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running
following
command to incorporate flair:
recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache
When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory"
Can someone guide what is happening? Is it that there are large
topological
error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage?
Thanks,
Sneha
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