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 <snp2...@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 <ahoo...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@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-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > > <fis...@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.
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