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 <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.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 <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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
