Hi all, What is the current best practice recommendation for using multiple T1s and/or T2s for recon-all where the sizes of the images are slightly different.
For instance: two T1w images of 0.9x0.9x0.9 and 1x1x1 resolution, however the 1x1x1 image seems to have better grey-white separation, etc... Separately, am I correct in my assessment that presently freesurfer will only use 1 T2 or FLAIR image and isn't doing averaging? -Alex ---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: alexander.coh...@childrens.harvard.edu (Medical/Science Email) E-mail: alexco...@gmail.com (Lifetime Email) ---------------------------------------------------------------- On Wed, Jan 18, 2017 at 1:10 PM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Re: mris_make_surfaces error with bbr-init-header (Sneha Pandya) > 2. Re: mris_make_surfaces error with bbr-init-header (Bruce Fischl) > 3. Re: WM lobes and Corpus Callosum (Bharadwaj, Pradyumna - (prad)) > 4. Re: WM lobes and Corpus Callosum (Yendiki, Anastasia) > 5. Re: mris_make_surfaces error with bbr-init-header (Sneha Pandya) > > > ---------- Forwarded message ---------- > From: Sneha Pandya <snp2...@med.cornell.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: > Date: Wed, 18 Jan 2017 17:11:17 +0000 > Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header > > 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 > > > > > > > > > > > ---------- Forwarded message ---------- > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: > Date: Wed, 18 Jan 2017 12:20:07 -0500 (EST) > 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 >> > >> > >> > >> > >> >> > > ---------- Forwarded message ---------- > From: "Bharadwaj, Pradyumna - (prad)" <p...@email.arizona.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: > Date: Wed, 18 Jan 2017 17:48:13 +0000 > Subject: Re: [Freesurfer] WM lobes and Corpus Callosum > > Hello Anastasia, > > > Thank you for your reply! > > > I had created the 4 WM lobes for each hemisphere to extract regional > volumes for white matter lesions in each lobe. > > > As some of our participants have WML in the corpus callosum very close to > the midline, they are not included in the WM lobes created earlier. > > > Do I need to manually edit the labels for the parts of the corpus > callosum between the hemispheres to have them be included in one of the > lobes ? > > > Or is there some alternate way to split the CC in aseg.mgz along > the hemispheric midline and assign its parts to the WM in each hemisphere ? > > > > Best, > > -Prad > > > > > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia < > ayend...@mgh.harvard.edu> > *Sent:* Tuesday, January 17, 2017 5:05 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] WM lobes and Corpus Callosum > > Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region > from the cortical parcellation. Which cortical region would you want to > assign the corpus callosum to? What's labeled as corpus callosum in the > aseg is the part of the corpus callosum between the 2 hemis. > > Best, > a.y > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna > - (prad) [p...@email.arizona.edu] > *Sent:* Tuesday, January 17, 2017 5:37 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] WM lobes and Corpus Callosum > > Hi, > > > I've been trying to create WM lobes using the following steps: > > > 1) mri_annotation2label --lobesStrict > > 2) Outputting the labels from step 1, & creating a simpler annotation > without limbic and insular lobes > > 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot > Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown > > > However, as the corpus callosum is not labelled as wm, it is not included > in any WM lobe. > > > Is there any workaround to assigning the corpus callosum to the different > WM lobes or do I have to manually edit aseg.mgz to change the corpus > callosum's value to match that of WM ? > > > > Thanks, > > -Prad > > > > > ---------- Forwarded message ---------- > From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: > Date: Wed, 18 Jan 2017 17:56:12 +0000 > Subject: Re: [Freesurfer] WM lobes and Corpus Callosum > Hi Prad - That part of the corpus callosum belongs neither to the left nor > to the right hemi, it connects the two. So any split would be arbitrary. > You could write a script that finds if a voxel is closer to the left or the > right hemi for example. > > Best, > a.y > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna > - (prad) [p...@email.arizona.edu] > *Sent:* Wednesday, January 18, 2017 12:48 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] WM lobes and Corpus Callosum > > Hello Anastasia, > > > Thank you for your reply! > > > I had created the 4 WM lobes for each hemisphere to extract regional > volumes for white matter lesions in each lobe. > > > As some of our participants have WML in the corpus callosum very close to > the midline, they are not included in the WM lobes created earlier. > > > Do I need to manually edit the labels for the parts of the corpus > callosum between the hemispheres to have them be included in one of the > lobes ? > > > Or is there some alternate way to split the CC in aseg.mgz along > the hemispheric midline and assign its parts to the WM in each hemisphere ? > > > > Best, > > -Prad > > > > > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia < > ayend...@mgh.harvard.edu> > *Sent:* Tuesday, January 17, 2017 5:05 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] WM lobes and Corpus Callosum > > Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region > from the cortical parcellation. Which cortical region would you want to > assign the corpus callosum to? What's labeled as corpus callosum in the > aseg is the part of the corpus callosum between the 2 hemis. > > Best, > a.y > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna > - (prad) [p...@email.arizona.edu] > *Sent:* Tuesday, January 17, 2017 5:37 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] WM lobes and Corpus Callosum > > Hi, > > > I've been trying to create WM lobes using the following steps: > > > 1) mri_annotation2label --lobesStrict > > 2) Outputting the labels from step 1, & creating a simpler annotation > without limbic and insular lobes > > 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot > Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown > > > However, as the corpus callosum is not labelled as wm, it is not included > in any WM lobe. > > > Is there any workaround to assigning the corpus callosum to the different > WM lobes or do I have to manually edit aseg.mgz to change the corpus > callosum's value to match that of WM ? > > > > Thanks, > > -Prad > > > > > ---------- Forwarded message ---------- > From: Sneha Pandya <snp2...@med.cornell.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: > Date: Wed, 18 Jan 2017 18:10:19 +0000 > Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header > > 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 > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > >
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