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.Cohen2@childrens.harvard.edu (Medical/Science Email) E-mail: alexcohen@gmail.com (Lifetime Email) ----------------------------------------------------------------
On Wed, Jan 18, 2017 at 1:10 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: mris_make_surfaces error with bbr-init-header (Sneha Pandya)
- Re: mris_make_surfaces error with bbr-init-header (Bruce Fischl)
- Re: WM lobes and Corpus Callosum (Bharadwaj, Pradyumna - (prad))
- Re: WM lobes and Corpus Callosum (Yendiki, Anastasia)
- Re: mris_make_surfaces error with bbr-init-header (Sneha Pandya)
---------- Forwarded message ---------- From: Sneha Pandya snp2003@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-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
---------- Forwarded message ---------- From: Bruce Fischl fischl@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-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
---------- Forwarded message ---------- From: "Bharadwaj, Pradyumna - (prad)" prad@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia < AYENDIKI@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna
- (prad) [prad@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:
mri_annotation2label --lobesStrict
Outputting the labels from step 1, & creating a simpler annotation
without limbic and insular lobes
- 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" AYENDIKI@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna
- (prad) [prad@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia < AYENDIKI@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bharadwaj, Pradyumna
- (prad) [prad@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:
mri_annotation2label --lobesStrict
Outputting the labels from step 1, & creating a simpler annotation
without limbic and insular lobes
- 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 snp2003@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-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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