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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 <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:

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" <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:

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 <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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