Hi Alex
you get to decide whether to average your data or not. It's a totally empirical question which one is better - why don't you run them each and visually inspect the results?
cheers
Bruce
On Wed, 18 Jan 2017, Alex Cohen wrote:
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:
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
<freesurfer-bounces@nmr.mgh.ha____________________________________________________________ ________________
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 rvard.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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