Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Priyanka, in the mri directory of each subject, you will find a file named: [lr]h.hippoSfLabels--.v10.1mm.mgz which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel space of that subject. Kind regards, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Priyanka Mehta" <priyankamehta0...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Sunday, September 13, 2015 10:14:34 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi again I want to use my hippocampal segmentation for masking 2380 brain volumes. Is there a way to find out using Freesurfer if the hippocampal subfields and the 2380 volumes are in the same space? The mean of the 2380 volumes and the hippocampal subfields align correctly when I use Freesurfer's freeview to view them. But does that also mean they are in the same voxel space? And if they aren't in the same space, is there any way using Freesurfer that I can have the two in the same space? I really appreciate any suggestions! Thanks, Priyanka Mehta On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > wrote: of course On Tue, 25 Aug 2015, Priyanka wrote: > Thanks Bruce. Just wanted to make sure I've got the correct output. > > Really appreciate the help. > > Thanks again, > Priyanka Mehta > >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu > >> wrote: >> >> Hi Priyanka >> >> that is what mri_extract_label is designed to do. This facilitates making >> density maps in a common space. If you want to get the original label # back >> you can use something like: >> >> mri_binarize --match 128 --binval or something like that >> >> cheers >> Bruce >> >> >>> On Tue, 25 Aug 2015, Priyanka Mehta wrote: >>> >>> Reposting my question: >>> This happens for all the segments that I've tried to extract using >>> mri_extract_label. They all show up as 128 nerve after mri_extract_label. >>> Is >>> this a bug in the dev version? >>> Any help is greatly appreciated! >>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka < priyankamehta0...@gmail.com > >>> wrote: >>> This happens for all the segments that I've tried to extract >>> using mri_extract_label. They all show up as 128 nerve after >>> mri_extract_label. Is this a bug in the dev version? >>> >>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell >>> < ltirr...@nmr.mgh.harvard.edu > wrote: >>> > >>> > It seems that the command: >>> > >>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii >>> > >>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 >>> in lh.hippoSfLabels-T1.v10.mgz. You can run: >>> > >>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii >>> > >>> > and then the correct label names from the Lookup Table will >>> show up. >>> > >>> > Best, >>> > Lee >>> > >>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: >>> >> >>> >> Hi Eugenio >>> >> Thank you for the explanation, it makes sense to me now. >>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it >>> aligns correctly. However, when I view the segmentation >>> >> with color map set to Lookup Table and 'show existing labels >>> only' checked, the lh.CA1.nii segment shows as 128 Nerve >>> >> label. Shouldn't it still be showing up as 206 CA1 label? I >>> am confused. >>> >> >>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias >>> < e.igles...@bcbl.eu > wrote: >>> >> Hi Prya, >>> >> that is because MriCron is not that great at overlaying >>> images that are in the same physical space but not >>> >> in the same voxel space. You have two options here: >>> >> 1. Use FreeSurfer's Freeview rather than MriCron to >>> visualize the output. FreeView will correctly overlay >>> >> the segmentation. >>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than >>> lh.hippoSfLabels-T1.v10.mgz) when you call >>> >> mri_extract_label. That volume lives in the same voxel >>> space as T1.nii, and should be prope
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi again I want to use my hippocampal segmentation for masking 2380 brain volumes. Is there a way to find out using Freesurfer if the hippocampal subfields and the 2380 volumes are in the same space? The mean of the 2380 volumes and the hippocampal subfields align correctly when I use Freesurfer's freeview to view them. But does that also mean they are in the same voxel space? And if they aren't in the same space, is there any way using Freesurfer that I can have the two in the same space? I really appreciate any suggestions! Thanks, Priyanka Mehta On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > of course > On Tue, 25 Aug 2015, Priyanka wrote: > > > Thanks Bruce. Just wanted to make sure I've got the correct output. > > > > Really appreciate the help. > > > > Thanks again, > > Priyanka Mehta > > > >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> > >> Hi Priyanka > >> > >> that is what mri_extract_label is designed to do. This facilitates > making density maps in a common space. If you want to get the original > label # back you can use something like: > >> > >> mri_binarize --match 128 --binval or something like > that > >> > >> cheers > >> Bruce > >> > >> > >>> On Tue, 25 Aug 2015, Priyanka Mehta wrote: > >>> > >>> Reposting my question: > >>> This happens for all the segments that I've tried to extract using > >>> mri_extract_label. They all show up as 128 nerve after > mri_extract_label. Is > >>> this a bug in the dev version? > >>> Any help is greatly appreciated! > >>> On Thu, Aug 20, 2015 at 3:45 PM, Priyanka <priyankamehta0...@gmail.com > > > >>> wrote: > >>> This happens for all the segments that I've tried to extract > >>> using mri_extract_label. They all show up as 128 nerve after > >>> mri_extract_label. Is this a bug in the dev version? > >>> > >>> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell > >>> <ltirr...@nmr.mgh.harvard.edu> wrote: > >>> > > >>> > It seems that the command: > >>> > > >>> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii > >>> > > >>> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 > >>> in lh.hippoSfLabels-T1.v10.mgz. You can run: > >>> > > >>> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii > >>> > > >>> > and then the correct label names from the Lookup Table will > >>> show up. > >>> > > >>> > Best, > >>> > Lee > >>> > > >>> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: > >>> >> > >>> >> Hi Eugenio > >>> >> Thank you for the explanation, it makes sense to me now. > >>> >> When I use Freeview to overlay my lh.CA1.nii on T1.nii, it > >>> aligns correctly. However, when I view the segmentation > >>> >> with color map set to Lookup Table and 'show existing labels > >>> only' checked, the lh.CA1.nii segment shows as 128 Nerve > >>> >> label. Shouldn't it still be showing up as 206 CA1 label? I > >>> am confused. > >>> >> > >>> >> On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias > >>> <e.igles...@bcbl.eu> wrote: > >>> >> Hi Prya, > >>> >> that is because MriCron is not that great at overlaying > >>> images that are in the same physical space but not > >>> >> in the same voxel space. You have two options here: > >>> >> 1. Use FreeSurfer's Freeview rather than MriCron to > >>> visualize the output. FreeView will correctly overlay > >>> >> the segmentation. > >>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than > >>> lh.hippoSfLabels-T1.v10.mgz) when you call > >>> >> mri_extract_label. That volume lives in the same voxel > >>> space as T1.nii, and should be properly overlayed > >>> >> by MriCron. However, the resolution of the segmentation > >>> will be 1 mm, rather than the 0.333 mm t
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Priyanka
that is what mri_extract_label is designed to do. This facilitates making
density maps in a common space. If you want to get the original label #
back you can use something like:
mri_binarize --match 128 --binval output label # or something like that
cheers
Bruce
On Tue, 25 Aug 2015, Priyanka Mehta wrote:
Reposting my question:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?
Any help is greatly appreciated!
On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:
This happens for all the segments that I've tried to extract
using mri_extract_label. They all show up as 128 nerve after
mri_extract_label. Is this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell
ltirr...@nmr.mgh.harvard.edu wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206
in lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will
show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
aligns correctly. However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels
only' checked, the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I
am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying
images that are in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to
visualize the output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel
space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation
will be 1 mm, rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject
${subject} -hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii,
however the alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was
extracted from the same T1 image, they should
technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt
response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Bruce. Just wanted to make sure I've got the correct output.
Really appreciate the help.
Thanks again,
Priyanka Mehta
On Aug 25, 2015, at 4:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Priyanka
that is what mri_extract_label is designed to do. This facilitates making
density maps in a common space. If you want to get the original label # back
you can use something like:
mri_binarize --match 128 --binval output label # or something like that
cheers
Bruce
On Tue, 25 Aug 2015, Priyanka Mehta wrote:
Reposting my question:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?
Any help is greatly appreciated!
On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:
This happens for all the segments that I've tried to extract
using mri_extract_label. They all show up as 128 nerve after
mri_extract_label. Is this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell
ltirr...@nmr.mgh.harvard.edu wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206
in lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will
show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
aligns correctly. However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels
only' checked, the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I
am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying
images that are in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to
visualize the output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel
space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation
will be 1 mm, rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject
${subject} -hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii,
however the alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was
extracted from the same T1 image, they should
technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt
response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Reposting my question:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label.
Is this a bug in the dev version?
Any help is greatly appreciated!
On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label.
Is this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu
wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
correctly. However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only'
checked, the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images
that are in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the
output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel space as
T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1
mm, rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz
206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was extracted
from the same T1 image, they should
technically be in the same space and therefore should align
correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get
from the previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are
interested in CA1 (label 206), you can
run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
of course
On Tue, 25 Aug 2015, Priyanka wrote:
Thanks Bruce. Just wanted to make sure I've got the correct output.
Really appreciate the help.
Thanks again,
Priyanka Mehta
On Aug 25, 2015, at 4:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Priyanka
that is what mri_extract_label is designed to do. This facilitates making
density maps in a common space. If you want to get the original label # back
you can use something like:
mri_binarize --match 128 --binval output label # or something like that
cheers
Bruce
On Tue, 25 Aug 2015, Priyanka Mehta wrote:
Reposting my question:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?
Any help is greatly appreciated!
On Thu, Aug 20, 2015 at 3:45 PM, Priyanka priyankamehta0...@gmail.com
wrote:
This happens for all the segments that I've tried to extract
using mri_extract_label. They all show up as 128 nerve after
mri_extract_label. Is this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell
ltirr...@nmr.mgh.harvard.edu wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206
in lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will
show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it
aligns correctly. However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels
only' checked, the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I
am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying
images that are in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to
visualize the output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel
space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation
will be 1 mm, rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra:
www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version
Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject
${subject} -hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii,
however the alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was
extracted from the same T1 image, they should
technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt
response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias
e.igles...@bcbl.eu wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is
this a bug in the dev version?
On Aug 20, 2015, at 3:20 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote:
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly.
However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only' checked,
the lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are
in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the
output. FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel space as T1.nii,
and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was extracted from
the same T1 image, they should
technically be in the same space and therefore should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from
the previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are
interested in CA1 (label 206), you can
run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in
the 6.0 dev version.
I used the following command: recon
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
It seems that the command:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
lh.hippoSfLabels-T1.v10.mgz. You can run:
mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
and then the correct label names from the Lookup Table will show up.
Best,
Lee
On Thu, 20 Aug 2015, Priyanka Mehta wrote:
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns correctly.
However, when I view the segmentation
with color map set to Lookup Table and 'show existing labels only' checked, the
lh.CA1.nii segment shows as 128 Nerve
label. Shouldn't it still be showing up as 206 CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are
in the same physical space but not
in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay
the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call
mri_extract_label. That volume lives in the same voxel space as T1.nii,
and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd
get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted
the left CA1 using mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206
lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached
picture).
I wonder what is causing this issue? Since the CA1 was extracted from the
same T1 image, they should
technically be in the same space and therefore should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are
interested in CA1 (label 206), you can
run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all
-hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v
lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
correctly. However, when I view the segmentation with color map set to
Lookup Table and 'show existing labels only' checked, the lh.CA1.nii
segment shows as 128 Nerve label. Shouldn't it still be showing up as 206
CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Prya,
that is because MriCron is not that great at overlaying images that are in
the same physical space but not in the same voxel space. You have two
options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume
lives in the same voxel space as T1.nii, and should be properly overlayed
by MriCron. However, the resolution of the segmentation will be 1 mm,
rather than the 0.333 mm that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
alignment is not correct (see attached picture).
I wonder what is causing this issue? Since the CA1 was extracted from the
same T1 image, they should technically be in the same space and therefore
should align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta
priyankamehta0...@gmail.com wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Prya,
that is because MriCron is not that great at overlaying images that are in the
same physical space but not in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume lives
in the same voxel space as T1.nii, and should be properly overlayed by MriCron.
However, the resolution of the segmentation will be 1 mm, rather than the 0.333
mm that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the alignment is
not correct (see attached picture).
I wonder what is causing this issue? Since the CA1 was extracted from the same
T1 image, they should technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta priyankamehta0...@gmail.com
wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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
Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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is
addressed. If you believe this e-mail was sent to you in error and the
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HelpLine at
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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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
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[Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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
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