Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer....
VP From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer....
VP
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz. That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So , I would like to export results of segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, with freesurfer I can have more parameters than with freesurfer. Does it exist another way for get measurements with surfaces ( not generated by Freesurfer)? Thx . VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer....
VP
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz. That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
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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.
it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So , I would like to export results of segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, with freesurfer I can have more parameters than with freesurfer. Does it exist another way for get measurements with surfaces ( not generated by Freesurfer)? Thx .
VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer....
VP
__
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz. That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created wi
th
Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
_______________________________________________ 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.
Hi bruce, I want cortical thickness, total surface area, instrinsec curvature index and folfing index. VP
Date: Wed, 20 Mar 2013 13:09:54 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So , I would like to export results of segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, with freesurfer I can have more parameters than with freesurfer. Does it exist another way for get measurements with surfaces ( not generated by Freesurfer)? Thx .
VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer....
VP
__
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz. That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created wi
th
Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way.
VP
_______________________________________________ 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
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.
I see. For thickness you will need both white and pial, and you can use mris_thickness to compute it. The easiest thing to do would be to run recon-all on a subject then replace the surfaces with your own when it has completed (and recompute the thickness) On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi bruce, I want cortical thickness, total surface area, instrinsec curvature index and folfing index.
VP
Date: Wed, 20 Mar 2013 13:09:54 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So
, I would like to export results of
segmentation with Brainsuite and make measurements with FreeSurfer. In Fac
t, with freesurfer I can have more parameters
than with freesurfer. Does it exist another way for get measurements with surfaces ( not generat
ed by Freesurfer)?
Thx .
VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't
open the file in Freesurfer with tksurfer....
VP
__
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would l
ike to get measurements with FreeSurfer. SO, I
convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to
be usable with Freesurfer. Then, I tried to get
measurements with the command .'mris_anatomical_stats' . with the file
created previously in Matlab (I called it
'rh.pial'). But I got this error like the system is not able to read wm
.mgz.
That's why I thought I could juste replace th 'rh.pial' of the segmentat
ion with Freesurfey by the 'rh.pial' created wi
th
Matalb and then run mris_anatomical_Stats. IS this a good approximation.
Could you recommand another way.
VP
_______________________________________________ Freesurfer mailing list Fr
eesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on 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 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Valtina Pouegue