Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface?
Thanks!
you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header
after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image?
Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab?
Thanks!
Date: Mon, 3 Mar 2014 14:20:55 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header
after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image?
It should be a functional image. If the ica maps come from an individual, then use the mean functional for that subject or whatever you used for fMRI motion correction (which should be aligned with the ica maps). If it is in a group space, then use the registration target (that is exactly the same size as your maps).
Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab?
For projfrac we usually use .5. You can ignore src_type. For output type, you can use nii (nifti) and then use MRIread.m doug
Thanks!
Date: Mon, 3 Mar 2014 14:20:55 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the
surface?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Dear Doug,
I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).
Thanks!
Date: Tue, 4 Mar 2014 10:37:19 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header
after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image?
It should be a functional image. If the ica maps come from an individual, then use the mean functional for that subject or whatever you used for fMRI motion correction (which should be aligned with the ica maps). If it is in a group space, then use the registration target (that is exactly the same size as your maps).
Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab?
For projfrac we usually use .5. You can ignore src_type. For output type, you can use nii (nifti) and then use MRIread.m doug
Thanks!
Date: Mon, 3 Mar 2014 14:20:55 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the
surface?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?
If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.
Bring up the overlay configuration window. You can control the frame/time point from there.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).
You can just specify the output file with a .nii extension doug
Thanks!
Date: Tue, 4 Mar 2014 10:37:19 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
Hi Doug, thanks for the quick reply. I've been playing around with
the
commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header
after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image?
It should be a functional image. If the ica maps come from an individual, then use the mean functional for that subject or whatever you used for fMRI motion correction (which should be aligned with the ica maps). If it is in a group space, then use the registration target (that is exactly the same size as your maps).
Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case? Also for --out_type, if I want an easy format to port to matlab?
For projfrac we usually use .5. You can ignore src_type. For output type, you can use nii (nifti) and then use MRIread.m doug
Thanks!
Date: Mon, 3 Mar 2014 14:20:55 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
you will need to create a registration between your volume
(maps) and
the anatomical. You can do this with bbregister. Then use
mri_vol2surf
to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
Hi,
I am trying to display the 20 ICA components in this nifti file
http://brainmap.org/icns/maps.zip
onto anatomical template they've provided here
http://brainmap.org/icns/colin_tlrc_1x1x1.nii
My question is:
How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the
surface?
Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?
Thanks again.
Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface following your instructions.
But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?
If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.
Bring up the overlay configuration window. You can control the frame/time point from there.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).
You can just specify the output file with a .nii extension
doug
Thanks!
> Date: Tue, 4 Mar 2014 10:37:19 -0500
> From: greve@nmr.mgh.harvard.edu
> To: andrewzhao@live.com.au; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
> > Hi Doug, thanks for the quick reply. I've been playing around with the
> > commands you suggested and managed to get what seemed like a good
> > registration by inspecting the green lines in tkregister.
> >
> > However, I wasn't actually sure if I put the correct input:
> >
> > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg
> > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1
> > --init-header
> >
> > after the '--mov' option should i be using the anatomical template or
> > the .nii file containing the 20 ICA components (4D)? I tried both
> > (changing the between the --t1 and --bold options) and the anatomical
> > template came out much better, but I thought the movable (--mov) is
> > meant to be the functional image?
> It should be a functional image. If the ica maps come from an
> individual, then use the mean functional for that subject or whatever
> you used for fMRI motion correction (which should be aligned with the
> ica maps). If it is in a group space, then use the registration target
> (that is exactly the same size as your maps).
> >
> > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac
> > options be set to in my case?
> > Also for --out_type, if I want an easy format to port to matlab?
> For projfrac we usually use .5. You can ignore src_type. For output
> type, you can use nii (nifti) and then use MRIread.m
> doug
> >
> > Thanks!
> >
> > > Date: Mon, 3 Mar 2014 14:20:55 -0500
> > > From: greve@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> > >
> > >
> > > you will need to create a registration between your volume (maps) and
> > > the anatomical. You can do this with bbregister. Then use mri_vol2surf
> > > to map your ICs to the surface
> > > doug
> > >
> > >
> > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
> > > >
> > > > Hi,
> > > >
> > > > I am trying to display the 20 ICA components in this nifti file
> > > >
> > > > http://brainmap.org/icns/maps.zip
> > > >
> > > > onto anatomical template they've provided here
> > > >
> > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii
> > > >
> > > > My question is:
> > > >
> > > > How do I extract only the cortical surface from the anatomical
> > > > template and overlay
> > > > it with only parts of each ICA component that intersects with the
> > surface?
> > > >
> > > >
> > > > Thanks!
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > 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.
> > >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> 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, 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.
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?
I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?
Can you be more specific? What are your vol2surf and fv command lines? Have you tried it in tksurfer?
Thanks again.
Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug, I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved: 1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.Bring up the overlay configuration window. You can control the frame/time point from there.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).You can just specify the output file with a .nii extension doug
Thanks! > Date: Tue, 4 Mar 2014 10:37:19 -0500 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > Hi Doug, thanks for the quick reply. I've been playing around with the > > commands you suggested and managed to get what seemed like a good > > registration by inspecting the green lines in tkregister. > > > > However, I wasn't actually sure if I put the correct input: > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 > > --init-header > > > > after the '--mov' option should i be using the anatomical template or > > the .nii file containing the 20 ICA components (4D)? I tried both > > (changing the between the --t1 and --bold options) and the anatomical > > template came out much better, but I thought the movable (--mov) is > > meant to be the functional image? > It should be a functional image. If the ica maps come from an > individual, then use the mean functional for that subject or whatever > you used for fMRI motion correction (which should be aligned with the > ica maps). If it is in a group space, then use the registration target > (that is exactly the same size as your maps). > > > > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac > > options be set to in my case? > > Also for --out_type, if I want an easy format to port to matlab? > For projfrac we usually use .5. You can ignore src_type. For output > type, you can use nii (nifti) and then use MRIread.m > doug > > > > Thanks! > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > > > > you will need to create a registration between your volume (maps) and > > > the anatomical. You can do this with bbregister. Then use mri_vol2surf > > > to map your ICs to the surface > > > doug > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > Hi, > > > > > > > > I am trying to display the 20 ICA components in this nifti file > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > onto anatomical template they've provided here > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > My question is: > > > > > > > > How do I extract only the cortical surface from the anatomical > > > > template and overlay > > > > it with only parts of each ICA component that intersects with the > > surface? > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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, 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 Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the layers seem to be also slightly offset in certain regions, I guess this again may be due to the fuzziness of the mov fmri data.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA components?
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?
I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?
Can you be more specific? What are your vol2surf and fv command lines? Have you tried it in tksurfer?
Thanks again.
Date: Tue, 4 Mar 2014 22:52:38 -0500
From: greve@nmr.mgh.harvard.edu
To: andrewzhao@live.com.au
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface following your instructions.
But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?
If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.
Bring up the overlay configuration window. You can control the frame/time point from there.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).
You can just specify the output file with a .nii extension
doug
Thanks!
> Date: Tue, 4 Mar 2014 10:37:19 -0500
> From: greve@nmr.mgh.harvard.edu
> To: andrewzhao@live.com.au; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
> > Hi Doug, thanks for the quick reply. I've been playing around with the
> > commands you suggested and managed to get what seemed like a good
> > registration by inspecting the green lines in tkregister.
> >
> > However, I wasn't actually sure if I put the correct input:
> >
> > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg
> > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1
> > --init-header
> >
> > after the '--mov' option should i be using the anatomical template or
> > the .nii file containing the 20 ICA components (4D)? I tried both
> > (changing the between the --t1 and --bold options) and the anatomical
> > template came out much better, but I thought the movable (--mov) is
> > meant to be the functional image?
> It should be a functional image. If the ica maps come from an
> individual, then use the mean functional for that subject or whatever
> you used for fMRI motion correction (which should be aligned with the
> ica maps). If it is in a group space, then use the registration target
> (that is exactly the same size as your maps).
> >
> > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac
> > options be set to in my case?
> > Also for --out_type, if I want an easy format to port to matlab?
> For projfrac we usually use .5. You can ignore src_type. For output
> type, you can use nii (nifti) and then use MRIread.m
> doug
> >
> > Thanks!
> >
> > > Date: Mon, 3 Mar 2014 14:20:55 -0500
> > > From: greve@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> > >
> > >
> > > you will need to create a registration between your volume (maps) and
> > > the anatomical. You can do this with bbregister. Then use mri_vol2surf
> > > to map your ICs to the surface
> > > doug
> > >
> > >
> > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
> > > >
> > > > Hi,
> > > >
> > > > I am trying to display the 20 ICA components in this nifti file
> > > >
> > > > http://brainmap.org/icns/maps.zip
> > > >
> > > > onto anatomical template they've provided here
> > > >
> > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii
> > > >
> > > > My question is:
> > > >
> > > > How do I extract only the cortical surface from the anatomical
> > > > template and overlay
> > > > it with only parts of each ICA component that intersects with the
> > surface?
> > > >
> > > >
> > > > Thanks!
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > 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.
> > >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> 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, 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.
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the layers seem to be also slightly offset in certain regions, I guess this again may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was generated from, so it should look perfect.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA components?
Sorry, what has to be mgz? What matlab command? What instructions? doug
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug, A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?Can you be more specific? What are your vol2surf and fv command lines? Have you tried it in tksurfer?
Thanks again. ------------------------------------------------------------------------ Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface On 3/4/14 7:18 PM, Xuelong Zhao wrote: Dear Doug, I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved: 1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient? If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size) 2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview. Bring up the overlay configuration window. You can control the frame/time point from there. 3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check). You can just specify the output file with a .nii extension doug Thanks! > Date: Tue, 4 Mar 2014 10:37:19 -0500 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > Hi Doug, thanks for the quick reply. I've been playing around with the > > commands you suggested and managed to get what seemed like a good > > registration by inspecting the green lines in tkregister. > > > > However, I wasn't actually sure if I put the correct input: > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 > > --init-header > > > > after the '--mov' option should i be using the anatomical template or > > the .nii file containing the 20 ICA components (4D)? I tried both > > (changing the between the --t1 and --bold options) and the anatomical > > template came out much better, but I thought the movable (--mov) is > > meant to be the functional image? > It should be a functional image. If the ica maps come from an > individual, then use the mean functional for that subject or whatever > you used for fMRI motion correction (which should be aligned with the > ica maps). If it is in a group space, then use the registration target > (that is exactly the same size as your maps). > > > > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac > > options be set to in my case? > > Also for --out_type, if I want an easy format to port to matlab? > For projfrac we usually use .5. You can ignore src_type. For output > type, you can use nii (nifti) and then use MRIread.m > doug > > > > Thanks! > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > > > > you will need to create a registration between your volume (maps) and > > > the anatomical. You can do this with bbregister. Then use mri_vol2surf > > > to map your ICs to the surface > > > doug > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > Hi, > > > > > > > > I am trying to display the 20 ICA components in this nifti file > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > onto anatomical template they've provided here > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > My question is: > > > > > > > > How do I extract only the cortical surface from the anatomical > > > > template and overlay > > > > it with only parts of each ICA component that intersects with the > > surface? > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
Date: Mon, 10 Mar 2014 11:25:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the layers seem to be also slightly offset in certain regions, I guess this again may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was generated from, so it should look perfect.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA components?
Sorry, what has to be mgz? What matlab command? What instructions? doug
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug, A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?Can you be more specific? What are your vol2surf and fv command lines? Have you tried it in tksurfer?
Thanks again. ------------------------------------------------------------------------ Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface On 3/4/14 7:18 PM, Xuelong Zhao wrote: Dear Doug, I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved: 1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient? If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size) 2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview. Bring up the overlay configuration window. You can control the frame/time point from there. 3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check). You can just specify the output file with a .nii extension doug Thanks! > Date: Tue, 4 Mar 2014 10:37:19 -0500 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > Hi Doug, thanks for the quick reply. I've been playing around with the > > commands you suggested and managed to get what seemed like a good > > registration by inspecting the green lines in tkregister. > > > > However, I wasn't actually sure if I put the correct input: > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 > > --init-header > > > > after the '--mov' option should i be using the anatomical template or > > the .nii file containing the 20 ICA components (4D)? I tried both > > (changing the between the --t1 and --bold options) and the anatomical > > template came out much better, but I thought the movable (--mov) is > > meant to be the functional image? > It should be a functional image. If the ica maps come from an > individual, then use the mean functional for that subject or whatever > you used for fMRI motion correction (which should be aligned with the > ica maps). If it is in a group space, then use the registration target > (that is exactly the same size as your maps). > > > > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac > > options be set to in my case? > > Also for --out_type, if I want an easy format to port to matlab? > For projfrac we usually use .5. You can ignore src_type. For output > type, you can use nii (nifti) and then use MRIread.m > doug > > > > Thanks! > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > > > > you will need to create a registration between your volume (maps) and > > > the anatomical. You can do this with bbregister. Then use mri_vol2surf > > > to map your ICs to the surface > > > doug > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > Hi, > > > > > > > > I am trying to display the 20 ICA components in this nifti file > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > onto anatomical template they've provided here > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > My question is: > > > > > > > > How do I extract only the cortical surface from the anatomical > > > > template and overlay > > > > it with only parts of each ICA component that intersects with the > > surface? > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au To: greve@nmr.mgh.harvard.edu Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
Date: Mon, 10 Mar 2014 11:25:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the layers seem to be also slightly offset in certain regions, I guess this again may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was generated from, so it should look perfect.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA components?
Sorry, what has to be mgz? What matlab command? What instructions? doug
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug, A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?Can you be more specific? What are your vol2surf and fv command lines? Have you tried it in tksurfer?
Thanks again. ------------------------------------------------------------------------ Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface On 3/4/14 7:18 PM, Xuelong Zhao wrote: Dear Doug, I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved: 1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient? If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size) 2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview. Bring up the overlay configuration window. You can control the frame/time point from there. 3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check). You can just specify the output file with a .nii extension doug Thanks! > Date: Tue, 4 Mar 2014 10:37:19 -0500 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > Hi Doug, thanks for the quick reply. I've been playing around with the > > commands you suggested and managed to get what seemed like a good > > registration by inspecting the green lines in tkregister. > > > > However, I wasn't actually sure if I put the correct input: > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 > > --init-header > > > > after the '--mov' option should i be using the anatomical template or > > the .nii file containing the 20 ICA components (4D)? I tried both > > (changing the between the --t1 and --bold options) and the anatomical > > template came out much better, but I thought the movable (--mov) is > > meant to be the functional image? > It should be a functional image. If the ica maps come from an > individual, then use the mean functional for that subject or whatever > you used for fMRI motion correction (which should be aligned with the > ica maps). If it is in a group space, then use the registration target > (that is exactly the same size as your maps). > > > > Also, wrt to mri_vol2surf, what should the --src_type, --projfrac > > options be set to in my case? > > Also for --out_type, if I want an easy format to port to matlab? > For projfrac we usually use .5. You can ignore src_type. For output > type, you can use nii (nifti) and then use MRIread.m > doug > > > > Thanks! > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > > > > you will need to create a registration between your volume (maps) and > > > the anatomical. You can do this with bbregister. Then use mri_vol2surf > > > to map your ICs to the surface > > > doug > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > Hi, > > > > > > > > I am trying to display the 20 ICA components in this nifti file > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > onto anatomical template they've provided here > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > My question is: > > > > > > > > How do I extract only the cortical surface from the anatomical > > > > template and overlay > > > > it with only parts of each ICA component that intersects with the > > surface? > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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 don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au To: greve@nmr.mgh.harvard.edu Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
Date: Mon, 10 Mar 2014 11:25:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the mov, whereas the target comparison looks very pristine. I was just wondering if this is expected. The mov, as I scroll through the
layers
seem to be also slightly offset in certain regions, I guess this
again
may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was generated from, so it should look perfect.
Regarding my second q:
I've got this working now- the segfault was due to me naively loading the surface image as a surface, instead of using it as an overlay, I can now successfully scroll through the various frames. However, I noticed that in the documentation to load into matlab, say the left pial surface (with the ICA components on it), I have to save it as a mgz file and then use MRI_read. However, freeview doesn't seem to offer this option once I load the pial surface and the the ICA
components?
Sorry, what has to be mgz? What matlab command? What instructions? doug
Date: Thu, 6 Mar 2014 10:19:25 -0500 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/6/14 6:39 AM, Xuelong Zhao wrote:
Hi Doug,
A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon-all. While, when I switch to the 'moveable' tab the green line seems to be slightly offset, but the underlying image is very fuzzy too. Is this an issue?
I don't know without seeing it. The mov is often lower resolution, so some fuzziness is expected.
Also, when I load the surface image in freeview produced by mri_vol2surf nothing seems to show up, even when I use the registration file. In fact, if I have other volumes loaded it causes freeview to segfault. When I do manage to load it successfully with the anatomical template in talairach space, it doesn't really show up and it seems that the anatomical template is really small and I have to zoom in a lot. Maybe I didn't process/register?
Can you be more specific? What are your vol2surf and fv command
lines?
Have you tried it in tksurfer?
Thanks again.
Date: Tue, 4 Mar 2014 22:52:38 -0500 From: greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
On 3/4/14 7:18 PM, Xuelong Zhao wrote:
Dear Doug,
I've managed to get functional information onto the cortical surface following your instructions. But, there's a few issues that are still not resolved:
1/ wrt to registration I believe the supplied anatomical template (in tailarach coords) is already aligned with the ica maps (which come from one individual). However, when I run mri_vol2surf I need a registration.dat file so in such a situation is the registration data from the anatomical template sufficient?
If the ica maps are in voxel-for-voxel alignment with the template then yes (i,e they must have the same dimension and voxel size)
2/ the nifti file for functional data actually contains 20 ICA components. After I ran mri_vol2surf how do I view each component independently? Currently it seems to only show one particular ICA component in freeview.
Bring up the overlay configuration window. You can control the frame/time point from there.
3/ using mri_vol2surf if I want .nii output do I specify thus: '--out_type nii' ? (i did this and it seemed to have worked, but just wanted to double check).
You can just specify the output file with a .nii extension doug
Thanks!
Date: Tue, 4 Mar 2014 10:37:19 -0500 From: greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au;
freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical
Surface
On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
Hi Doug, thanks for the quick reply. I've been playing
around with the
commands you suggested and managed to get what seemed like
a good
registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg
~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1
--init-header
after the '--mov' option should i be using the anatomical
template or
the .nii file containing the 20 ICA components (4D)? I
tried both
(changing the between the --t1 and --bold options) and the
anatomical
template came out much better, but I thought the movable
(--mov) is
meant to be the functional image?
It should be a functional image. If the ica maps come from an individual, then use the mean functional for that subject or
whatever
you used for fMRI motion correction (which should be aligned
with the
ica maps). If it is in a group space, then use the
registration target
(that is exactly the same size as your maps).
Also, wrt to mri_vol2surf, what should the --src_type,
--projfrac
options be set to in my case? Also for --out_type, if I want an easy format to port to
matlab?
For projfrac we usually use .5. You can ignore src_type. For
output
type, you can use nii (nifti) and then use MRIread.m doug
Thanks!
Date: Mon, 3 Mar 2014 14:20:55 -0500 From: greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on
Cortical Surface
you will need to create a registration between your
volume (maps) and
the anatomical. You can do this with bbregister. Then
use mri_vol2surf
to map your ICs to the surface doug
On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > Hi, > > I am trying to display the 20 ICA components in this
nifti file
> > http://brainmap.org/icns/maps.zip > > onto anatomical template they've provided here > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > My question is: > > How do I extract only the cortical surface from the
anatomical
> template and overlay > it with only parts of each ICA component that
intersects with the
surface?
> > > Thanks! > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the
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the e-mail
contains patient information, please contact the
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HelpLine at
http://www.partners.org/complianceline . If the e-mail
was sent to
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dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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.
Okay, I think I'm getting close to what I want in the matlab object. I've successfully imported both the pial surface (using read_surf.m) and the ICA components on the surface in mgh format using MRIread.m
I've had a look at the MRIread.m script and it says I can use vox2ras1 to convert column, row, and slice to XYZ coordinates. Which field of the matlab structure should I apply this to? I"m guessing its voxels but wanted to make sure, and also I'd have to do this for each individual frame? Thanks.
Date: Mon, 10 Mar 2014 23:54:18 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
I don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au
To: greve@nmr.mgh.harvard.edu
Date: Tue, 11 Mar 2014 11:54:10 +1100
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
> Date: Mon, 10 Mar 2014 11:25:23 -0400
> From: greve@nmr.mgh.harvard.edu
> To: andrewzhao@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> > Hi Doug,
> >
> > To clarify my previous question:
> >
> > There is definitely some fuzziness when comparing with the mov,
> > whereas the target comparison looks very pristine. I was just
> > wondering if this is expected. The mov, as I scroll through the layers
> > seem to be also slightly offset in certain regions, I guess this again
> > may be due to the fuzziness of the mov fmri data.
> Yes this is somewhat expected. The target is the data the surface was
> generated from, so it should look perfect.
> >
> > Regarding my second q:
> >
> > I've got this working now- the segfault was due to me naively loading
> > the surface image as a surface, instead of using it as an overlay, I
> > can now successfully scroll through the various frames. However, I
> > noticed that in the documentation to load into matlab, say the left
> > pial surface (with the ICA components on it), I have to save it as a
> > mgz file and then use MRI_read. However, freeview doesn't seem to
> > offer this option once I load the pial surface and the the ICA components?
>
> Sorry, what has to be mgz? What matlab command? What instructions?
> doug
>
> >
> >
> > ------------------------------------------------------------------------
> > Date: Thu, 6 Mar 2014 10:19:25 -0500
> > From: greve@nmr.mgh.harvard.edu
> > To: andrewzhao@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/6/14 6:39 AM, Xuelong Zhao wrote:
> >
> > Hi Doug,
> >
> > A follow-up. I've gone back and re-done the registration using
> > nifti file with the ICA20 maps. I noticed in tkregister2 that when
> > I press on the TARGET tab there is extremely good alignment ( i
> > think it is to 'orig.mgz' in the mri folder of my subject which I
> > had processed using recon-all. While, when I switch to the
> > 'moveable' tab the green line seems to be slightly offset, but the
> > underlying image is very fuzzy too. Is this an issue?
> >
> > I don't know without seeing it. The mov is often lower resolution, so
> > some fuzziness is expected.
> >
> >
> > Also, when I load the surface image in freeview produced by
> > mri_vol2surf nothing seems to show up, even when I use the
> > registration file. In fact, if I have other volumes loaded it
> > causes freeview to segfault. When I do manage to load it
> > successfully with the anatomical template in talairach space, it
> > doesn't really show up and it seems that the anatomical template
> > is really small and I have to zoom in a lot. Maybe I didn't
> > process/register?
> >
> > Can you be more specific? What are your vol2surf and fv command lines?
> > Have you tried it in tksurfer?
> >
> >
> > Thanks again.
> >
> > ------------------------------------------------------------------------
> > Date: Tue, 4 Mar 2014 22:52:38 -0500
> > From: greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/4/14 7:18 PM, Xuelong Zhao wrote:
> >
> > Dear Doug,
> >
> > I've managed to get functional information onto the cortical
> > surface following your instructions.
> > But, there's a few issues that are still not resolved:
> >
> > 1/ wrt to registration I believe the supplied anatomical
> > template (in tailarach coords) is already aligned with the ica
> > maps (which come from one individual). However, when I run
> > mri_vol2surf I need a registration.dat file so in such a
> > situation is the registration data from the anatomical
> > template sufficient?
> >
> > If the ica maps are in voxel-for-voxel alignment with the template
> > then yes (i,e they must have the same dimension and voxel size)
> >
> >
> > 2/ the nifti file for functional data actually contains 20 ICA
> > components. After I ran mri_vol2surf how do I view each
> > component independently? Currently it seems to only show one
> > particular ICA component in freeview.
> >
> > Bring up the overlay configuration window. You can control the
> > frame/time point from there.
> >
> >
> > 3/ using mri_vol2surf if I want .nii output do I specify thus:
> > '--out_type nii' ? (i did this and it seemed to have worked,
> > but just wanted to double check).
> >
> > You can just specify the output file with a .nii extension
> > doug
> >
> >
> >
> > Thanks!
> >
> > > Date: Tue, 4 Mar 2014 10:37:19 -0500
> > > From: greve@nmr.mgh.harvard.edu
> > mailto:greve@nmr.mgh.harvard.edu
> > > To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au;
> > freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical
> > Surface
> > >
> > >
> > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
> > > > Hi Doug, thanks for the quick reply. I've been playing
> > around with the
> > > > commands you suggested and managed to get what seemed like
> > a good
> > > > registration by inspecting the green lines in tkregister.
> > > >
> > > > However, I wasn't actually sure if I put the correct input:
> > > >
> > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg
> > > >
> > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat
> > --t1
> > > > --init-header
> > > >
> > > > after the '--mov' option should i be using the anatomical
> > template or
> > > > the .nii file containing the 20 ICA components (4D)? I
> > tried both
> > > > (changing the between the --t1 and --bold options) and the
> > anatomical
> > > > template came out much better, but I thought the movable
> > (--mov) is
> > > > meant to be the functional image?
> > > It should be a functional image. If the ica maps come from an
> > > individual, then use the mean functional for that subject or
> > whatever
> > > you used for fMRI motion correction (which should be aligned
> > with the
> > > ica maps). If it is in a group space, then use the
> > registration target
> > > (that is exactly the same size as your maps).
> > > >
> > > > Also, wrt to mri_vol2surf, what should the --src_type,
> > --projfrac
> > > > options be set to in my case?
> > > > Also for --out_type, if I want an easy format to port to
> > matlab?
> > > For projfrac we usually use .5. You can ignore src_type. For
> > output
> > > type, you can use nii (nifti) and then use MRIread.m
> > > doug
> > > >
> > > > Thanks!
> > > >
> > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500
> > > > > From: greve@nmr.mgh.harvard.edu
> > mailto:greve@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] Resting State Networks on
> > Cortical Surface
> > > > >
> > > > >
> > > > > you will need to create a registration between your
> > volume (maps) and
> > > > > the anatomical. You can do this with bbregister. Then
> > use mri_vol2surf
> > > > > to map your ICs to the surface
> > > > > doug
> > > > >
> > > > >
> > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I am trying to display the 20 ICA components in this
> > nifti file
> > > > > >
> > > > > > http://brainmap.org/icns/maps.zip
> > > > > >
> > > > > > onto anatomical template they've provided here
> > > > > >
> > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii
> > > > > >
> > > > > > My question is:
> > > > > >
> > > > > > How do I extract only the cortical surface from the
> > anatomical
> > > > > > template and overlay
> > > > > > it with only parts of each ICA component that
> > intersects with the
> > > > surface?
> > > > > >
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > Freesurfer mailing list
> > > > > > Freesurfer@nmr.mgh.harvard.edu
> > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
> > > > > --
> > > > > Douglas N. Greve, Ph.D.
> > > > > MGH-NMR Center
> > > > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > > > > Phone Number: 617-724-2358
> > > > > Fax: 617-726-7422
> > > > >
> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > mailto: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.
> > > > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > _______________________________________________ Freesurfer mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> > mailto: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.
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
_______________________________________________ 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.
You would apply it to the column, row, and slice of a voxel. Note that the volume structure is volume(row,col,slice). But I'm not sure why you need to do this. If you read in the ICA maps after running mri_vol2surf, there will be a value for each vertex, no need to do any mapping
doug
On 3/11/14 7:00 PM, Xuelong Zhao wrote:
Okay, I think I'm getting close to what I want in the matlab object. I've successfully imported both the pial surface (using read_surf.m) and the ICA components on the surface in mgh format using MRIread.m
I've had a look at the MRIread.m script and it says I can use vox2ras1 to convert column, row, and slice to XYZ coordinates. Which field of the matlab structure should I apply this to? I"m guessing its voxels but wanted to make sure, and also I'd have to do this for each individual frame? Thanks.
Date: Mon, 10 Mar 2014 23:54:18 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
I don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks. ------------------------------------------------------------------------ From: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> To: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface Regarding matlab: Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components. I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks. > Date: Mon, 10 Mar 2014 11:25:23 -0400 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/09/2014 09:12 AM, Xuelong Zhao wrote: > > Hi Doug, > > > > To clarify my previous question: > > > > There is definitely some fuzziness when comparing with the mov, > > whereas the target comparison looks very pristine. I was just > > wondering if this is expected. The mov, as I scroll through the layers > > seem to be also slightly offset in certain regions, I guess this again > > may be due to the fuzziness of the mov fmri data. > Yes this is somewhat expected. The target is the data the surface was > generated from, so it should look perfect. > > > > Regarding my second q: > > > > I've got this working now- the segfault was due to me naively loading > > the surface image as a surface, instead of using it as an overlay, I > > can now successfully scroll through the various frames. However, I > > noticed that in the documentation to load into matlab, say the left > > pial surface (with the ICA components on it), I have to save it as a > > mgz file and then use MRI_read. However, freeview doesn't seem to > > offer this option once I load the pial surface and the the ICA components? > > Sorry, what has to be mgz? What matlab command? What instructions? > doug > > > > > > > ------------------------------------------------------------------------ > > Date: Thu, 6 Mar 2014 10:19:25 -0500 > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> > > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/6/14 6:39 AM, Xuelong Zhao wrote: > > > > Hi Doug, > > > > A follow-up. I've gone back and re-done the registration using > > nifti file with the ICA20 maps. I noticed in tkregister2 that when > > I press on the TARGET tab there is extremely good alignment ( i > > think it is to 'orig.mgz' in the mri folder of my subject which I > > had processed using recon-all. While, when I switch to the > > 'moveable' tab the green line seems to be slightly offset, but the > > underlying image is very fuzzy too. Is this an issue? > > > > I don't know without seeing it. The mov is often lower resolution, so > > some fuzziness is expected. > > > > > > Also, when I load the surface image in freeview produced by > > mri_vol2surf nothing seems to show up, even when I use the > > registration file. In fact, if I have other volumes loaded it > > causes freeview to segfault. When I do manage to load it > > successfully with the anatomical template in talairach space, it > > doesn't really show up and it seems that the anatomical template > > is really small and I have to zoom in a lot. Maybe I didn't > > process/register? > > > > Can you be more specific? What are your vol2surf and fv command lines? > > Have you tried it in tksurfer? > > > > > > Thanks again. > > > > ------------------------------------------------------------------------ > > Date: Tue, 4 Mar 2014 22:52:38 -0500 > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> > > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/4/14 7:18 PM, Xuelong Zhao wrote: > > > > Dear Doug, > > > > I've managed to get functional information onto the cortical > > surface following your instructions. > > But, there's a few issues that are still not resolved: > > > > 1/ wrt to registration I believe the supplied anatomical > > template (in tailarach coords) is already aligned with the ica > > maps (which come from one individual). However, when I run > > mri_vol2surf I need a registration.dat file so in such a > > situation is the registration data from the anatomical > > template sufficient? > > > > If the ica maps are in voxel-for-voxel alignment with the template > > then yes (i,e they must have the same dimension and voxel size) > > > > > > 2/ the nifti file for functional data actually contains 20 ICA > > components. After I ran mri_vol2surf how do I view each > > component independently? Currently it seems to only show one > > particular ICA component in freeview. > > > > Bring up the overlay configuration window. You can control the > > frame/time point from there. > > > > > > 3/ using mri_vol2surf if I want .nii output do I specify thus: > > '--out_type nii' ? (i did this and it seemed to have worked, > > but just wanted to double check). > > > > You can just specify the output file with a .nii extension > > doug > > > > > > > > Thanks! > > > > > Date: Tue, 4 Mar 2014 10:37:19 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au>; > > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical > > Surface > > > > > > > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > > > Hi Doug, thanks for the quick reply. I've been playing > > around with the > > > > commands you suggested and managed to get what seemed like > > a good > > > > registration by inspecting the green lines in tkregister. > > > > > > > > However, I wasn't actually sure if I put the correct input: > > > > > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > > > > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat > > --t1 > > > > --init-header > > > > > > > > after the '--mov' option should i be using the anatomical > > template or > > > > the .nii file containing the 20 ICA components (4D)? I > > tried both > > > > (changing the between the --t1 and --bold options) and the > > anatomical > > > > template came out much better, but I thought the movable > > (--mov) is > > > > meant to be the functional image? > > > It should be a functional image. If the ica maps come from an > > > individual, then use the mean functional for that subject or > > whatever > > > you used for fMRI motion correction (which should be aligned > > with the > > > ica maps). If it is in a group space, then use the > > registration target > > > (that is exactly the same size as your maps). > > > > > > > > Also, wrt to mri_vol2surf, what should the --src_type, > > --projfrac > > > > options be set to in my case? > > > > Also for --out_type, if I want an easy format to port to > > matlab? > > > For projfrac we usually use .5. You can ignore src_type. For > > output > > > type, you can use nii (nifti) and then use MRIread.m > > > doug > > > > > > > > Thanks! > > > > > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Subject: Re: [Freesurfer] Resting State Networks on > > Cortical Surface > > > > > > > > > > > > > > > you will need to create a registration between your > > volume (maps) and > > > > > the anatomical. You can do this with bbregister. Then > > use mri_vol2surf > > > > > to map your ICs to the surface > > > > > doug > > > > > > > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > > > > > Hi, > > > > > > > > > > > > I am trying to display the 20 ICA components in this > > nifti file > > > > > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > > > > > onto anatomical template they've provided here > > > > > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > > > > > My question is: > > > > > > > > > > > > How do I extract only the cortical surface from the > > anatomical > > > > > > template and overlay > > > > > > it with only parts of each ICA component that > > intersects with the > > > > surface? > > > > > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Hmm, it seems I may have misinterpreted the fields in the matlab structure after using MRIRead
rsn20_surf = MRIread('rsn20_surf.nii')
I thought perhaps the data would be in the 'volsize' field?
rsn20_surf =
srcbext: '' analyzehdr: [] bhdr: [] vol: [4-D double] niftihdr: [1x1 struct] fspec: 'rsn20_surf.nii' pwd: '~/rsn_smith09' flip_angle: 0 tr: 1000 te: 0 ti: 0 vox2ras0: [4x4 double] volsize: [1 139732 1] height: 1 width: 139732 depth: 1 nframes: 20 vox2ras: [4x4 double] nvoxels: 139732 xsize: 1 ysize: 1 zsize: 1 x_r: -1 x_a: 0 x_s: 0 y_r: 0 y_a: 1 y_s: 0 z_r: 0 z_a: 0 z_s: 1 c_r: -1 c_a: -17 c_s: 19 vox2ras1: [4x4 double] Mdc: [3x3 double] volres: [1 1 1] tkrvox2ras: [4x4 double]
Date: Wed, 12 Mar 2014 10:55:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
You would apply it to the column, row, and slice of a voxel. Note that the volume structure is volume(row,col,slice). But I'm not sure why you need to do this. If you read in the ICA maps after running mri_vol2surf, there will be a value for each vertex, no need to do any mapping
doug
On 3/11/14 7:00 PM, Xuelong Zhao wrote:
Okay, I think I'm getting close to what I want in the matlab object. I've successfully imported both the pial surface (using read_surf.m) and the ICA components on the surface in mgh format using MRIread.m
I've had a look at the MRIread.m script and it says I can use vox2ras1 to convert column, row, and slice to XYZ coordinates. Which field of the matlab structure should I apply this to? I"m guessing its voxels but wanted to make sure, and also I'd have to do this for each individual frame? Thanks.
Date: Mon, 10 Mar 2014 23:54:18 -0400
From: greve@nmr.mgh.harvard.edu
To: andrewzhao@live.com.au
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
I don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks.
From: andrewzhao@live.com.au
To: greve@nmr.mgh.harvard.edu
Date: Tue, 11 Mar 2014 11:54:10 +1100
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks.
> Date: Mon, 10 Mar 2014 11:25:23 -0400
> From: greve@nmr.mgh.harvard.edu
> To: andrewzhao@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> > Hi Doug,
> >
> > To clarify my previous question:
> >
> > There is definitely some fuzziness when comparing with the mov,
> > whereas the target comparison looks very pristine. I was just
> > wondering if this is expected. The mov, as I scroll through the layers
> > seem to be also slightly offset in certain regions, I guess this again
> > may be due to the fuzziness of the mov fmri data.
> Yes this is somewhat expected. The target is the data the surface was
> generated from, so it should look perfect.
> >
> > Regarding my second q:
> >
> > I've got this working now- the segfault was due to me naively loading
> > the surface image as a surface, instead of using it as an overlay, I
> > can now successfully scroll through the various frames. However, I
> > noticed that in the documentation to load into matlab, say the left
> > pial surface (with the ICA components on it), I have to save it as a
> > mgz file and then use MRI_read. However, freeview doesn't seem to
> > offer this option once I load the pial surface and the the ICA components?
>
> Sorry, what has to be mgz? What matlab command? What instructions?
> doug
>
> >
> >
> > ------------------------------------------------------------------------
> > Date: Thu, 6 Mar 2014 10:19:25 -0500
> > From: greve@nmr.mgh.harvard.edu
> > To: andrewzhao@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/6/14 6:39 AM, Xuelong Zhao wrote:
> >
> > Hi Doug,
> >
> > A follow-up. I've gone back and re-done the registration using
> > nifti file with the ICA20 maps. I noticed in tkregister2 that when
> > I press on the TARGET tab there is extremely good alignment ( i
> > think it is to 'orig.mgz' in the mri folder of my subject which I
> > had processed using recon-all. While, when I switch to the
> > 'moveable' tab the green line seems to be slightly offset, but the
> > underlying image is very fuzzy too. Is this an issue?
> >
> > I don't know without seeing it. The mov is often lower resolution, so
> > some fuzziness is expected.
> >
> >
> > Also, when I load the surface image in freeview produced by
> > mri_vol2surf nothing seems to show up, even when I use the
> > registration file. In fact, if I have other volumes loaded it
> > causes freeview to segfault. When I do manage to load it
> > successfully with the anatomical template in talairach space, it
> > doesn't really show up and it seems that the anatomical template
> > is really small and I have to zoom in a lot. Maybe I didn't
> > process/register?
> >
> > Can you be more specific? What are your vol2surf and fv command lines?
> > Have you tried it in tksurfer?
> >
> >
> > Thanks again.
> >
> > ------------------------------------------------------------------------
> > Date: Tue, 4 Mar 2014 22:52:38 -0500
> > From: greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/4/14 7:18 PM, Xuelong Zhao wrote:
> >
> > Dear Doug,
> >
> > I've managed to get functional information onto the cortical
> > surface following your instructions.
> > But, there's a few issues that are still not resolved:
> >
> > 1/ wrt to registration I believe the supplied anatomical
> > template (in tailarach coords) is already aligned with the ica
> > maps (which come from one individual). However, when I run
> > mri_vol2surf I need a registration.dat file so in such a
> > situation is the registration data from the anatomical
> > template sufficient?
> >
> > If the ica maps are in voxel-for-voxel alignment with the template
> > then yes (i,e they must have the same dimension and voxel size)
> >
> >
> > 2/ the nifti file for functional data actually contains 20 ICA
> > components. After I ran mri_vol2surf how do I view each
> > component independently? Currently it seems to only show one
> > particular ICA component in freeview.
> >
> > Bring up the overlay configuration window. You can control the
> > frame/time point from there.
> >
> >
> > 3/ using mri_vol2surf if I want .nii output do I specify thus:
> > '--out_type nii' ? (i did this and it seemed to have worked,
> > but just wanted to double check).
> >
> > You can just specify the output file with a .nii extension
> > doug
> >
> >
> >
> > Thanks!
> >
> > > Date: Tue, 4 Mar 2014 10:37:19 -0500
> > > From: greve@nmr.mgh.harvard.edu
> > mailto:greve@nmr.mgh.harvard.edu
> > > To: andrewzhao@live.com.au mailto:andrewzhao@live.com.au;
> > freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical
> > Surface
> > >
> > >
> > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote:
> > > > Hi Doug, thanks for the quick reply. I've been playing
> > around with the
> > > > commands you suggested and managed to get what seemed like
> > a good
> > > > registration by inspecting the green lines in tkregister.
> > > >
> > > > However, I wasn't actually sure if I put the correct input:
> > > >
> > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg
> > > >
> > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat
> > --t1
> > > > --init-header
> > > >
> > > > after the '--mov' option should i be using the anatomical
> > template or
> > > > the .nii file containing the 20 ICA components (4D)? I
> > tried both
> > > > (changing the between the --t1 and --bold options) and the
> > anatomical
> > > > template came out much better, but I thought the movable
> > (--mov) is
> > > > meant to be the functional image?
> > > It should be a functional image. If the ica maps come from an
> > > individual, then use the mean functional for that subject or
> > whatever
> > > you used for fMRI motion correction (which should be aligned
> > with the
> > > ica maps). If it is in a group space, then use the
> > registration target
> > > (that is exactly the same size as your maps).
> > > >
> > > > Also, wrt to mri_vol2surf, what should the --src_type,
> > --projfrac
> > > > options be set to in my case?
> > > > Also for --out_type, if I want an easy format to port to
> > matlab?
> > > For projfrac we usually use .5. You can ignore src_type. For
> > output
> > > type, you can use nii (nifti) and then use MRIread.m
> > > doug
> > > >
> > > > Thanks!
> > > >
> > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500
> > > > > From: greve@nmr.mgh.harvard.edu
> > mailto:greve@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > mailto:freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] Resting State Networks on
> > Cortical Surface
> > > > >
> > > > >
> > > > > you will need to create a registration between your
> > volume (maps) and
> > > > > the anatomical. You can do this with bbregister. Then
> > use mri_vol2surf
> > > > > to map your ICs to the surface
> > > > > doug
> > > > >
> > > > >
> > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I am trying to display the 20 ICA components in this
> > nifti file
> > > > > >
> > > > > > http://brainmap.org/icns/maps.zip
> > > > > >
> > > > > > onto anatomical template they've provided here
> > > > > >
> > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii
> > > > > >
> > > > > > My question is:
> > > > > >
> > > > > > How do I extract only the cortical surface from the
> > anatomical
> > > > > > template and overlay
> > > > > > it with only parts of each ICA component that
> > intersects with the
> > > > surface?
> > > > > >
> > > > > >
> > > > > > Thanks!
> > > > > >
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > Freesurfer mailing list
> > > > > > Freesurfer@nmr.mgh.harvard.edu
> > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
> > > > > --
> > > > > Douglas N. Greve, Ph.D.
> > > > > MGH-NMR Center
> > > > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > > > > Phone Number: 617-724-2358
> > > > > Fax: 617-726-7422
> > > > >
> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > mailto: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.
> > > > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > _______________________________________________ Freesurfer mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> > mailto: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.
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
_______________________________________________ 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.
it is in the 'vol' field On 03/12/2014 08:54 PM, Xuelong Zhao wrote:
Hmm, it seems I may have misinterpreted the fields in the matlab structure after using MRIRead
rsn20_surf = MRIread('rsn20_surf.nii')
I thought perhaps the data would be in the 'volsize' field?
rsn20_surf =
srcbext: '' analyzehdr: [] bhdr: [] vol: [4-D double] niftihdr: [1x1 struct] fspec: 'rsn20_surf.nii' pwd: '~/rsn_smith09' flip_angle: 0 tr: 1000 te: 0 ti: 0 vox2ras0: [4x4 double] volsize: [1 139732 1] height: 1 width: 139732 depth: 1 nframes: 20 vox2ras: [4x4 double] nvoxels: 139732 xsize: 1 ysize: 1 zsize: 1 x_r: -1 x_a: 0 x_s: 0 y_r: 0 y_a: 1 y_s: 0 z_r: 0 z_a: 0 z_s: 1 c_r: -1 c_a: -17 c_s: 19 vox2ras1: [4x4 double] Mdc: [3x3 double] volres: [1 1 1] tkrvox2ras: [4x4 double]
Date: Wed, 12 Mar 2014 10:55:23 -0400 From: greve@nmr.mgh.harvard.edu To: andrewzhao@live.com.au CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
You would apply it to the column, row, and slice of a voxel. Note that the volume structure is volume(row,col,slice). But I'm not sure why you need to do this. If you read in the ICA maps after running mri_vol2surf, there will be a value for each vertex, no need to do any mapping
doug
On 3/11/14 7:00 PM, Xuelong Zhao wrote:
Okay, I think I'm getting close to what I want in the matlab object. I've successfully imported both the pial surface (using read_surf.m) and the ICA components on the surface in mgh format using MRIread.m I've had a look at the MRIread.m script and it says I can use vox2ras1 to convert column, row, and slice to XYZ coordinates. Which field of the matlab structure should I apply this to? I"m guessing its voxels but wanted to make sure, and also I'd have to do this for each individual frame? Thanks. ------------------------------------------------------------------------ Date: Mon, 10 Mar 2014 23:54:18 -0400 From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface I don't know of anything that will do this (or what a single object would mean in this case). If you have the overlay in a volume format (eg, mgz), you can use MRIread.m. This gives you a value for each vertex, not face, so you'd have to write something to assign the value to a face. doug On 3/10/14 11:27 PM, Xuelong Zhao wrote: Should also add that I can import the cortical surface into matlab without any issues using read_surf.m what I would like to have is the ICA overlay also imported into matlab as corresponding colors for each face on the cortical mesh. Thanks. ------------------------------------------------------------------------ From: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> To: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Date: Tue, 11 Mar 2014 11:54:10 +1100 CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface Regarding matlab: Currently, I have in freesurfer the surface extracted via recon-all. I also have the overlay from running mri_vol2surf on the ICA components. I would like to export the pial surface + overlay into matlab together as a single object. Is there a matlab script for this, or do I need to do some further processing? Thanks. > Date: Mon, 10 Mar 2014 11:25:23 -0400 > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > On 03/09/2014 09:12 AM, Xuelong Zhao wrote: > > Hi Doug, > > > > To clarify my previous question: > > > > There is definitely some fuzziness when comparing with the mov, > > whereas the target comparison looks very pristine. I was just > > wondering if this is expected. The mov, as I scroll through the layers > > seem to be also slightly offset in certain regions, I guess this again > > may be due to the fuzziness of the mov fmri data. > Yes this is somewhat expected. The target is the data the surface was > generated from, so it should look perfect. > > > > Regarding my second q: > > > > I've got this working now- the segfault was due to me naively loading > > the surface image as a surface, instead of using it as an overlay, I > > can now successfully scroll through the various frames. However, I > > noticed that in the documentation to load into matlab, say the left > > pial surface (with the ICA components on it), I have to save it as a > > mgz file and then use MRI_read. However, freeview doesn't seem to > > offer this option once I load the pial surface and the the ICA components? > > Sorry, what has to be mgz? What matlab command? What instructions? > doug > > > > > > > ------------------------------------------------------------------------ > > Date: Thu, 6 Mar 2014 10:19:25 -0500 > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> > > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/6/14 6:39 AM, Xuelong Zhao wrote: > > > > Hi Doug, > > > > A follow-up. I've gone back and re-done the registration using > > nifti file with the ICA20 maps. I noticed in tkregister2 that when > > I press on the TARGET tab there is extremely good alignment ( i > > think it is to 'orig.mgz' in the mri folder of my subject which I > > had processed using recon-all. While, when I switch to the > > 'moveable' tab the green line seems to be slightly offset, but the > > underlying image is very fuzzy too. Is this an issue? > > > > I don't know without seeing it. The mov is often lower resolution, so > > some fuzziness is expected. > > > > > > Also, when I load the surface image in freeview produced by > > mri_vol2surf nothing seems to show up, even when I use the > > registration file. In fact, if I have other volumes loaded it > > causes freeview to segfault. When I do manage to load it > > successfully with the anatomical template in talairach space, it > > doesn't really show up and it seems that the anatomical template > > is really small and I have to zoom in a lot. Maybe I didn't > > process/register? > > > > Can you be more specific? What are your vol2surf and fv command lines? > > Have you tried it in tksurfer? > > > > > > Thanks again. > > > > ------------------------------------------------------------------------ > > Date: Tue, 4 Mar 2014 22:52:38 -0500 > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> > > CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface > > > > > > On 3/4/14 7:18 PM, Xuelong Zhao wrote: > > > > Dear Doug, > > > > I've managed to get functional information onto the cortical > > surface following your instructions. > > But, there's a few issues that are still not resolved: > > > > 1/ wrt to registration I believe the supplied anatomical > > template (in tailarach coords) is already aligned with the ica > > maps (which come from one individual). However, when I run > > mri_vol2surf I need a registration.dat file so in such a > > situation is the registration data from the anatomical > > template sufficient? > > > > If the ica maps are in voxel-for-voxel alignment with the template > > then yes (i,e they must have the same dimension and voxel size) > > > > > > 2/ the nifti file for functional data actually contains 20 ICA > > components. After I ran mri_vol2surf how do I view each > > component independently? Currently it seems to only show one > > particular ICA component in freeview. > > > > Bring up the overlay configuration window. You can control the > > frame/time point from there. > > > > > > 3/ using mri_vol2surf if I want .nii output do I specify thus: > > '--out_type nii' ? (i did this and it seemed to have worked, > > but just wanted to double check). > > > > You can just specify the output file with a .nii extension > > doug > > > > > > > > Thanks! > > > > > Date: Tue, 4 Mar 2014 10:37:19 -0500 > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > To: andrewzhao@live.com.au <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au> <mailto:andrewzhao@live.com.au>; > > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Resting State Networks on Cortical > > Surface > > > > > > > > > On 03/03/2014 11:25 PM, Xuelong Zhao wrote: > > > > Hi Doug, thanks for the quick reply. I've been playing > > around with the > > > > commands you suggested and managed to get what seemed like > > a good > > > > registration by inspecting the green lines in tkregister. > > > > > > > > However, I wasn't actually sure if I put the correct input: > > > > > > > > bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg > > > > > > ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat > > --t1 > > > > --init-header > > > > > > > > after the '--mov' option should i be using the anatomical > > template or > > > > the .nii file containing the 20 ICA components (4D)? I > > tried both > > > > (changing the between the --t1 and --bold options) and the > > anatomical > > > > template came out much better, but I thought the movable > > (--mov) is > > > > meant to be the functional image? > > > It should be a functional image. If the ica maps come from an > > > individual, then use the mean functional for that subject or > > whatever > > > you used for fMRI motion correction (which should be aligned > > with the > > > ica maps). If it is in a group space, then use the > > registration target > > > (that is exactly the same size as your maps). > > > > > > > > Also, wrt to mri_vol2surf, what should the --src_type, > > --projfrac > > > > options be set to in my case? > > > > Also for --out_type, if I want an easy format to port to > > matlab? > > > For projfrac we usually use .5. You can ignore src_type. For > > output > > > type, you can use nii (nifti) and then use MRIread.m > > > doug > > > > > > > > Thanks! > > > > > > > > > Date: Mon, 3 Mar 2014 14:20:55 -0500 > > > > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Subject: Re: [Freesurfer] Resting State Networks on > > Cortical Surface > > > > > > > > > > > > > > > you will need to create a registration between your > > volume (maps) and > > > > > the anatomical. You can do this with bbregister. Then > > use mri_vol2surf > > > > > to map your ICs to the surface > > > > > doug > > > > > > > > > > > > > > > On 03/02/2014 04:21 AM, Xuelong Zhao wrote: > > > > > > > > > > > > Hi, > > > > > > > > > > > > I am trying to display the 20 ICA components in this > > nifti file > > > > > > > > > > > > http://brainmap.org/icns/maps.zip > > > > > > > > > > > > onto anatomical template they've provided here > > > > > > > > > > > > http://brainmap.org/icns/colin_tlrc_1x1x1.nii > > > > > > > > > > > > My question is: > > > > > > > > > > > > How do I extract only the cortical surface from the > > anatomical > > > > > > template and overlay > > > > > > it with only parts of each ICA component that > > intersects with the > > > > surface? > > > > > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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
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Douglas Greve -
Douglas N Greve
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Xuelong Zhao