Hi Bruce,
I carefully followed your orientations. Kindly I still need more clarification regarding the following point:
I have statistical map in MNI152 space (volume) as an output of permutation analysis using " randomise/FSL". I want to visualize this map on an inflated surface in Freesurfer.
1. Can I directly use the command "
2. Whay I need to do segmentation to MNI152 then running the command mri_vol2surf? Whar are the cons and pros of doing or not doing these steps?tksurfer fsaverage rh inflated -overlay-reg $FREESURFER_HOME/average/mni152.register.dat -o "my tstat map"
Thanks a lot!
John
John
Sent: Friday, January 08, 2016 at 2:57 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform statistical map in MNI to surface
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform statistical map in MNI to surface
Hi John
you would run recon-all on the MNI 152 T1 image (NOT your map), then use
mri_vol2surf to map the stats map onto the resulting surfaces. Note that
this won't give you great results as a bunch of your clusters will
probably not be near the cortical surface (since in general subjects
cortices don't align well in MNI 152)
cheers
Bruce
On Fri, 8 Jan 2016, John Anderson
wrote:
> Thanks Bruce,
> if my statistical map "stat1.nii.gz" is in MNI152 standard space what are
> the command lines that I need ( or if possible any link to wiki)
> Thanks a lot!
>
>
> John
> Sent: Friday, January 08, 2016 at 2:49 PM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> you wouldn't run it on the stats map - you would run it on the
> T1-weighted MNI152 volume
>
> > Sent: Friday, January 08, 2016 at 1:41 PM
> > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> > If it is in mni152 space, then you can run recon-all on the mni152 T1
> > map, then use mri_vol2surf with --regheader to map the volume tothe
> > surface, then use tksurfer or freeview to view the resulting map
> >
> > On 01/08/2016 12:49 PM, John Anderson wrote:
> > > Hi Experts,
> > > I have statistical map in MNI space and I want to view it using
> > > tksurfer how can i transform this map to a surface ?
> > >
> > > Bests,
> > > John
> > >
> > >
> > > _______________________________________________
> > > 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
> > gr...@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
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> >
> >
> >_______________________________________________
> 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
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you would run recon-all on the MNI 152 T1 image (NOT your map), then use
mri_vol2surf to map the stats map onto the resulting surfaces. Note that
this won't give you great results as a bunch of your clusters will
probably not be near the cortical surface (since in general subjects
cortices don't align well in MNI 152)
cheers
Bruce
On Fri, 8 Jan 2016, John Anderson
wrote:
> Thanks Bruce,
> if my statistical map "stat1.nii.gz" is in MNI152 standard space what are
> the command lines that I need ( or if possible any link to wiki)
> Thanks a lot!
>
>
> John
> Sent: Friday, January 08, 2016 at 2:49 PM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> you wouldn't run it on the stats map - you would run it on the
> T1-weighted MNI152 volume
>
> > Sent: Friday, January 08, 2016 at 1:41 PM
> > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> > If it is in mni152 space, then you can run recon-all on the mni152 T1
> > map, then use mri_vol2surf with --regheader to map the volume tothe
> > surface, then use tksurfer or freeview to view the resulting map
> >
> > On 01/08/2016 12:49 PM, John Anderson wrote:
> > > Hi Experts,
> > > I have statistical map in MNI space and I want to view it using
> > > tksurfer how can i transform this map to a surface ?
> > >
> > > Bests,
> > > John
> > >
> > >
> > > _______________________________________________
> > > 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
> > gr...@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
> > 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
> 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.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
