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
you wouldn't run it on the stats map - you would run it on the T1-weighted MNI152 volume
On Fri, 8 Jan 2016, John Anderson wrote:
Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis Bests, John Sent: Friday, January 08, 2016 at 1:41 PM From: "Douglas N Greve" greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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" fischl@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
On Fri, 8 Jan 2016, John Anderson wrote:
Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis Bests, John Sent: Friday, January 08, 2016 at 1:41 PM From: "Douglas N Greve" greve@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 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.
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On 1/22/16 6:27 AM, John Anderson wrote:
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.
- Can I directly use the command "
tksurfer fsaverage rh inflated -overlay-reg $FREESURFER_HOME/average/mni152.register.dat -o "my tstat map"
That will work. I don't know whether it gives you something better or worse than running recon-all on the mni152 .
- 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?
It will create surfaces that may be more consistent with your activation.
Thanks a lot! John *Sent:* Friday, January 08, 2016 at 2:57 PM *From:* "Bruce Fischl" fischl@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" fischl@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" greve@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 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 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
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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 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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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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John Anderson