Thanks so much, I appreciate the help. However, I am not sure what I am supposed to do with the output of the recon-all process. Can I simply use the .dat file that is outputted there in MRI_vol2surf?
Lotte
Date: Wed, 22 Mar 2017 13:01:42 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] display SPM results on inflated surface? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 41134c50-bb0b-792c-c52b-b6850bcecf3c@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
If you have the T1 for the mni152 (which is somewhere in the bowels of the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz
On 3/21/17 1:27 PM, Schoot, Lotte wrote:
Hi Doug and others,
A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct:
bbregister --s fsaverage --mov con_0001.nii --init-spm --reg register.dat --bold
Thanks! Lotte
If your results are on the MNI152, you can run the mni152 through freesurfer, then use mri_vol2surf to map the data to the surface then view it with freeview (or tksurfer). You should not confuse this with doing the fMRI analysis on the surface. You will not have the benefits of surface-based analysis
On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
/Hi all, />//>/I was wondering if you knew of a way to display SPM results onto the />/inflated surface in Freesurfer. />//>/I have tried using SurfRend but there seem to be problems which might />/be due to the fact the results are obtained with SPM12 and SurfRend />/was designed to work with SPM5. />//>/Thanks, />/Lotte />//>//>/_______________________________________________ />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer / -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Phone Number: 617-724-2358 Fax: 617-726-7422
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just map your mni152-spm volume to the surface with mri_vol2surf and --regheader, eg,
mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s mni152 --o lh.yourspm152.nii.gz
then visualize
tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz
On 3/22/17 3:46 PM, Schoot, Lotte wrote:
Thanks so much, I appreciate the help. However, I am not sure what I am supposed to do with the output of the recon-all process. Can I simply use the .dat file that is outputted there in MRI_vol2surf?
Lotte
Date: Wed, 22 Mar 2017 13:01:42 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] display SPM results on inflated surface? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 41134c50-bb0b-792c-c52b-b6850bcecf3c@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
If you have the T1 for the mni152 (which is somewhere in the bowels of the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz
On 3/21/17 1:27 PM, Schoot, Lotte wrote:
Hi Doug and others,
A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct:
bbregister --s fsaverage --mov con_0001.nii --init-spm --reg register.dat --bold
Thanks! Lotte
If your results are on the MNI152, you can run the mni152 through freesurfer, then use mri_vol2surf to map the data to the surface then view it with freeview (or tksurfer). You should not confuse this with doing the fMRI analysis on the surface. You will not have the benefits of surface-based analysis
On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
/Hi all, />//>/I was wondering if you knew of a way to display SPM results onto the />/inflated surface in Freesurfer. />//>/I have tried using SurfRend but there seem to be problems which might />/be due to the fact the results are obtained with SPM12 and SurfRend />/was designed to work with SPM5. />//>/Thanks, />/Lotte />//>//>/_______________________________________________ />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer / -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Phone Number: 617-724-2358 Fax: 617-726-7422
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
I am wondering, where did you find the mini 152 T1 map? :)
Regarding this... Would it be better to instead run recon-all on a higher-res MNI atlas? and then run mri_vol2surf for that segmentation?
Cheers,
*Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.
Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney
*E* Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au | *W* https://kevinaquino.github.io http://www.physics.usyd.edu.au/~aquino/
----------------------------------------------
The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost
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On Thu, Mar 23, 2017 at 7:53 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Just map your mni152-spm volume to the surface with mri_vol2surf and --regheader, eg,
mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s mni152 --o lh.yourspm152.nii.gz
then visualize
tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz
On 3/22/17 3:46 PM, Schoot, Lotte wrote:
Thanks so much, I appreciate the help. However, I am not sure what I am supposed to do with the output of the
recon-all process.
Can I simply use the .dat file that is outputted there in MRI_vol2surf?
Lotte
Date: Wed, 22 Mar 2017 13:01:42 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] display SPM results on inflated surface? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 41134c50-bb0b-792c-c52b-b6850bcecf3c@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
If you have the T1 for the mni152 (which is somewhere in the bowels of
the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard. edu/safelinks/greve/mni152.tar.gz
On 3/21/17 1:27 PM, Schoot, Lotte wrote:
Hi Doug and others,
A while ago, I got this reply to my question below (thanks!). I tried
to look in to it, but I am a bit confused (probably because I am very new to Freesurfer).
My results are on the MNI 152, but I don't understand what you mean
with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf?
What would you recommend to get the register.dat file? Is it possible
to use bbregister for that? I have tried this, but I don't know whether it is correct:
bbregister --s fsaverage --mov con_0001.nii --init-spm --reg register.dat --bold
Thanks! Lotte
If your results are on the MNI152, you can run the mni152 through freesurfer, then use mri_vol2surf to map the data to the surface then view it with freeview (or tksurfer). You should not confuse this with doing the fMRI analysis on the surface. You will not have the benefits of surface-based analysis
On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
/Hi all, />//>/I was wondering if you knew of a way to display SPM results onto the />/inflated surface in Freesurfer. />//>/I have tried using SurfRend but there seem to be problems which might />/be due to the fact the results are obtained with SPM12 and SurfRend />/was designed to work with SPM5. />//>/Thanks, />/Lotte />//>//>/_______________________________________________ />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer / -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Phone Number: 617-724-2358 Fax: 617-726-7422
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I got it from FSL in the $FSLDIR/data/standard, but it is distributed with SPM as well
On 4/5/17 9:39 PM, Kevin Aquino wrote:
Hi Douglas,
I am wondering, where did you find the mini 152 T1 map? :)
Regarding this... Would it be better to instead run recon-all on a higher-res MNI atlas? and then run mri_vol2surf for that segmentation?
Cheers,
*Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.
Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney
*E* Kevin.aquino@nottingham.ac.uk mailto:Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au mailto:aquino@physics.usyd.edu.au | *W* *MailScanner has detected a possible fraud attempt from "www.physics.usyd.edu.au" claiming to be* https://kevinaquino.github.io http://www.physics.usyd.edu.au/%7Eaquino/
The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office.
Robert Frost
CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments.
Please think of our environment and only print this e-mail if necessary.
On Thu, Mar 23, 2017 at 7:53 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Just map your mni152-spm volume to the surface with mri_vol2surf and --regheader, eg, mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s mni152 --o lh.yourspm152.nii.gz then visualize tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz On 3/22/17 3:46 PM, Schoot, Lotte wrote: > Thanks so much, I appreciate the help. > However, I am not sure what I am supposed to do with the output of the recon-all process. > Can I simply use the .dat file that is outputted there in MRI_vol2surf? > > Lotte > > > Date: Wed, 22 Mar 2017 13:01:42 -0400 > From: Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] display SPM results on inflated surface? > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <41134c50-bb0b-792c-c52b-b6850bcecf3c@nmr.mgh.harvard.edu <mailto:41134c50-bb0b-792c-c52b-b6850bcecf3c@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="windows-1252" > > If you have the T1 for the mni152 (which is somewhere in the bowels of the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz> > > > > On 3/21/17 1:27 PM, Schoot, Lotte wrote: >> Hi Doug and others, >> >> A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). >> My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? >> What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct: >> >> bbregister --s fsaverage --mov con_0001.nii --init-spm --reg >> register.dat --bold >> >> >> Thanks! >> Lotte >> >> >>> If your results are on the MNI152, you can run the mni152 through >>> freesurfer, then use mri_vol2surf to map the data to the surface then >>> view it with freeview (or tksurfer). You should not confuse this with >>> doing the fMRI analysis on the surface. You will not have the >>> benefits of surface-based analysis >> >> On 02/15/2017 03:37 PM, Schoot, Lotte wrote: >>> /Hi all, />//>/I was wondering if you knew of a way to display SPM >>> results onto the />/inflated surface in Freesurfer. />//>/I have >>> tried using SurfRend but there seem to be problems which might />/be >>> due to the fact the results are obtained with SPM12 and SurfRend >>> />/was designed to work with SPM5. />//>/Thanks, />/Lotte >>> />//>//>/_______________________________________________ >>> />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> / >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >
freesurfer@nmr.mgh.harvard.edu
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Schoot, Lotte