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
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