Is this individual data or group? If individual, are you planning to do a surface-based group analysis? If so, make sure that the fMRI data are in the native functional space. doug

Bruce Fischl wrote:

yes, use bbregister to register your functional maps, then mri_vol2surf to sample them onto the surface and load them in tksurfer.

cheers Bruce On Thu, 16 Feb 2012, LAOUCHEDI MAKHLOUF wrote:

...

hi all excuse me for this "simple question" but i am quiet new to freesurfer (i use it just for the parcellations). i've some functionnal maps (i've used spm for that) that i want to use as an overlay on the pial surface of the subject. is there an easy way to do it

thanks

---

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Laouchedi

it looks like you might be loading individual subject overlay on the fsaverage subject. What is your command line for tksurfer? And what exact file name do you type in? You can also load the overlay directly on the tksurfer command line with -overlay <overlay file name>. You can check the surfaces and volumes to see if they match with mris_euler_number lh.orig and mri_info cor-001.nii. The # of vertices in the surface should match the # of (rows x cols x slices) in the volume

cheers Bruce

On Mon, 20 Feb 2012, LAOUCHEDI MAKHLOUF wrote:

--- En date de : Jeu 16.2.12, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : hi all        i used bbregister my functional map (i have to inform you that the 3D volume to which i want to superimpose my functional map as an overlay is obtained using recon-all with notalairach option), before running i was asked to add a flag (use --bold, --dti, --t2, or --t1); i chose --bold, the result is a vollume named vol0000.nii.gz (which i attached to this mail) then i used mri_vol2surf on the result of bbregister. the result is a file named cor-001.nii. i tried to load it as an overlay using tksurfer but nothing was loaded and an error was generated :

  mri_read(): couldn't determine type of file
  /mnt/winlinux/fs/cor-001
  surfer: couldn't load /mnt/winlinux/fs/cor-001.
   If you were trying to load a functional volume, make sure
  you selected the right registration method, and if necessary,
  that the registration file exists.
  If you were trying to load a volume-encoded value file,
  make sure it has the same number of values as this surface
  does vertices (166454).

  thanks a lot for your help

  De: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  Objet: Re: [Freesurfer] overlay question
  À: "LAOUCHEDI MAKHLOUF" <laoumakhl@yahoo.fr>
  Cc: freesurfer@nmr.mgh.harvard.edu
  Date: Jeudi 16 février 2012, 16h59

  yes, use bbregister to register your functional maps, then
  mri_vol2surf to sample them onto the surface and load them in
  tksurfer.

  cheers
  Bruce
  On Thu, 16 Feb 2012, LAOUCHEDI MAKHLOUF wrote:

  > hi all
  >        excuse me for this "simple question" but i am quiet new
  to freesurfer
  > (i use it just for the parcellations).  i've some functionnal
  maps (i've
  > used spm for that) that i want to use as an overlay on the
  pial surface of
  > the subject. is there an easy way to do it
  >
  > thanks
  >
  >


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