Re: [Freesurfer] running recon-all for FSL-based ROIs

It is not done with recon-all. Use mri_label2vol to map your ROIs to fsaverage space using the registration below doug

On 10/21/2013 11:54 AM, Paul Beach wrote:

Hi Doug,

Thank you for the response.

You'll have to pardon my ignorance here, but how would I integrate this into the actual recon-all command? What kind of flag would I utilize?

The setup is that I have a folder named "anterior_Salience" in my subjects directory - this folder has the NIFTI file anterior_Salience.nii.gz:

/recon-all -s anterior_Salience / /-i /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/anterior_Salience/anterior_Salience.nii.gz *-flag?? */*/$FREESURFER_HOME//average/mni152.register.dat/* */ /* */ /* Thanks

On Mon, Oct 21, 2013 at 11:19 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

If you are trying to get them into fsaverage/mni305 space, then use
$FREESURFER_HOME//average/mni152.register.dat

doug

On 10/21/2013 10:58 AM, Paul Beach wrote:
> Hello FS experts,
>
> I am interested in utilizing the functional ROIs made by the
Greicius
> lab out of Stanford (found here
> <http://findlab.stanford.edu/functional_ROIs.html>). However, these
> ROIs were made using FSL and the coordinate system for them is not
> responding to simple resampling commands (such as mri_convert or
> 3dresample). The resulting file from utilizing these commands
"works"
> in the sense that it puts them in the proper orientation, but
the ROIs
> are still way out of whack, somehow.
>
> Thus, I would like to try utilizing recon-all to get these ROIs
(which
> correspond to MNI152-2mm) into the standard space I'm utilizing
> (Freesurfer-defined MNI305, based on the subjects' talairach.m3z
> file). However, I have no idea how to do this. Could I have some
> general guidance on the steps and options for recon-all that would
> accomplish this?
>
> I have some additional information about the ROIs below.
>
> *_This is the 3dinfo output for the ROIs (in this case,
> anterior-salience)_*
> Template Space:  TLRC
> Dataset Type:    Anat Bucket (-abuc)
> Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:    NIFTI
> Storage Space:   3,610,516 (3.6 million [mega]) bytes
> Geometry String: "MATRIX(2,0,0,-90,0,-2,0,126,0,0,2,-72):91,109,91"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Posterior-to-Anterior
>   third  (z) = Inferior-to-Superior   [-orient RPI]
> R-to-L extent:   -90.000 [R] -to-    90.000 [L] -step-     2.000
mm [
> 91 voxels]
> A-to-P extent:   -90.000 [A] -to-   126.000 [P] -step-     2.000 mm
> [109 voxels]
> I-to-S extent:   -72.000 [I] -to-   108.000 [S] -step-     2.000
mm [
> 91 voxels]
>
>
> Thanks!
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
>    - Bozoki Lab: Neurology/Radiology
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
  • Bozoki Lab: Neurology/Radiology