Hello FS experts,
I am interested in utilizing the functional ROIs made by the Greicius lab out of Stanford (found herehttp://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!
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Paul Beach