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Hi there freesurfer experts,

I am fairly new to freesurfer. I am attempting to convert freesurfer overlay files and eventually create individual-specific annotation files which will then be used to create a segmentation file to be used for drawing white matter tracts.

When I run mri_info on the overlay files I get the following:

Volume information for Net_10_ROIs_1_lh.mgh
          type: MGH
    dimensions: 253237 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 253237.000
           dof: 1
        xstart: -126618.5, xend: 126618.5
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =   1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.5000
              : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =  1281.0000
              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =     0.5000

talairach xfm :
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                1.0000   0.0000   0.0000 -126618.0000
                0.0000   1.0000   0.0000  1280.5000
                0.0000   0.0000   1.0000     0.0000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 1

ras to voxel transform:
                1.0000   0.0000   0.0000 126618.0000
                0.0000   1.0000   0.0000 -1280.5000
                0.0000   0.0000   1.0000     0.0000
                0.0000   0.0000   0.0000     1.0000

My initial thought was to run mri_label2label --> mri_label2vol --> mris_label2annot --mri_label2vol --> mri_concat = segmentation in native volume

Running WSL2 Ubuntu 18_x86_64-7.2.0

FS:   freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

Any guidance would be greatly appreciated.

Thank you!

--

Benjamin L. Deck

Doctoral Student

Applied Cognitive and Brain Sciences

Department of Psychological and Brain Sciences

Drexel University

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