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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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