sorry, I'm not sure what your question is. You can an overlay, but your proposed processing stream starts with mri_label2label. It looks like your overlay is on the surface (the number of vertices looks quite high).
On 5/29/2022 11:32 AM, Benjamin Deck wrote:
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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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