On 4/15/2020 11:17 AM, Safi Ullah . wrote:

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Dear Freesurfers,

I recently started working on an brain sMRI related project. I have a minor (may be a major) issue.

when I generate label files for a tissue e.g midbrain by using the command

mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173
--l midbrain.label

or in voxel space
mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz --id 173 --l midbrain1.label
👉Now I want to lad the label file and the MRI volume, brainstemSsLabels.v10 , in Matlab (I can do this by using MRIread function given in FSmatlab directory. the function read mri in a matlab struct, which along with other info also contain a 'vol' 3D data matrix)

read_label.m will read in the label
MRIread.m will load the volume

👉 Using the coordinates given in label file, how to extract a specific slice, row, column from a matlab matrix? as the label file need some transformation, I dont know this part.

See this page for converting between coordinates https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

Any help shall be highly appreciated.

Regards,

Safi

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