I have some questions about how to manually correct the white matter regions .
It's the same manually edit the volume "brainmask.mgz" and use control points? Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as white matter with the value 110. Is it right to do this?
My second question is: Is it possible to edit the volumes with a third party program? My intention here is to turn the volume "brainmask.mgz" to " brainmask.nii" using "mri_convert" command. Then edit the values of the voxels manually with a third party software or painting tool, and finally, turn the volume back to "brainmask.mgz", replace the file in their respective directory, and finally execute "-autorecon2- wm". Is it right to do this? Or this may compromise my data?
Thanks in advance, Alberto.
Alberto,
I included detailed replies below, but I have a question before you get to those. Why don't you want to follow the FreeSurfer techniques for reconstruction? You suggested several other ways, but I don't understand your motivation for not wanting to follow the instructions for FreeSurfer.
On 10/2/15 5:49 AM, Julio Alberto González Torre wrote:
I have some questions about how to manually correct the white matter regions.
It's the same manually edit the volume "brainmask.mgz" and use control points?Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as white matter with the value 110. Is it right to do this?
Why don't you want to use control points? They do more than replace the value with 110. They let FreeSurfer know that that voxel is definitely white matter even though the intensity is different. It can then tweak what it sees as white matter locally in that space and get you a good measure of the border. Remember the border is likely to occur in the middle of voxels with partial voluming effects, where the intensity is not 110, and also where you should not make the volume 110.
My second question is: Is it possible to edit the volumes with a third party program? My intention here is to turn the volume "brainmask.mgz" to "brainmask.nii" using "mri_convert" command. Then edit the values of the voxels manually with a third party software or painting tool, and finally, turn the volume back to "brainmask.mgz", replace the file in their respective directory, and finally execute "-autorecon2- wm". Is it right to do this? Or this may compromise my data?
While I am not a FreeSurfer dev, I would strongly discourage you from doing this. First, it will be easier to get help, troubleshoot and do things properly, if follow the FreeSurfer techniques, plus you will need their tools to do any corrections to the Talairach etc. Second, the NIFTI format is pretty bad and lacks a lot of data which the mgz format preserves.
Thanks in advance, Alberto.
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Hi Alberto
1. No, this is not the same. The control points are used to estimate the bias field, which can affect an entire regions. Replacing a voxel in the brainmask with a 110 will only affect that voxel.
2. You can do this if you want but you have to be careful how you edit. When we turn something "off" we set it to 1, not 0 so we can track and preserve it, and similarly when we turn it "on" we set it to 255.
cheers Bruce
On Fri, 2 Oct 2015, Julio Alberto González Torre wrote:
I have some questions about how to manually correct the white matter regions.
It's the same manually edit the volume "brainmask.mgz" and use control points? Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as white matter with the value 110. Is it right to do this?
My second question is: Is it possible to edit the volumes with a third party program? My intention here is to turn the volume "brainmask.mgz" to "brainmask.nii" using "mri_convert" command. Then edit the values of the voxels manually with a third party software or painting tool, and finally, turn the volume back to "brainmask.mgz", replace the file in their respective directory, and finally execute "-autorecon2- wm". Is it right to do this? Or this may compromise my data?
Thanks in advance, Alberto.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
dgw -
Julio Alberto González Torre