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| Question: I have successfully run a subject's data through FreeSurfer. FreeSurfer creates volumes in 1mm^3, 256^3 space, but I want the FreeSurfer results in the space of my original anatomical. How do I do this? | Question: I have successfully run a subject's data through FreeSurfer. FreeSurfer creates volumes in 1mm^3^, 256^3^ space, but I want the FreeSurfer results in the space of my original anatomical. How do I do this? |
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| cd $SUBJECTS_DIR/subject mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz |
cd $SUBJECTS_DIR/<subjid>/mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg |
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| "rawavg.mgz" is a file created by FreeSurfer and is in the native space of your anatomical. The output is brain-in-rawavg.mgz and will be in the native space of the anatomical. | "rawavg.mgz" is a file created by FreeSurfer and is in the native space of your anatomical so we use that volume as a target space. The output is brain-in-rawavg.mgz and will be in the native space of the anatomical. Substitute brain.mgz with whatever other images you want in native space. |
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| cd $SUBJECTS_DIR/subject mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz}}} |
cd $SUBJECTS_DIR/<subjid>/mri mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz }}} |
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| After running these two commands, tkmedit should show the aseg overlaid properly on the brain | If you ran both of the commands above, tkmedit should show the aseg (in native space) overlaid properly on the brain (in native space) all matching up well with the rawavg.mgz (your native space target). |
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| tkmedit -f brain-in-rawavg.mgz -seg aseg-in-rawavg.mgz | tkmedit -f brain-in-rawavg.mgz -aux rawavg.mgz -seg aseg-in-rawavg.mgz |
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You can also map a surface into the native anatomical space First, create a registration matrix between the conformed space (orig.mgz) and the native anatomical (rawavg.mgz) {{{ tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader }}} Next, map the surface to the native space: {{{ mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname }}} The output will be stored in $SUBJECTS_DIR/subjectname/surf/lh.pial.native To verify that this worked, run {{{ freeview -v rawavg.mgz -f lh.pial.native }}} |
How to Convert from FreeSurfer Space Back to Native Anatomical Space
Question: I have successfully run a subject's data through FreeSurfer. FreeSurfer creates volumes in 1mm3, 2563 space, but I want the FreeSurfer results in the space of my original anatomical. How do I do this?
The exact command you use depends on what you want to convert, an image (like brain.mgz) or a segmentation (like aseg.mgz).
For an image:
cd $SUBJECTS_DIR/<subjid>/mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg
"rawavg.mgz" is a file created by FreeSurfer and is in the native space of your anatomical so we use that volume as a target space. The output is brain-in-rawavg.mgz and will be in the native space of the anatomical. Substitute brain.mgz with whatever other images you want in native space.
For a segmentation (aseg.mgz, aparc+aseg.mgz, wmparc.mgz, etc):
cd $SUBJECTS_DIR/<subjid>/mri mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
If you ran both of the commands above, tkmedit should show the aseg (in native space) overlaid properly on the brain (in native space) all matching up well with the rawavg.mgz (your native space target).
tkmedit -f brain-in-rawavg.mgz -aux rawavg.mgz -seg aseg-in-rawavg.mgz
You can also map a surface into the native anatomical space
First, create a registration matrix between the conformed space (orig.mgz) and the native anatomical (rawavg.mgz)
tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader
Next, map the surface to the native space:
mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname
The output will be stored in $SUBJECTS_DIR/subjectname/surf/lh.pial.native
To verify that this worked, run
freeview -v rawavg.mgz -f lh.pial.native