The hemi just refers to either lh or rh to load the proper surface. The
command have no idea what you are transferring to the surface.
Before the mri_vol2label stage, try loading surf.MDROI onto the surface
as an overlay and see if the ROIs are showing up in the right place
On 8/6/2020 11:41 AM, Eleni Nikalexi wrote:
External Email - Use Caution
Dear Freesurfer developers,
We have a volume that assigns unique numerical labels to each of the
ROIs it contains, in NIFTI format. I want to register it to MNI152
(1mm) space, so that I can map it on my subjects and use
mris_anatomical_stats.
I have tried the following command:
1. tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg
registrationMD/MDROI.lta
to get : "LTA input is not RAS to RAS...converting...".
Then I run:
2. mri_vol2surf --src MDROI.nii --src_type nii --out
registrationMD/surf.MDROI.mgh --reg
registrationMD/MDROI.lta --hemi lh --surf white
--projdist-max 0 1 0.1
3. mri_vol2surf --src MDROI.nii --src_type nii --out
registrationMD/surf.MDROI_rh.mgh --reg
registrationMD/MDROI.lta --hemi rh --surf white
--projdist-max 0 1 0.1
The 2 commands above demand the --hemi argument, but I wasn't sure
what to put, as the ROIs are mixed and are in both hemispheres. Thus I
run the command once for the left and once for the right hemisphere,
creating different .mgh files.
Last, I continued with:
4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l
lab.MDROI_lh.label --surf MNI_1mm l
which failed, as I get "ERROR: found no voxels matching id 1"
Could you please tell me, if the commands make sense, and if I should
change something?
Thank you so much for your help!
Best regards,
Eleni
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
