Your mri_vol2label command is fine (since these are surfaces)
On 8/7/2020 10:52 AM, Eleni Nikalexi wrote:
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Dear Douglas,
Thank you for the reply,
The MDROI.nii is a set of ROIs, which I want to transform in separate
labels. So how can I extract the ROIs??
I already tried:
mri_extract_label MDROI.nii 1 label1.mgz
but it extracts the labels according to the inherent anatomical ROIs
from freesurfer
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT),
and not the ones the volume is showing.
I also tried:
mri_annotation2label --subject MNI_1mm/ --annotation MDROI.nii
--outdir MNI_1mm/trial_MD_2_labels/
but it needs a corresponding .annot file for the --annotation argument
On Friday, August 7, 2020, 05:11:40 PM GMT+3, Douglas N. Greve
<[email protected]> wrote:
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:
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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
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