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 <dgreve@mgh.harvard.edu> 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:

        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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer