Dear Dr. Greve,

Thanks a lot for your email.

Yes, ROI.mgh is correctly aligned in fsaverage, it is the Xnew.label file which is far away from ROI.mgh.
Here I am attaching 5 files:
(1). ROI_vol_MNI.nii.gz: This is ROI volume file in standard space (correctly aligned in orig.mgz, I checked using mricron also).
(2). ROI_surf_MNI.nii.gz: This is ROI vol2surface file in standard space (correctly aligned in fsaverage lh inflated)
(3). X.label: This is label generated using step 1 from my previous email
(4). Xnew.label: This is label generated using step 3 from my previous email
(5). ROI_Label_Surface: Screen shot after overlaying ROI in standard space (red color) and Xnew.label (yellow color).

I am hoping these files might help you to figure out the issue.

Thanks again for your time.

Regards,
Sahil

On Thu, Apr 28, 2016 at 12:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
First, you should look at your ROI in fsaverage space to see if it
overlaps at all, eg,
tkmedit fsaverage orig.mgz -ov ROI.mgh -fminmax .5 1 -surfs
If the surface does not intersect, then none of this will work. If it
does not intersect, then you will need to register the ROI to fsaverage
(or run recon-all on an MNI brain)


On 04/28/2016 01:04 PM, Sahil Bajaj wrote:
> Dear FreeSurfer experts,
>
> I have a surface ROI defined in MNI co-ordinate system, ROI.mgh, I am
> interested in converting it into label. I tried following steps:
> (1). mri_cor2label --i ROI.mgz --id 1 --l X.label
> (2). mri_label2label --srclabel X.label --s fsaverage --trglabel
> Xnew.label --hemi lh --paint 30
>
> This gives me final .label file as Xnew.label, then I tried to check
> if this is correct using:
> (3). tksurfer fsaverage lh inflated -overlay ROI.mgh -fthresh 0.5
> and then on top of it File>load label>Xnew.label
>
> Now the new Xnew.label is not matching with ROI.mgz.
> Can someone please help me to figure out what I am doing wrong here?
> Also, how can I view the label in FreeView i.e. is there any way to
> load this new label just like LookUp Table?
>
> Thanks,
> Sahil
> --
> -------------------------------------------------
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.brain@gmail.com <mailto:E-mail%3Asahil.phy@gmail.com>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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--
-- 
-------------------------------------------------
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)