Hi Douglas,

Indeed you have already helped me !
Thank you for your help and for your time.

I have tried to do, as you said.
I have used the brain image for the registration and then I have tried to convert my ROI nifti volumetric file into a surface file using this registration file.

I do not know what is wrong with my command line and I tried many many things.

I have attached two files
(MNI152_T1_2mm_brain.nii is the brain file, multdemand_MCC_SMA_thr50.nii.gz is the ROI file).

I have tried the following commands :
1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152.dat --tw --init-coreg

2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat --hemi lh --o ./multidem.mgh

I do not know if the output format .mgh is correct.
Anyway when I launch it with :
tksurfer fsaverage lh inflated -label multidem.mgh

the multidem.mgh file does not appear.

Thank you by advance for your advice,

Best,

Redwan

On 9 March 2017 at 09:09, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

didn't I respond to this earlier this week? the images appear to be
binarized regions of interest and not whole (or ever partial) brain. To
run the registration, you will need an actual brain. If you created the
ROI from a brain image, then use that image to create the reg, then run
vol2surf using that reg with the ROI as input

On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> Hi experts,
>
> I try to convert my volumetric nifti file to surface files.
>
> My nifti volumetric file looks like : 1. screenshot
> I have first registered the volumetric file using bbregister with this
> command line :
> *bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1
> --init-coreg*
>
> then I have used the following command line and the file looks like
> screenshot 1 attached :
> *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
>
> And after that, I have tried to convert my volumetric file to surface
> file with this command line :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.nii --float2int round*
>
> But with this command when I load the file with freeview it does not
> work and with tkregister the file is empty.
>
> Or this one :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.w --out_type paint --float2int tkregister*
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Could you please help me to convert my volumetric files because I am
> probably doing someting wrong. All my files come from an Atlas and I
> just need to convert them to surfaces files.
>
> Thank you for your help,
> Redwan
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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