Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and I don't know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot As you said, i have first registered the volumetric file using bbregister. I have used this command line : tkregister2 --mov segment_7.nii --reg register7.dat --surf (knowing that segment_7.nii is my volumetric file which looks like 1.screenshot). With this command line, my output is this file : 2.screenshot (attached).

Am I satisfied with this file ? if not what can I do to improve the result and the matching ?

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

Thank you by advance for your precious help, Have a nice day, Redwan

On 1 March 2017 at 07:31, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

Hi Redwan,

You'll need to register your volume to an FS-analyzed data set (probably using bbregister). Then apply mri_vol2surf (run with --help to get examples)

doug

On 2/28/17 5:17 PM, Redwan Maatoug wrote:

Hi all !

I would like to convert my files : volumetrics nifti files to surfaces files. My volumetrics nifti files come from an Atlas and I would like to convert them to surfaces files (i need the surfaces files).

Could you please tell me the process because I have tried many things like :

mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out thepathwayIwantToputmySurfaceFileAfterConversion

And it did not work.

Thank you for your help, Redwan

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

What is that input file? It looks like a mask of some part of the brain

On 03/03/2017 06:14 PM, Redwan Maatoug wrote:

Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and I don't know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot As you said, i have first registered the volumetric file using bbregister. I have used this command line : tkregister2 --mov segment_7.nii --reg register7.dat --surf (knowing that segment_7.nii is my volumetric file which looks like 1.screenshot). With this command line, my output is this file : 2.screenshot (attached).

Am I satisfied with this file ? if not what can I do to improve the result and the matching ?

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 the following warning : Warning: all vertex values are zero

Thank you by advance for your precious help, Have a nice day, Redwan

On 2 March 2017 at 10:07, Redwan Maatoug <redwanmaatoug@gmail.com mailto:redwanmaatoug@gmail.com> wrote:

Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and
I don't know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot
As you said, i have first registered the volumetric file
 using bbregister.
 I have used this command line :
tkregister2 --mov segment_7.nii --reg register7.dat --surf
 (knowing that segment_7.nii is my volumetric file which looks
like 1.screenshot).
With this command line, my output is this file : 2.screenshot
(attached).

Am I satisfied with this file ? if not what can I do to improve
the result and the matching ?

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

Thank you by advance for your precious help,
Have a nice day,
Redwan

On 1 March 2017 at 07:31, Douglas Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi Redwan,

    You'll need to register your volume to an FS-analyzed data set
    (probably using bbregister). Then apply mri_vol2surf (run with
    --help to get examples)

    doug


    On 2/28/17 5:17 PM, Redwan Maatoug wrote:

...

    Hi all !

    I would like to convert my files : volumetrics nifti files to
    surfaces files.
    My volumetrics nifti files come from an Atlas and I would
    like to convert them to surfaces files (i need the surfaces
    files).

    Could you please tell me the process because I have tried
    many things like :

    mri_vol2surf --src pathwaytomyfile --hemi lh --float2int
    round --out thepathwayIwantToputmySurfaceFileAfterConversion

    And it did not work.

    Thank you for your help,
    Redwan



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