Bruce, 

I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. 

Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this information. 

I was able to create the volume by adding --identity, --template, and --mkmask. 

The required surfval and volreg, are taken from the -mkmask and  identity respectively. 

The surface is created using the template from T1.mgz,, -mkmask works for me.  However the orientation is wrong (and  thus the registration). I wonder which file contains the correct registration (to give it as input to volreg. I tried using fstal 1 (this sets the template to mni305.cor.subfov1res.mgz and registration from mni305.cor.subfov1res.reg: That also gave me an unregistered output. 

I guess the only piece of the puzzle I am missing is which registration file to use, so that the final volume is registered to the T1.mgz. This file must be there, as when loading the images into tkmedit they are registered. 

here is the output of the execution. The reg files comes from using --identity. I wonder which reg file can I use. 

test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz  --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id
gdiagno = -1
Using identity matrix for registration
Overriding reg subject user_id with user_id
Qa2v: SurfXYZ to VolCRS: ------------------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000  -1.000   128.000;
 0.000   1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
--------------------------------------------------
subjects dir   /home/test/Desktop/surftovol/
hemi           lh
mksurfmask     1
projfrac       0
outvol   path  out.nii.gz
template path  mri/T1.mgz
------- Anat2Vol Registration (TkReg)----
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
-----------------------------------------
height = 256
 width = 256
 depth = 256
 xsize = 1.000000
 ysize = 1.000000
 zsize = 1.000000
  cdc  = -1.000000 0.000000 0.000000
  rdc  = 0.000000 0.000000 -1.000000
  sdc  = 0.000000 1.000000 -0.000000
  xyz0 = -8.411377 8.796127 -0.092697
Gdiag_no  -1
Reading surface /home/test/Desktop/surftovol//user_id/surf/lh.white
Done reading source surface
surf nframes = 1
INFO: mapping vertices to closest voxel
INFO: resampling surface to volume
INFO: sampled 61045 voxels in the volume
INFO: writing output volume to out.nii.gz
done
test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz  --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id

On Tue, May 16, 2017 at 11:08 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

If you run it with --help, it will print out examples. Did you try that?
On 5/16/17 9:26 AM, Bruce Fischl wrote:
Hi gAbE

you could try using mris_fill, or even mris_compute_volume_fractions

cheers
Bruce
On Mon, 15 May 2017, Gamaliz wrote:

My idea is to convert the registered white surface into a volume, so it can be shown in a volume viewer (not a surface viewer). I need to display a DTI image and mark the edges of the white matter as a line on top if it.
This is not the exact command, I am not sitting in front of my station, but it goes something like it. I tried many combinations, the general error was related to the template files not on the correct format (it could have been they couldn't be found to be opened too, the error seemed generic).
mri_surf2vol --surfval white --hemi lh --outvol test.mgz --template T1.mgz
--volreg T1.mgz --sd /home/user/Desktop/sf/sub1
I am at a loss for the --volreg flag.
The sd seems to indicate the directory of freesurfer (but then how is the co
mmand aware of the specficic subject I am trying to process? I tried using: --identity subject no luck.
'sub1' us my subject, located not in the default freesurfer directory.
There are no examples or a lot of help using it
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol

If this is not enough I can get back to you with the specific error tomorrow
.
On Mon, May 15, 2017 at 10:02 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu>

wrote:

      what was your mri_surf2vol cmd line? And what was the terminal
      output?

      On 5/15/17 9:59 PM, Gamaliz wrote:
      I looked at the ribbon.mgz, but it is a pial surface, not
      really delineated white matter the way I need it. There is
      a command called mri_sur2vol, I have tried to use it, but
      unsuccessfully, no idea if that is the solution to my
      problem.

On Mon, May 15, 2017 at 9:57 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu> wrote:

      not sure what you mean. Have you looked at the
      ribbon.mgz file?

      On 5/15/17 5:20 PM, Gamaliz wrote:
      I need to create an image which overlaps the
      T1/mgz and the outer surface of the white
      matter. How do I convert the surface into a
      mgz volume?

--
gAbE

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The information in this e-mail is intended only for the person to whom
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addressed. If you believe this e-mail was sent to you in error and the
e-mail
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

gAbE