Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas N Greve]

I don't know about mri_morphology, but you can use mri_binarize to 
erode. It has several options to allow control of how the erosion is done


On 05/22/2017 12:48 PM, Gamaliz wrote:
> Douglas,
>
> I just realized that I was  using the wrong feeesurfer output. I had 3 
> processed MRIs for the same subject, and I just happened to pick the 
> wrong one. The output of mri_surf2vol is indeed perfectly registered 
> to the T1.mgz. So my problem is resolved.  It still bugs me that the 
> --identity works even if you type anything as the subjectid, luckily 
> this does not affect me at all.
>
>
> Thanks for your help.
>
> On another accord, I used the mri_morphology to erode the white matter 
> and noticed that it erodes quite a lot in a single iteration, is there 
> any other command which provides better controls in how much gets 
> eroded? Also. is the erosion always happening inwards?
>
> Gabriel
>
> On Thu, May 18, 2017 at 12:29 PM, Gamaliz  > wrote:
>
> I thing I noticed is that if I change the  "--identity" parameter
> it provides the same result. I am just typing anything and it
> still produces the same volume that gets created when the
> subject_id is used.
>
> On Thu, May 18, 2017 at 12:16 PM, Gamaliz  > wrote:
>
> Douglas,
>
> I am looking at them in freeview and mango. They are not
> aligned. I am able to align them using flirt, and they come
> out perfect. I have tried 5 cases. 3 of them they are aligned,
> two were not. I am loading below the wm and lh.wm. They are
> supposed to be aligned (wm is aligned with T1).
>
> I got a surface by using Bruce's method, but it's much more
> irregular than the one obtained from mri_surf2vol. I wonder
> why the inconsistency. I guess I can create the surface and
> flirt using a solid transform to the T1. It takes longer, but
> it works.
>
> Gabriel
>
> Inline image 1
>
>
>
>
> -- 
> gAbE
>
>
>
>
> -- 
> gAbE
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas N Greve]

how were you examining the registration? When I run the command, the 
rh.white.mgz aligns perfectly with the T1.mgz


On 05/16/2017 05:38 PM, Gamaliz wrote:
> Douglas,
>
> The previous message had an images attached that seemed to be too big. 
> it was "bounced" automatically. I guess too many images were attached.
>
> I ran the command for the rh.white and lh.white and the image is not 
> perfectly registered. I tried a lot of things, but nothing worked. I 
> ended up using the idea from Bruce. I Binarized the aseg+aparc file, 
> extracting the wm regions, eroded, and subtracted. That gave me a 
> surface as a volumen. This also can be done with only the images (no 
> need to extract the whole freesurfer output)  The image from 
> mri_surf2vol had better quality, but I couldn't get it to register. If 
> by any chance someone figures this registration problem out, I will 
> use certainly use it.
>
> Thanks for all your help.
>
> Gabriel
>
>
> previous message:
>
> Douglas,
>
> I extracted the whole directory and ran:
>
> mri_surf2vol --mkmask --surf white --hemi rh --o rh.white.mgz 
> --template ../subjects/subject/mri/T1.mgz --sd ../subjects --subject 
> subject --identity subject
> gdiagno = -1
> Using identity matrix for registration
> Overriding reg subject subject with subject
> 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   ../subjects
> hemi rh
> mksurfmask 1
> projfrac 0
> outvol path  rh.white.mgz
> template path  ../subjects/subject/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 = 1.00
>  ysize = 1.00
>  zsize = 1.00
>   cdc  = -1.00 0.00 0.00
>   rdc  = 0.00 0.00 -1.00
> sdc  = 0.00 1.00 0.00
> xyz0 = 3.373505 20.515587 -6.721008
> Gdiag_no -1
> Reading surface ../subjects/subject/surf/rh.white
> Done reading source surface
> surf nframes = 1
> INFO: mapping vertices to closest voxel
> INFO: resampling surface to volume
> INFO: sampled 84160 voxels in the volume
> INFO: writing output volume to rh.white.mgz
> done
>
> I did both hemispheres, they are not registered. I tried using as 
> template the T1.mgz, and T1 converted to nifti. I also tried output as 
> mgz and then mri_convert to nifti, the also output to nifti. I always 
> obtained the same volumes, and they were always unregistered.
>
>
> both hemispheres, they are not registered. I tried using as
> template the T1.mgz, and T1 converted to nifti. I also tried
> output as mgz and then mri_convert to nifti, the also output to
> nifti.
>
> Inline image 2
>
>
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

Try visualizing it in freeview instead of fslview.


On 5/16/17 12:11 PM, Gamaliz wrote:

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.


Inline image 2

Inline image 1

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 = 1.00
 ysize = 1.00
 zsize = 1.00
  cdc  = -1.00 0.00 0.00
  rdc  = 0.00 0.00 -1.00
  sdc  = 0.00 1.00 -0.00
  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 
> 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 

 

wrote:

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


  On 5/15/17 9:59 PM, Gamaliz 

Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

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.

[image: Inline image 2]

[image: Inline image 1]

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 = 1.00
 ysize = 1.00
 zsize = 1.00
  cdc  = -1.00 0.00 0.00
  rdc  = 0.00 0.00 -1.00
  sdc  = 0.00 1.00 -0.00
  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 
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
>
>  
>
> 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
> 

Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

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 



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
 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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-- gAbE

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--
gAbE





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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Bruce Fischl]

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 



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
 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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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

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 command 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 
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 
> 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
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e
>> du/mailman/listinfo/freesurfer 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.
>
> --
> gAbE
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
> 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.
>
>


-- 
gAbE
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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

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 
> 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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___ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu

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


--
gAbE

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

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 
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
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
> 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.
>
>


-- 
gAbE
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.