Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

External Email - Use Caution

Firstly I used the command line to extract whole cc, mri_vol2label --c
aseg.auto.mgz --id 192 --l cc.label. Then, I tried to get the labels of the
subregions of cc using the command, mri_vol2label --c cc.mgz --id 251 --l
cc1.label.
Please find the attached full terminal output.
Thanks for your support.


I’m
protected online with Avast Free Antivirus. Get it here — it’s free forever.

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Fri, Jul 19, 2019 at 1:34 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> please send the command line and full terminal output
>
> On 7/18/2019 12:27 PM, Sadia Sheikh wrote:
>
> External Email - Use Caution
> Thanks for your response.
> I tried mri_vol2label initially but I was facing this error. error: found
> no voxels matching id 192. The problem is with my given command or this
> command is not possible for corpus callosum? Please find the attached
> output of the command line.
>
>
> On Fri, Jul 19, 2019 at 12:25 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> you can try mri_vol2label
>>
>> On 7/17/19 11:16 PM, Sadia Sheikh wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello Bruce
>> >
>> > I don't have much experience in Freesurfer and I want to get the
>> > labels of CC. Is there any other way to get corpus callosum labels or
>> > voxels without using Matlab? It will be really helpful to me.
>> >
>> > Thanks in advance
>> > Sadia
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://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
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] voxel coordinates of corpus collosum

[Greve, Douglas N.,Ph.D.]

please send the command line and full terminal output

On 7/18/2019 12:27 PM, Sadia Sheikh wrote:

External Email - Use Caution

Thanks for your response.
I tried mri_vol2label initially but I was facing this error. error: found no 
voxels matching id 192. The problem is with my given command or this command is 
not possible for corpus callosum? Please find the attached output of the 
command line.


On Fri, Jul 19, 2019 at 12:25 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
you can try mri_vol2label

On 7/17/19 11:16 PM, Sadia Sheikh wrote:
>
> External Email - Use Caution
>
> Hello Bruce
>
> I don't have much experience in Freesurfer and I want to get the
> labels of CC. Is there any other way to get corpus callosum labels or
> voxels without using Matlab? It will be really helpful to me.
>
> Thanks in advance
> Sadia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://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



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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

Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

External Email - Use Caution

Thanks for your response.
I tried mri_vol2label initially but I was facing this error. error: found
no voxels matching id 192. The problem is with my given command or this
command is not possible for corpus callosum? Please find the attached
output of the command line.


On Fri, Jul 19, 2019 at 12:25 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> you can try mri_vol2label
>
> On 7/17/19 11:16 PM, Sadia Sheikh wrote:
> >
> > External Email - Use Caution
> >
> > Hello Bruce
> >
> > I don't have much experience in Freesurfer and I want to get the
> > labels of CC. Is there any other way to get corpus callosum labels or
> > voxels without using Matlab? It will be really helpful to me.
> >
> > Thanks in advance
> > Sadia
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] voxel coordinates of corpus collosum

[Greve, Douglas N.,Ph.D.]

you can try mri_vol2label

On 7/17/19 11:16 PM, Sadia Sheikh wrote:
>
> External Email - Use Caution
>
> Hello Bruce
>
> I don't have much experience in Freesurfer and I want to get the 
> labels of CC. Is there any other way to get corpus callosum labels or 
> voxels without using Matlab? It will be really helpful to me.
>
> Thanks in advance
> Sadia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://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

Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

External Email - Use Caution

Hello Bruce

I don't have much experience in Freesurfer and I want to get the labels of
CC. Is there any other way to get corpus callosum labels or voxels without
using Matlab? It will be really helpful to me.

Thanks in advance
Sadia
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

External Email - Use Caution

I tried to extract cc labels from aseg.auto.mgz file and extract the labels
subregions of cc from the cc.mgz file (cc.mgz contain the segmented
subregions of corpus callosum) using mri_vol2label command.

On Fri, Jun 21, 2019 at 11:23 PM Bruce Fischl 
wrote:

> can you send us the full command line and screen output? Doug might have
> an easy way to do it, but personally I would do it in matlab
> cheers
> Bruce
> On Fri, 21 Jun
> 2019, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Thanks for your reply. I want to get the voxel coordinates of  CC and
> its subregions. I tried using
> > the command mri_vol2label for cc subregions also. But still I am getting
> the error message: found no
> > voxels matching id 251.
> > What is the right command to get the coordinates of CC?
> >
> > Thanks in advance.
> > Sadia
> >
> >
> > On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Sadia
> >
> >   we subdivide the cc into multiple components:
> >
> >   251 CC_Posterior0   0   64  0
> >   252 CC_Mid_Posterior0   0   112 0
> >   253 CC_Central  0   0   160 0
> >   254 CC_Mid_Anterior 0   0   208 0
> >   255 CC_Anterior 0   0   255 0
> >
> >
> >   cheers
> >   Bruce
> >
> >   On Thu, 20 Jun
> >   2019, Sadia
> >   Sheikh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear Freesurfer experts
> >   > How can I get the voxel coordinates of the segmented corpus
> callosum? I tried using
> >   the command
> >   > mri_vol2label and id of the corpus callosum as 192  as given in
> Freesurfer LUT,
> >   > but it gives an error: found no voxels matching id 192
> >   >
> >   > Thanks in advance
> >   >
> >   > Sadia
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] voxel coordinates of corpus collosum

[Bruce Fischl]

can you send us the full command line and screen output? Doug might have 
an easy way to do it, but personally I would do it in matlab

cheers
Bruce
On Fri, 21 Jun 
2019, Sadia Sheikh wrote:




External Email - Use Caution

Thanks for your reply. I want to get the voxel coordinates of  CC and its 
subregions. I tried using
the command mri_vol2label for cc subregions also. But still I am getting the 
error message: found no
voxels matching id 251.
What is the right command to get the coordinates of CC?

Thanks in advance.
Sadia
 

On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl  
wrote:
  Hi Sadia

  we subdivide the cc into multiple components:

  251 CC_Posterior                            0   0   64  0
  252 CC_Mid_Posterior                        0   0   112 0
  253 CC_Central                              0   0   160 0
  254 CC_Mid_Anterior                         0   0   208 0
  255 CC_Anterior                             0   0   255 0


  cheers
  Bruce

  On Thu, 20 Jun
  2019, Sadia
  Sheikh wrote:

  >
  > External Email - Use Caution
  >
  > Dear Freesurfer experts
  > How can I get the voxel coordinates of the segmented corpus callosum? I 
tried using
  the command
  > mri_vol2label and id of the corpus callosum as 192  as given in 
Freesurfer LUT, 
  > but it gives an error: found no voxels matching id 192 
  >
  > Thanks in advance
  >
  > Sadia
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://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

Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

External Email - Use Caution

Thanks for your reply.
I want to get the voxel coordinates of  CC and its subregions. I tried
using the command mri_vol2label for cc subregions also. But still I am
getting the error message: found no voxels matching id 251.
What is the right command to get the coordinates of CC?

Thanks in advance.
Sadia


On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl 
wrote:

> Hi Sadia
>
> we subdivide the cc into multiple components:
>
> 251 CC_Posterior0   0   64  0
> 252 CC_Mid_Posterior0   0   112 0
> 253 CC_Central  0   0   160 0
> 254 CC_Mid_Anterior 0   0   208 0
> 255 CC_Anterior 0   0   255 0
>
>
> cheers
> Bruce
>
> On Thu, 20 Jun
> 2019, Sadia
> Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts
> > How can I get the voxel coordinates of the segmented corpus callosum? I
> tried using the command
> > mri_vol2label and id of the corpus callosum as 192  as given in
> Freesurfer LUT,
> > but it gives an error: found no voxels matching id 192
> >
> > Thanks in advance
> >
> > Sadia
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://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

Re: [Freesurfer] voxel coordinates of corpus collosum

[Bruce Fischl]

Hi Sadia

we subdivide the cc into multiple components:

251 CC_Posterior0   0   64  0
252 CC_Mid_Posterior0   0   112 0
253 CC_Central  0   0   160 0
254 CC_Mid_Anterior 0   0   208 0
255 CC_Anterior 0   0   255 0


cheers
Bruce

On Thu, 20 Jun 
2019, Sadia 
Sheikh wrote:




External Email - Use Caution

Dear Freesurfer experts
How can I get the voxel coordinates of the segmented corpus callosum? I tried 
using the command
mri_vol2label and id of the corpus callosum as 192  as given in Freesurfer LUT, 
but it gives an error: found no voxels matching id 192 

Thanks in advance

Sadia

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer