Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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.

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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
>> >
>> > ___
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>>
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Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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
>
>
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Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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
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Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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
> >   >
> >   >___
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> >
> >
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Re: [Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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
> >
> >___
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[Freesurfer] voxel coordinates of corpus collosum

[Sadia Sheikh]

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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
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Re: [Freesurfer] Alignment of segmented brainstem in Freesurfer

[Sadia Sheikh]

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Thankyou, Sir.
It really helped me a lot.

On Sat, Apr 20, 2019 at 11:46 PM Bruce Fischl 
wrote:

> What command did you use to apply the transform? If mri_convert add -rt
> nearest to your command line.
> The issue is that you are using trilinear interpolation our a label map
> instead of nearest neighbor
>
> On Apr 20, 2019, at 5:22 AM, Sadia Sheikh 
> wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts
>
> I did brainstem segmentation using BrainstemSubstructure method. Then
> after segmentation, I aligned all my segmented brainstem to Talairach
> coordinates using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.
> Alignment seems to be fine. But the boundary of the aligned brainstem
> looks distorted with different other colors. Why does the boundary look
> like this? and how can I improve this?
> I have attached the image of brainstem after alignment.
>
> Thanks in advance.
>
> Regards
> Sadia
> Research Student
>
>
>
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[Freesurfer] Alignment of segmented brainstem in Freesurfer

[Sadia Sheikh]

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Dear FreeSurfer experts

I did brainstem segmentation using BrainstemSubstructure method. Then after
segmentation, I aligned all my segmented brainstem to Talairach coordinates
using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.
Alignment seems to be fine. But the boundary of the aligned brainstem looks
distorted with different other colors. Why does the boundary look like
this? and how can I improve this?
I have attached the image of brainstem after alignment.

Thanks in advance.

Regards
Sadia
Research Student



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Re: [Freesurfer] Alignment to ACPC

[Sadia Sheikh]

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Thanks for your response Sir

I did that using mri_convert for the orig.mgz file and brainstem segmented
file.
(mri_convert orig.mgz --apply_transform transforms/talairach.xfm -o
orig.talairach.mgz). but the image doesn't seem like to be aligned.
How can I confirm that the image is ACPC aligned or not and how is the
transformation matrix in transforms.xfm file is evaluated.

Thanks in advance
Sadia

On Sat 23 Feb, 2019, 12:38 AM Bruce Fischl  Hi Sadia
>
> we don't align to AC-PC, but we do compute a talairach transformation in
> $SUBJECTS_DIR/$subjects/mri/transforms/talairach.xfm that should do so.
> You
> can apply it using mri_convert or mri_vol2vol.
>
> cheers
> Bruce
>
> On
> Fri, 22 Feb 2019, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer experts
> > Freesurfer preprocessed data by(recon-all) are ACPC aligned?
> > If not how can I align my files to ACPC? I read the documents but I am
> still very confused about the
> > alignment and coordinate system in freesurfer.
> >
> > Thanks in advance
> >
> > Regards
> > Sadia
> > Research Student
> >
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[Freesurfer] Alignment to ACPC

[Sadia Sheikh]

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Hello Freesurfer experts

Freesurfer preprocessed data by(recon-all) are ACPC aligned?
If not how can I align my files to ACPC? I read the documents but I am
still very confused about the alignment and coordinate system in freesurfer.

Thanks in advance

Regards
Sadia
Research Student
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Re: [Freesurfer] automatically save the selected plane

[Sadia Sheikh]

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Hello

My purpose is to get the specific(required) plane of axial view that lies
in the midbrain region. For that i m thinking firstly to get all the planes
of axial view from the midbrain region and then choose the best plane.i
want to get the mickey mouse sign that lies in the axial direction from
large number of data.
So, i want to do this automatically.

Thanks
Sadia

On Sat, Feb 16, 2019 at 12:17 AM Bruce Fischl 
wrote:

> Hi Sadia
>
> can you elaborate what you are trying to do. What seleected plane?
>
> cheers
> Bruce
>
> On Fri, 15
> Feb 2019, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear FreeSurfer experts
> >
> > It is possible to automatically save the selected planes or set of
> planes from the specific region?
> > Since I have a large number of data and I want to save all the planes
> that lie in the midbrain region.
> >
> > Regards
> > Sadia
> > Research Student
> >
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Re: [Freesurfer] voxel cordinates

[Sadia Sheikh]

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Thankyou Sir for your reply.
Actually using mri_binarize is segmented the regions from the aseg.mgz.
Now, i want to get the shape and then compare   using voxel cordinates .

On Tue, Jan 1, 2019 at 1:17 AM Bruce Fischl 
wrote:

> can you explain a bit more about what you are trying to do? If you
> extracted ROIs into label files it is just a list of coordinates, although
> probably not voxel indices. This page (thanks Doug!) explains our various
> coordinate systems and how to go from one to another:
>
> http://freesurfer.net/fswiki/CoordinateSystems
>
> cheers
> Bruce
>
>
> On Sun, 30 Dec 2018, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts
> > I am using freesurfer version 6.0. I have extracted ROI's from the
> aseg.mgz file. Now is it possible
> > to get the cordinates of each voxel for a particular ROI?
> >
> > Thanks in advance
> > Regards
> > Research student
> >
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[Freesurfer] voxel cordinates

[Sadia Sheikh]

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Dear Freesurfer experts

I am using freesurfer version 6.0. I have extracted ROI's from the aseg.mgz
file. Now is it possible to get the cordinates of each voxel for a
particular ROI?

Thanks in advance
Regards
Research student
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