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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
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
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 fischl@nmr.mgh.harvard.edu 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 CautionDear 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
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 fischl@nmr.mgh.harvard.edu 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
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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 fischl@nmr.mgh.harvard.edu 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 CautionThanks 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 <
fischl@nmr.mgh.harvard.edu> 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 corpuscallosum? I tried using
the command > mri_vol2label and id of the corpus callosum as 192 as given inFreesurfer 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
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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
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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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. < DGREVE@mgh.harvard.edu> wrote:
you can try mri_vol2label
On 7/17/19 11:16 PM, Sadia Sheikh wrote:
External Email - Use CautionHello 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
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. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: you can try mri_vol2label
On 7/17/19 11:16 PM, Sadia Sheikh wrote:
External Email - Use CautionHello 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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=default3&tag=3530826a-819e-47f1-a448-b4bc56ebebed I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=default3&tag=3530826a-819e-47f1-a448-b4bc56ebebed <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Fri, Jul 19, 2019 at 1:34 AM Greve, Douglas N.,Ph.D. < DGREVE@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 CautionThanks 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. < DGREVE@mgh.harvard.edu> wrote:
you can try mri_vol2label
On 7/17/19 11:16 PM, Sadia Sheikh wrote:
External Email - Use CautionHello 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 listFreesurfer@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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Sadia Sheikh