Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work.
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
Hi all --
Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ? h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab.
Apologies if this question has come up before... a quick google didn't reveal anything.
Many thanks -=R
On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote:
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much for the quick answer and happy holidays.
Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work.
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
Hi all --
Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ? h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab.
Apologies if this question has come up before... a quick google didn't reveal anything.
Many thanks -=R
On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote:
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello experts,
After several days of trying, I have accomplished to get what you thought I was asking for. Unfortunately I was not asking for that.
First, I have to say that there is no --lobes option in mri_annotation2label (It is not documented, and if you try it, nothing happens).
Then I ran these commands:
[1] mri_annotation2label --subject XXX --hemi rh --outdir ../subjects/XXX/tmp/ --annotation lobes
[2] mri_label2vol --label ../subjects/XXX/rh.temporal.label --subject XXX --o test.nii --temp ../subjects/XXX/mri/orig.mgz --identity
I have seen that what I get in test.nii is a volume with the segmentation of the border between the white matter and grey matter in the temporal lobe. I am afraid I was not clear enough, as I was looking for a volume with the segmentation of the grey matter of the temporal lobe. I have tried changing the parameters in the first command, but it does not seem to work.
Does anybody know how can I do this?
Thanks in advance.
Fidel.
Thank you very much for the quick answer and happy holidays.
Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work.
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
Hi all --
Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ? h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab.
Apologies if this question has come up before... a quick google didn't reveal anything.
Many thanks -=R
On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote:
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I guess you could use the ribbon.mgz and mask it with various labels in the aparc+aseg.mgz
cheers Bruce On Wed, 29 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Hello experts,
After several days of trying, I have accomplished to get what you thought I was asking for. Unfortunately I was not asking for that.
First, I have to say that there is no --lobes option in mri_annotation2label (It is not documented, and if you try it, nothing happens).
Then I ran these commands:
[1] mri_annotation2label --subject XXX --hemi rh --outdir ../subjects/XXX/tmp/ --annotation lobes
[2] mri_label2vol --label ../subjects/XXX/rh.temporal.label --subject XXX --o test.nii --temp ../subjects/XXX/mri/orig.mgz --identity
I have seen that what I get in test.nii is a volume with the segmentation of the border between the white matter and grey matter in the temporal lobe. I am afraid I was not clear enough, as I was looking for a volume with the segmentation of the grey matter of the temporal lobe. I have tried changing the parameters in the first command, but it does not seem to work.
Does anybody know how can I do this?
Thanks in advance.
Fidel.
Thank you very much for the quick answer and happy holidays.
Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work.
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
> Hi all -- > > Is there a simple way to create an annotation for > frontal/temporal/occipital/parietal lobes based off the ? > h.aparc.annot > files in a FS 'label' dir? Ideally speaking, I'd like to have a > ?h.lobar.annot with corresponding lobar.annot.ctab. > > Apologies if this question has come up before... a quick google > didn't > reveal anything. > > Many thanks > -=R > >
On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote:
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Which version of FS are you using? It should be in version 5 (though it is undocumented). Are you sure it did not create a lobes annotation in the subject's label dir? The reason that it is undocumented is that it does not quite do what people really want (it keeps pre and post central gyrus for example). I would use --lobesStrict instead of --lobes (this is in version 5.1). You can also create your own by merging the aparc labels (mri_mergelabels) and then creating a new annot from the merged labels (mris_label2annot).
doug
On 12/29/10 11:38 AM, FIDEL ALFARO ALMAGRO wrote:
Hello experts,
After several days of trying, I have accomplished to get what you thought I was asking for. Unfortunately I was not asking for that.
First, I have to say that there is no --lobes option in mri_annotation2label (It is not documented, and if you try it, nothing happens).
Then I ran these commands:
[1] mri_annotation2label --subject XXX --hemi rh --outdir ../subjects/XXX/tmp/ --annotation lobes
[2] mri_label2vol --label ../subjects/XXX/rh.temporal.label --subject XXX --o test.nii --temp ../subjects/XXX/mri/orig.mgz --identity
I have seen that what I get in test.nii is a volume with the segmentation of the border between the white matter and grey matter in the temporal lobe. I am afraid I was not clear enough, as I was looking for a volume with the segmentation of the grey matter of the temporal lobe. I have tried changing the parameters in the first command, but it does not seem to work.
Does anybody know how can I do this?
Thanks in advance.
Fidel.
Thank you very much for the quick answer and happy holidays.
Forwarding a previous answer from doug. I tried it before (and recently). It does seem to work.
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
> Hi all -- > > Is there a simple way to create an annotation for > frontal/temporal/occipital/parietal lobes based off the ? > h.aparc.annot > files in a FS 'label' dir? Ideally speaking, I'd like to have a > ?h.lobar.annot with corresponding lobar.annot.ctab. > > Apologies if this question has come up before... a quick google > didn't > reveal anything. > > Many thanks > -=R > >
On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote:
Hello,
I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution.
So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain?
Thanks.
Hi Fidel,
that is deprecated code. What are you trying to do?
cheers (and happy holidays)
Bruce On Fri, 24 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Happy holidays for those who celebrate it today,
Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any.
Thanks in advance.
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.
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
FIDEL ALFARO ALMAGRO -
ythomas