External Email - Use Caution
Hi Freesurfer community,
I have an issue in adding a surface label to an annot file.
I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument) to create a surface label for the mask.
I also have a custom parcellation of fsaverage which I have mapped to individual native space using mri_surf2surf.
My issue is I want to combine the outputted binarymask.label file with the custom parcellation. My understanding is that I would need to combine the binarymask.label with the custom.parc.annot file. In order to do this wopuld I break down the annot file with mri_annot2label and then rebuild including the new binarymask.label?
Could I also just add another row to the LUT from the custom.parc.annot file to allow this?
And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised?
BW
James
External Email - Use Caution
Good Morning All,
Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended!
Any help would be greatly appreciated.
BW James
On Tue, Jun 26, 2018 at 1:20 PM, James Hobart jameshobart2@gmail.com wrote:
Hi Freesurfer community,
I have an issue in adding a surface label to an annot file.
I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument) to create a surface label for the mask.
I also have a custom parcellation of fsaverage which I have mapped to individual native space using mri_surf2surf.
My issue is I want to combine the outputted binarymask.label file with the custom parcellation. My understanding is that I would need to combine the binarymask.label with the custom.parc.annot file. In order to do this wopuld I break down the annot file with mri_annot2label and then rebuild including the new binarymask.label?
Could I also just add another row to the LUT from the custom.parc.annot file to allow this?
And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised?
BW
James
Hi James
yes, I guess that is the right workflow. YOu will also need to modify the color lut to include your new parcel. As for overlap you could just remove it in matlab I guess. Or maybe mris_label2annot handles it, I'm not sure (Doug may know)
cheers Bruce On Mon, 23 Jul 2018, James Hobart wrote:
External Email - Use Caution
Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended!
Any help would be greatly appreciated.
BW James
On Tue, Jun 26, 2018 at 1:20 PM, James Hobart jameshobart2@gmail.com wrote:
Hi Freesurfer community, I have an issue in adding a surface label to an annot file. I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument) to create a surface label for the mask. I also have a custom parcellation of fsaverage which I have mapped to individual native space using mri_surf2surf. My issue is I want to combine the outputted binarymask.label file with the custom parcellation. My understanding is that I would need to combine the binarymask.label with the custom.parc.annot file. In order to do this wopuld I break down the annot file with mri_annot2label and then rebuild including the new binarymask.label? Could I also just add another row to the LUT from the custom.parc.annot file to allow this? And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised? BW James
Your workflow looks right. Once you have a set of labels you want to combine, use mris_label2annot. You will have to supply a color tab (--ctab) that you have modified to include the new label. To mediate between multiple labels having the same vertex, use the --maxstatwinner option. You will have to include a "stat" as the last column in the label file. This is usually 0, so change it to 1 in your custom label.
On 07/23/2018 10:13 AM, Bruce Fischl wrote:
Hi James
yes, I guess that is the right workflow. YOu will also need to modify the color lut to include your new parcel. As for overlap you could just remove it in matlab I guess. Or maybe mris_label2annot handles it, I'm not sure (Doug may know)
cheers Bruce On Mon, 23 Jul 2018, James Hobart wrote:
External Email - Use Caution
Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended!
Any help would be greatly appreciated.
BW James
On Tue, Jun 26, 2018 at 1:20 PM, James Hobart jameshobart2@gmail.com wrote:
Hi Freesurfer community,
I have an issue in adding a surface label to an annot file.
I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument) to create a surface label for the mask.
I also have a custom parcellation of fsaverage which I have mapped to individual native space using mri_surf2surf.
My issue is I want to combine the outputted binarymask.label file with the custom parcellation. My understanding is that I would need to combine the binarymask.label with the custom.parc.annot file. In order to do this wopuld I break down the annot file with mri_annot2label and then rebuild including the new binarymask.label?
Could I also just add another row to the LUT from the custom.parc.annot file to allow this?
And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised?
BW
James
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Bruce Fischl -
Douglas N. Greve -
James Hobart