Hi Freesurfer experts,
I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen
Hi Karen
This is typically caused because the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes
cheers Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Freesurfer experts,
I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a lot of labels. However, I can't find an option called close in mri_label2label. Can you give me another hint?
Best, Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote:
Hi Karen
This is typically caused because the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes
cheers Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Freesurfer experts,
I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen
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
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.
Try using the --paint option to mri_label2label doug
On 3/24/14 10:53 AM, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a lot of labels. However, I can't find an option called close in mri_label2label. Can you give me another hint?
Best, Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote:
Hi Karen
This is typically caused because the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes
cheers Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Freesurfer experts,
I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen
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
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
Hi Karen
you need to grab a new version then:
mri_label2label --help|grep close --close N close the label N times before writing --paint dmax surfname : map to closest vertex on source surfname if d < dmax the closest surface vertices:
what hardware/software environment are you running in? Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a lot of labels. However, I can't find an option called close in mri_label2label. Can you give me another hint?
Best, Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote: Hi Karen
This is typically caused because the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes cheers Bruce On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote: Hi Freesurfer experts, I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf: mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled? After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot. Best, Karen _______________________________________________ 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
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.
Hi Bruce,
The freesurfer version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I am running on a Linux Mint 16 machine.
Best, Karen
On 03/24/2014 05:06 PM, Bruce Fischl wrote:
Hi Karen
you need to grab a new version then:
mri_label2label --help|grep close --close N close the label N times before writing --paint dmax surfname : map to closest vertex on source surfname if d < dmax the closest surface vertices:
what hardware/software environment are you running in? Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a lot of labels. However, I can't find an option called close in mri_label2label. Can you give me another hint?
Best, Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote: Hi Karen
This is typically caused because the surface just misses thevoxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes
cheers Bruce On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote: Hi Freesurfer experts, I have a volume label only which is only different fromzero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --outvolume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay intksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surfaceto labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen _______________________________________________ Freesurfer mailing list Freesurfer@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
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
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Karen Marie Sandø Ambrosen